tag:blogger.com,1999:blog-10164605196360428772024-03-07T23:24:27.917-08:00Coral Reef Diversity and Conservation (2012) James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.comBlogger14125tag:blogger.com,1999:blog-1016460519636042877.post-70727063899780484472013-01-23T03:16:00.000-08:002013-01-23T03:16:24.623-08:00January 23, 2013 class notesOral presentations today - 10 groups gave presentations.<br />
<br />
Overall impressions: Very unique - and realistic. Should be interesting seeing the marks and reports!<br />
<br />
お疲れさま to everyone!<br />
<br />
<br />James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-58961230102631584832013-01-23T03:15:00.000-08:002013-01-23T03:15:00.835-08:00January 16, 2013 class notes<b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Outline</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span></b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. Introduction: Problems facing taxonomy and diversity.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. Accelerating “taxonomy”: DNA barcoding.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. Promoting taxonomy: Census of Marine Life.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. Images from one CoML Project (Creefs).</span><br /><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;"><br /></span></span><b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. Introduction: Problems facing taxonomy and diversity.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span></b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Problems facing taxonomy 1</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Too many species! Diversity confounds our best efforts to examine it.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Keep finding new species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Extinction rates increasing.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Problems facing taxonomy 2</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Not enough taxonomists.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Pay poor, work long.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Everyone says “important” but not considered essential.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Many groups have no active workers.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Potential solutions 1</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Increasing technology and information available.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Global information systems.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Molecular experiment techniques.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Potential solutions 2</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Increasing international research collaboration.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Growing awareness of biodiversity and importance.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. Accelerating “taxonomy”: DNA barcoding.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span></b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">What is “DNA barcoding”?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">遺伝子バーコードというのは?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">A DNA barcode is a short sequence, taken from standardized portions of the genome,used to identify species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">遺伝子バーコードとはひとつの配列を利用して、全生物の種類区別を行うこと。</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">If a genome project is deep and narrow, DNA barcoding is broad and shallow.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Genome projectは深くて、狭いが、遺伝子バーコードは浅くて、広い。</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Requirements of a DNA barcoding marker</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">A sequence/marker used to barcode should:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">be easy to amplify</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">not possess paralogues</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">have conserved regions to design primers efficiently for a broad taxonomic sampling</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">be variable enough to distinguish species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">but conserved enough within species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Choosing the correct DNA marker is critical.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Point:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Barcoding does not aim to solve phylogeny!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Reasons for DNA barcoding</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. Works with fragments.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. Works with all stages of life: Can link male/females. Different stages of same organism. E.g. Amphipods (White & Reimer 2012)</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. Cryptic species detection. E.g.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">Astraptes</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. Reduces ambiguity (set DNA code).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">5. Makes expertise go further.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">6. Democratizes access to data. E.g. Barcode of Life project</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">7. Opens the way for handheld barcoders.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">8. Finds new diversity.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">9. Demonstrates value of museum collections. Sequencing of collections vital.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">10. Speeds up discovery of new species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Additional strong point</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Does not need expert knowledge.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Weak points</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. DNA (specifically COI) does not always work for each group of organisms.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. Handheld technology has not succeeded, despite many advances.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. Different taxa have different DNA protocols, so standardization is difficult.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. The “barcoding gap”</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Barcoding implies that the level of DNA divergence between and within species is different.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">But evolution not neat - hybrids, incomplete lineage sorting, etc.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">This gap is not always present – so taxonomy comes back to “judgement”.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Results</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">DNA barcoding proposed in 2003 as a “solution” to taxonomy.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Two large projects: Barcode of Life and Ocean Genome Legacy.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Encyclopedia of Life on the internet.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Common method of identification.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Gaining acceptance as a practical method to obtain much data.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">But has not solved taxonomy, instead a new approach or “sub-field”.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">For zoanthids (and corals), > 1 DNA marker is needed.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">mt DNA evolves very slowly.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Still, better than no experts at all!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. Promoting taxonomy: Census of Marine Life.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span></b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Scientific Framework</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">What has lived in the oceans?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">What does live in the oceans?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">What will live in the oceans?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">The Census consisted of four major component programs organized around these questions.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. Investigating the Past</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Census researchers undertook the challenge of constructing the history of marine animal populations since human predation became important, roughly the last 500 years. This program component was called HMAP.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Teams of fisheries scientists, historians, economists and others conducted case studies in southern Africa, Australia, and approximately a dozen other regions.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Together, these case studies created the first reliable picture of life in the oceans before fishing.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">The long historical records of marine populations help distinguish the contributions of natural fluctuations in the environment from the effects of human activities.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. Assessing the Present</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">The largest component of the Census involved investigating what now lives in the world's oceans through 14 field projects.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Each sampled important kinds of biota in one of six realms of the global oceans using a range of technologies.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">This included CReefs.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. Forecasting the Future</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">To speak about what will live in the oceans required numerical modeling and simulation. This component program is the Future of Marine Animal Populations (FMAP).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Integrating data from many different sources and creating new statistical and analytical tools to predict marine populations and composition of ecosystems in the future</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. Living Legacy</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Such a global initiative required a state-of-the-art data assimilation framework, and this is:Ocean Biogeographic Information System (OBIS).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Numbers</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2,700 scientists</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">80+ nations</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">540 expeditions</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">US$ 650 million</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2,600+ scientific publications</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">6,000+ potential new species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">30 million distribution records and counting</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. Example: CReefs:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span></b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Heron Island Trip</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">November 8th – December 1st, 2010</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Census of Coral Reef Ecosystems (www.creefs.org), part of Census of Marine Life (CoML – www.coml.org).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Large international effort to understand biodiversity, use data for conservation.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Many researchers from different institutions, focused on different taxa, many “ignored”.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">I focused on zoanthids (of course)!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Location:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Heron Island</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Many seabirds nest here. Always noisy, and dangerous to walk without a hat!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Rails also live on the island.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">The island is an important nesting site for green and loggerhead sea turtles.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Heron Island Research Station is run by the University of Queensland. Most of the station is very new.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">There are excellent facilities for experiments, sample collection, and analyses, indoors and outside.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Scientists from all over the world, most based in Australia, but others from USA, Japan, Iceland, etc.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Most scientists had much field experience, and were good divers. Many also had boat licenses and first aid training.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">There were also dive officers, who acted as boat captains, guides, diving assistants, etc.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Outreach included a professional photographer, and a professional blogger with stories and images posted every day.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">A professional chef ensured everyone was well-fed. The food was amazing!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Every night at dinner, based on everyone’s ideas, weather conditions, and tides, the next day’s schedule was decided.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Boats were launched from the harbor, 3-10 people per boat. Often boats were out for over 7 hours.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Diving was always done under the buddy system, with very strict guidelines on diving protocol.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Special permits were obtained to allow specimen collection. Work underwater was intense and focused.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">I was able to collect 270 specimens in 33 dives. Other groups collected up to >2000 specimens!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Samples were also collected on reef walks, and by snorkeling. Other groups used ARMS and the “carpet of death”.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Some groups found many new species, others new records for the southern GBR. This genus was found in the southern Pacific Ocean for the 1st time, likely a new species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Another potential new species of zoanthid.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Many people also collected for other groups.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Back in the lab, data were collected, and specimens numbered. All data were given to the CReefs data manager as well.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">All sites were assigned numbers, and all had GPS coordinates. 130 sites were visited in 3 weeks!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Samples will be shipped to institutions all over the world and analyzed further.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Of course, work was not 24 hours a day…</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Sunset drinks were the one time of day when everyone would relax and take a break.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">And the sunsets were amazing…</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">References cited:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span></b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. CP Meyer, G Paulay. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3(12) e422.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. Consortium for Barcoding of Life homepage.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. Census of Marine Life homepage.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. OBIS homepage.</span>James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-63326508171782967212013-01-23T03:12:00.002-08:002013-01-23T03:12:24.088-08:00January 15, 2013 class notes<br />
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; line-height: 1.4; position: relative; width: 586px;">
January 15th class notes</div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<br /></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<b>Outline</b>:</div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 1.4;">1. </span><span class="Apple-style-span" style="line-height: 18px;">Community conservation in the Philippines.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
2. Conservation History on the Great Barrier Reef</div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
3. The future</div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
4. Conclusions</div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<br /></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<b><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 1.4;">Part 1</span></span></b></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="display: inline !important; font-weight: bold; line-height: 18px; position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;">Community conservation in the Philippines.</span></div>
</div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small; line-height: 18px;">History</span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Philippines consist of 7000+ islands.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Centuries have used reefs for livelihood.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Since 1970s, threatened by over-exploitation and destructive fishing methods.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;"><br /></span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Conservation started in 1974. Many projects failed.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Politics tied to conservation.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Local governments have authority but not knowledge or budget.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">To be successful, combination of local and national people.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Within local group, must include users of reef; fishermen, resort owners, coastal residents, scuba divers.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Start of conservation</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">MDCP started in 1986 on three islands (62-166 households); Apo, Pamilacan, Balicasag.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">All had less fish catch, increasing destruction and poverty.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;"><br /></span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">MCDP plan</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Marine reserves with buffer areas to increase number and diversity fish.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Development of local knowledge and alternative work.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Community center.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Outreach and replication program.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">MCDP steps</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Integration into community.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Education - marine ecology and resource management.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Group building, formalizing, strengthening.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Results</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Apo & Pamilacan remain strong.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Balicasag protection groups somewhat weakened due to large PTA resort and less local “ownership”.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">PTA has good points too.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">All islands have stronger municipal laws now.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Results</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Local fisherman believe sanctuary has helped.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Comparison of 1985-86 data with 1992 shows increases in fish, stable coral cover.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Conclusions</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">MPAs work on small islands by preventing destructive fishing and making locals understand value of conservation.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Small islands easier to implement plans.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Immediate benefits must be seen.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Baseline data necessary.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Local fishermen help with MPA location decisions.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Conclusions</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Locals must understand how problem and answer related.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Management groups must have respected members.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Link with all potentially helpful groups.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">All plans vulnerable to politics and outside groups.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<b><br /></b></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<b><br /></b></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<b><br /></b></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<b>Part 2 - Conservation History on the Great Barrier Reef:</b></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<br />The Great Barrier Reef = GBR<br />Great Barrier Reef Marine Park<br /><br />Outline<br />Background<br />Why was rezoning of GBR necessary?<br />Representative Areas Program (RAP) (only part of solution)<br />Phase 1 and 2<br />Final zoning plan<br />Implementation phase<br />Monitoring<br />Other actions<br />Reef Water Quality Plan<br />Reducing fishing and policing<br /><br />The Great Barrier Reef = GBR<br />345,000 km2<br />> 2000 km long<br />2900 separate reefs<br />> 900 islands<br /><br />Formation of the Park<br />Late 1960’s – early 1970’s—much agitation for a park, reinforced by plans to mine Ellison Reef (off Innisfail)<br />Politicians promised that the GBR should be protected as a Park<br />Park established in 1975, under Great Barrier Reef Marine Park Act (Federal Parliament Act)<br />Implementation<br />Park boundaries are non-negotiable, can only be changed by Act of Parliament<br />No mining within the Park<br />Development & implementation of zoning plans is a Federal responsibility<br />Day to day management is the responsibility of Queensland Parks & Wildlife Service<br />Zoning Plans<br />First areas to be zoned Capricorn and Bunker, finished in 1977<br />Subsequently the other regions were zoned<br />Zoning plans reviewed at regular intervals, with public participation, and plans changed over time and even the type of zones changed<br /><br />GBRMPA<br />Based in Townsville<br />Responsible to Minister for Science<br />Issues permits and licences, including those for scientific research<br />GBR declared World Heritage Area in 1981— such listing requires regular report card to ensure the reef is being maintained<br /><br /><br />During the 1990’s<br />Increasing use of the reef by tourists<br />Increased scientific knowledge of the reef<br />Increasing awareness of the connectivity of reefs (mass spawning)<br />Increasing evidence of decline of some habitats, especially inshore<br />The Great Barrier Reef Is ‘Under Pressure’<br /><br /><br />Downstream effects of land use (water quality issues)<br />Coral bleaching<br />Coastal developments<br />Increasing fishing effort and impacts<br />Shipping & pollution incidents<br />Increasing tourism and recreation<br />Trends in Regional Biodiversity Are Negative<br />Fishing effort increasing substantially in intensity & spatial extent (coral trout fishery—effort x2 since 1995; shark catch x5 since 1991)<br />Turtles–all 6 species threatened; 2 are endangered (Loggerhead and Olive Ridley)<br />Dugong population south of Cooktown has declined >90% since mid-1980’s<br />Humpbacks listed as vulnerable; other cetaceans (Irrawaddy & Indo-Pacific hump-backed dolphins) listed as rare<br />Trends for most species unknown<br />GBR Is Not Isolated From World Trends<br />10% of world’s reefs destroyed or severely degraded<br />58% of world’s reefs potentially threatened<br />70% reefs already degraded in Indonesia & Philippines<br />On current trends 70% of the world’s reefs will have gone in 40 years<br />Minimising the<br />‘Pressures’<br />Downstream effects of land use ==> Reef Water Quality Action Plan (results not immediate)<br />Coastal developments ==> Aquaculture Regs; GBRMP permit requirements<br />Increasing fishing effort and impacts ==> Queensland FS fisheries management plans (ECTMP, Reef Line)<br />Minimising the<br />‘Pressures’<br />Shipping & pollution incidents ==> Australia Marine Shipping Authority shipping review, compulsory pilotage, mandatory reporting, etc<br />Increasing tourism and recreation ==> PoMs; new tourism framework<br />Threatened species ==> new policies; species recovery plans; seasonal closures, RAP<br />Protecting biodiversity ==> RAP<br />Why was rezoning of the GBR necessary?<br /><br />Queenslanders depend on the GBR<br />Important for economy—tourism, commercial fishing, recreational fishing, shipping<br />Important for Traditional Owners—connection with Sea Country<br />Important for communities—relaxation, lifestyles<br />>90% Australians (including Queenslanders) wanted more no-take zones<br />Important for building knowledge—education, research<br />Better protection = insurance for all these values<br /><br />Connectivity in the GBR<br /><br />An overview of RAP<br />Representative examples of the entire diversity of habitats protected<br />RAP reviewed the existing zoning of the Marine Park<br />RAP attempted to minimise negative impacts for users and stakeholders while aiming to achieve protection of biodiversity<br />RAP has meant an increase in Green Zones to protect biodiversity<br />RAP is a crucial part of the solution to a complex problem<br /><br /><br />Other Issues Addressed During Rezoning<br />Some current zoning plans had been in existence for 16 years<br />Ensured consistent zone names and zone provisions throughout GBR<br />Coastal areas zoned for first time<br />Clearer delineation of zone boundaries (GPS co-ordinates)<br /><br />Developing the Zoning Plan<br />The Zoning Plan was developed using environmental, economic, and social information<br />Clear Principles on how to use the environmental and social information were followed<br />These principles were set out in the first round of community participation (CP1)<br />Environmental Information<br />Bioregions<br />Bioregions were mapped between 1999 and 2002 using expert knowledge and best available data and methods<br />30 reef bioregions 40 non-reef bioregions<br />Many bioregions previously lacked adequate protection<br />At least 20% of each bioregion included in a no-take zone<br />The GBR Marine Park<br /><br />Non reef bioregions<br /><br /><br />Environmental Information<br />Other key issues:<br /><br />Special and unique places<br />Critical habitats such as turtle nesting sites<br />Deep & shallow water sea-grass, fish spawning sites etc.<br /><br />Special and unique places<br />Critical turtle nesting areas<br />Environmental Information<br />Biophysical Principles guided selection and use of environmental information<br />The Principles :<br />were developed by independent reef scientists<br />published in CP1<br />said that at least 20% of each bioregion had to be in no-take zones<br />No-take zones must be<br />large<br />arranged to form viable network, allowing connectivity, provides insurance policy<br /><br /><br />Social & Economic Information<br />Sources:<br />Recreational fishing diaries, and tag and release records<br />Commercial fishing log-books<br />The location of boat-ramps and coastal developments<br />Historic ship-wrecks<br />Visitor use data<br /><br />Over 10,000 submissions received in Phase 1 & >21,000 in Phase 2<br />All submissions read to identify community issues<br />All submissions were taken into account<br />Recreational fishing sites<br />Commercial fishing values<br />Using Social Information<br />Social, Economic, Cultural and Management Principles were:<br />developed by an independent panel of experts<br />published in Community Phase 1<br /><br />The SEC Principles attempted to<br />minimise impact on existing users of the Marine Park<br />be fair—ie not impacting on one group or community more than another<br />but needed a Zoning plan easy to enforce<br />Previous Zoning<br />Previous Zoning, plus Trawl Plans<br />New green zones—environmental data only<br />Green zones—using economic data too<br />Green zones—revising boundaries<br />The Plan<br />What Does This Plan Do?<br />Provides strong, medium and long-term protection for future generations<br />Green zones mean more and bigger fish<br />Green zone spill-over, better fishing for reef communities<br />Natural values which attracts tourists and $ will be maintained<br />Protects at least 20% of each bioregion, special and unique areas, important habitats, and nesting areas—over 33% achieved<br /><br />Phases of RAP<br />Classification (map biodiversity)<br />Reviewed existing protection<br />informal consultation with user groups<br />formal Community Participation phase 1<br />Identification of possible network options<br />Selection of most acceptable network<br />Draft zoning plan<br />formal Community Participation phase 2 (over 21,000 submissions)<br />Ministerial & parliamentary approval March 2004<br />Implemented July 1st 2004<br /><br />Representative Areas Program<br />A new and effective network of ‘no-take’ areas representative of all bioregions helps to:<br />maintain biological diversity<br />maintain ecological processes and systems<br />provide an ecological safety margin, and if necessary, enable species and habitats to recover<br />ensure viable and sustainable industries<br />Current Status<br />Distribution of information and many maps to fishers, tourist operators, dive, boat and bait shops<br />Revised maps at boat ramps<br />Sorting out current permits in relation to new zoning, research stations issuing permits<br />Working with GPS manufacturers to incorporate zoning plans into charts, some available<br />Website available to download zoning plans for particular areas of interest<br /><br />Related Activities<br />Reef Water Quality Protection Plan-implemented<br />Fisheries related: Reduction of number of fishing boats<br />Reduction in areas where trawling allowed<br />compensation being paid<br />Increased surveillance, penalties imposed<br />Dugong protected areas and reduce netting areas<br />Qld zoned adjacent coastal parks<br />Recognition of RAP<br />Authority awarded a Eureka Prize for Biodiversity Research and Banksia Environmental Award<br />WWF Australia acknowledges its importance for conserving biodiversity<br />Recognition overseas of importance of this approach to marine park management<br />Best practise<br />Relevance to Other Areas<br />Zoning with scientific basis<br />Problems facing the GBR faced by all reefal areas<br />Methods for zoning multi-use parks relevant to all areas in Australia and elsewhere<br />Such community involvement results in ownership and stewardship of the reef– schools adopting reefs, communities becoming effective policers<br />Other Management Strategies<br />Reef Water Quality Protection Plan<br />being implemented but ongoing and results will take years to be apparent<br />Reduction in number of fishing licences, compensation being paid<br />Increasing policing and enforcement<br />Global warming— the big question<br />increased rates of bleaching<br />increased cyclones activity<br />What is the long term future for the GBR?<br /></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<b>Part 3 - Looking towards the future (De'ath et al. 2012)</b></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">~50% of coral lost in GBR in last 27 years!!</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Loss due to:</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Storms (48%)</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">COTS (42%)</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Bleaching (10%)</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small; line-height: 18px;"><br /></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small; line-height: 18px;">So, is conservation really working?</span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">What can be done to stop this loss?</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">Focus on COTS possible.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;"><br /></span></span></div>
</div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<b>Conclusions (1):</b></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">1. Increased connections in the world are increasing biological invasions.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">2. Invasions can be rapid and irreversible.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">3. Large scale management often needed, and international cooperation.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">4. Coral reef biodiversity patterns different from land; different management needed.</span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<b>Conclusions (2):</b></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
</div>
</div>
<div>
<div>
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">1. Coral reefs are linked to other ecosystems, both marine and on land.</span></span></div>
<div>
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">2. Conservation plans must protect linked areas and ecosystems, and not “islands”.</span></span></div>
<div>
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">3. Protected areas should be decided based on endemism, geographic features, neighboring ecosystems, etc.</span></span></div>
<div>
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">4. Successful conservation involves all levels of people, but most important are locals.</span></span></div>
<div>
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">5. Without demonstration of monetary value, coral reef protection very vulnerable to politics.</span></span></div>
<div>
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;"><div>
6. In the future, more conservation plans will be implemented.</div>
<div>
7. The gap between well protected areas and those not protected will widen.</div>
<div>
<div>
8. Very few non-protected reefs will survive.</div>
</div>
</span></span></div>
<div>
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small; line-height: 18px;"><b>We must do MORE!</b></span></div>
<div style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4;">
<b>Conclusions (Okinawa)</b></div>
<div style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4;">
<span class="Apple-style-span" style="font-weight: normal;">Points to consider for Okinawa/Ryukyu Islands:</span></div>
</div>
</div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
Only three major governments (National, 2 Prefectural).<br />However, management is very ambiguous.<br />Local fisheries have strong power; no no-take zones anywhere in Japan, aquaculture common.<br />Competing interests within national government have different agendas (Construction, Environment).<br />National laws for parks weak.<br />Okinawa Prefecture likely has strong wishes, but needs money from National government.<div style="clear: both;">
</div>
</div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<br /></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<b>References cited:</b></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">1. White & Vogt. 2000. Philippine coral reefs under threat: lessons learned after 25 years of community-based reef conservation. Mar Poll Bull 40: 537-550. </span></span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="position: relative; width: 586px;">
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;">2. GBRMPA Conservation Plan. </span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small; line-height: 18px;">3. De’ath et al. 2012. The 27–year decline of coral cover on the Great Barrier Reef and its causes. PNAS 10.1073/pnas.1208909109</span></div>
<div class="post-body entry-content" id="post-body-1156894883561196480" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<br /></div>
</div>
<div class="post-footer" style="color: white; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.6; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 1.5em;">
</div>
James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-41567284618421587332013-01-23T03:01:00.007-08:002013-01-23T03:17:31.405-08:00January 9, 2013 class notes<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><b>Outline</b></span><br />
<div class="post-body entry-content" id="post-body-6432907804209323926" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
1. Quick introduction to diseases.<br />
2. Common coral reef diseases.<br />
3. Why are diseases becoming common?<br />
4. How do diseases affect conservation?<br />
5. <span style="font-style: italic;">Terpios</span>: a new threat<br />
6. Conclusions</div>
<div class="post-body entry-content" id="post-body-6432907804209323926" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<br /></div>
<div class="post-body entry-content" id="post-body-6432907804209323926" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<b>Part 1: Disease</b>Example 1: Plague in humans<br />
<br />
• Plagues have struck humans many times.<br />
• Often kill 10-50% of population.<br />
• Caused by an influenza virus.<br />
• Two most infamous cases are 13th century Black Plague, and 1919-1920 Spanish Influenza.<br />
• No one knows where plagues came from.<br />
• Spread through common routes of trade.<br />
• Spread faster in modern cases.<br />
• Often affects young adults worse due to “cytokine storms”.<br />
Spanish Influenza<br />
• In some countries fatalities were as high as 50%.<br />
• Killed more people than WWI.<br />
<br />
How does this happen?<br />
• New mutation in influenza virus that most humans do not have capability to respond to.<br />
• Genetic variation provides resistance.<br />
• SARS is a more recent case.<br />
<br />
<br />
Example 2:<br />
Introduction of a new disease into an isolated area<br />
Elm trees common in North America and Eurasia.<br />
Preyed upon by two species of bark beetles.<br />
Beginning in the 1910s, some elms began to die.<br />
Die-offs became rapid in 1960s.<br />
Bark beetles somehow involved in the disease.<br />
<br />
Survival of elms close to 0%.<br />
• The causative agents of DED are ascomycete microfungi.<br />
• Carried by the elm bark beetles.<br />
<br />
• Three species are now recognized: <span style="font-style: italic;">Ophiostoma ulmi</span>, which afflicted Europe in 1910, reaching North America on imported timber in 1928, <span style="font-style: italic;">Ophiostoma himal-ulmi</span>, a species endemic to the western Himalaya, and the extremely virulent species, <span style="font-style: italic;">Ophiostoma novo-ulmi</span>, which was first described in Europe and North America in the 1940s and has devastated elms in both areas since the late 1960s.<br />
• The origin of <span style="font-style: italic;">O. novo-ulmi</span> remains unknown but may have arisen as a hybrid between <span style="font-style: italic;">O. ulmi </span>and<span style="font-style: italic;">O. himal-ulmi</span>.</div>
<div class="post-body entry-content" id="post-body-6432907804209323926" itemprop="description articleBody" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 1.4; position: relative; width: 586px;">
<br />
<b>Part 2: Common coral reef diseases</b>Introduction to<br />
coral reef diseases<br />
• Bacteria observed in corals in early 1900s.<br />
• Diseases noticed in 1970s, seemingly increasing over last 30 years.<br />
• 34 mass events, affecting sponges, seagrasses, cetaceans, urchins, fish, molluscs, corals.<br />
• Have changed composition of reefs.<br />
<br />
Diseases affecting Scleractinia<br />
• Many diseases named, but very little known.<br />
• Most pathogens still unknown.<br />
• Most common in Atlantic (Green & Bruckner).<br />
• Not to be confused with coral bleaching.<br />
Green & Bruckner 2000<br />
Black Band Disease (BBD) Caused by numerous cyanobacteria (500 spp.) as a microbial mat.<br />
Mat makes the colored band.<br />
First observed in 1973.<br />
Moves 3mm to 1cm/day.<br />
Found in 42 spp. of coral.<br />
<br />
Kuta & Richardson 2002<br />
• BBD correlates strongly with depth, temperature, nitrites.<br />
• Also correlates with diversity and orthophosphate.<br />
White band disease: Pathogen unknown, may be bacteria. Noticed in 1981.<br />
Tissue loss from base to tip.<br />
Affects two species, <span style="font-style: italic;">Acropora cervicornis</span> and <span style="font-style: italic;">A. palmata.</span><br />
Moves 3mm to 1cm/day.<br />
• WBD has drastically altered Caribbean reefs.<br />
• Shifts in coral species.<br />
• Loss of overall coral cover; algae increasing.<br />
<br />
• Both species now “threatened”.<br />
• Losses of over 98% of <span style="font-style: italic;">A. cervicornis</span>. Locally extinct.<br />
White plague: Affects many species, but no acroporoids.<br />
Caused by <span style="font-style: italic;">Aurantimonas</span> bacteria.<br />
First observed in 1977.<br />
<br />
Aspergillosis: Caused by terrestrial fungi.<br />
Affect mainly Atlantic gorgonians.<br />
Also affects waterfowl.<br />
Noted in 1997.<br />
<br />
Tumors: Similar to cancer.<br />
Affects mainly <span style="font-style: italic;">A. palmata</span>.<br />
Irregular growth, no zooxanthellae.<br />
Noted in 1960s and 1970s.<br />
<br />
Other diseases: Many other diseases.<br />
Mostly known from Atlantic.<br />
Yellow band disease, yellow spot disease, white pox disease, brown band disease.<br />
Most noted for first time in last 20 years.<br />
Pathogens usually unknown.<br />
<br />
<b>Part 3: Why are diseases becoming common?</b>1. Global warming?<br />
• Many people blame global warming.<br />
• But likely much more complex.<br />
2. Nutrient enrichment - Bruno et al. 2003<br />
• Experiments done with YBD and <span style="font-style: italic;">Aspergillosis</span>.<br />
• Controls were disease only, experimental with added nitrogen and phosphorus.<br />
Results - <span style="font-style: italic;">Aspergillosis</span><br />
• Nutrients increased severity of disease in sea fans.<br />
Results - YBD<br />
• Presence of nutrients increased rate at which YBD developed in two species of coral.<br />
3. Dust? -<br />
Garrison et al. 2003<br />
• Airborne dust from Africa and Asia carries many contaminants to reefs.<br />
• Global warming and desertification increasing dust, therefore increasing contaminants.<br />
<br />
<b>Part 4: How do diseases affect conservation?</b>Effects are widespread<br />
Many studies have documented widespread coral decline in almost ALL coral species.<br />
Porter et al. 2001 showed many declines 1996-1998 NOT due to coral bleaching but disease.<br />
<br />
• Porter et al. 2001 cont<br />
• Green & Bruckner 2000<br />
<br />
• Green & Bruckner 2000<br />
Many examples of diseases spreading, many examples of reef degradation (show many photos).<br />
<br />
Overview of disease<br />
• All diseases have negative effects.<br />
• Only WBD has changed communities drastically.<br />
• Pacific 15 years behind Atlantic.<br />
• Compounded negative influences more severe for coral reefs.<br />
<br />
<b>Part 5: Preliminary results of field surveys of <span style="font-style: italic;">Terpios</span> outbreaks in the Nansei Islands, Japan</b><br />
<span style="font-style: italic;">Terpios hoshinota</span> Rützler and Muzik 1993<br />
<span style="font-style: italic;">Terpios</span> in the Nansei Islands - history<br />
Outbreak noticed in Mariana Is. 1973. (Bryan 1973 )<br />
Terpios-Nansei project<br />
Assess the current distribution of Terpios in the Nansei Islands.<br />
Establish monitoring sites.<br />
If present, characterize sexual reproduction & ecology.<br />
Methods<br />
Survey all major islands by snorkel/scuba (Reimer).<br />
Monthly/bi-monthly sampling at designated locations – histology (Hirose), genetics (Chen).<br />
Permanent transects at massive outbreak (Reimer), analyses (Reimer, Nozawa).<br />
Preliminary results<br />
Three situations observed: none, small amounts, massive outbreak<br />
Disappearance?<br />
Yonama, Tokunoshima had massive outbreak (87.9% cover) in 1986 (Marine Park Center Foundation 1986).<br />
Discussion<br />
<span style="font-style: italic;">Terpios</span> absent or present in small numbers in most reefs in Nansei Islands (38/39 examined locations).<br />
Coverage does not appear to fluctuate much in most locations.<br />
Discussion & Questions<br />
Massive outbreaks still occur in Nansei Islands.<br />
How long do outbreaks last?<br />
“Recovery” observed at Yonama, but is this true recovery? At least, not a dead-end.<br />
Results suggest outbreaks are linked to reef degradation, but factors not clear.<br />
Future work<br />
Permanent transect results & analyses.<br />
Try to quantify speed at which massive outbreaks can occur.<br />
Combine analyses with genetic, histological results.<br />
Examine Yakomo (current outbreak location) to understand causes of outbreaks. Why this location?<br />
<br />
<b>Part 6: Conclusions.</b>Conclusion 1<br />
• Disease more widespread on reefs in Caribbean.<br />
• More research? Partially.<br />
• Monitoring in Pacific very critical.<br />
Conclusion 2<br />
• Only one disease has permanently changed community structure (WBD).<br />
• Other diseases locally important.<br />
Conclusion 3<br />
• Very few studies have investigated in detail mortality rates.<br />
• Monitoring of individual colonies needed.<br />
Conclusion 4<br />
• Diseases increasing.<br />
• Bleaching appears to be more critical, but two problems appear related.<br />
Conclusion 5<br />
• Diseases not well understood.<br />
• Many diseases affect many species; possibly more or less diseases.<br />
• Pathogens need to be investigated.<br />
Conclusion 6<br />
• While bleaching currently more serious, foolish to ignore diseases.<br />
• May be “indicator” of serious problems, similar to amphibians.<br />
What needs to be done<br />
• <3% of reefs in danger have low human impact.<br />
• More research needed on human influences and pathogens.<br />
• Management and conservation then follow.<br />
References:<br />
1. Green & Bruckner. 2000. The significance of coral disease epizootiology for coral reef conservation. Biological Conservation 96: 347-361.<br />
2. Aronson & Precht. 2001. White-band disease and the changing face of Caribbean coral reefs. Hydrobiologia 460: 25-38.<br />
3. Garrison et al. 2003. African and Asian dust: from desert soils to coral reefs. BioScience 53: 469-481.<br />
4. Bruno et al. 2003. Nutrient enrichment can increase the severity of coral diseases. Ecology Letters 6: 1056-1061.<br />
5. Kuta & Richardson. 2002. Ecological aspects of black band disease of corals: relationships between disease incidence and environmental factors. Coral Reefs 21: 393-398.<br />
6. Porter et al. 2001. Patterns of spread of disease in the Florida Keys. Hydrobiologia 460: 1-24.<br />
7. Reimer, Hirose, et al. new <span style="font-style: italic;">Terpios</span> papers.</div>
James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-8814642634022109922013-01-23T02:58:00.000-08:002013-01-23T03:02:14.219-08:00December 21, 2012 class notes<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Outline</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. Introduction: What is a species?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. Taxonomic species: Amphipods in the Ryukyus.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. Biological species: Fish species complex!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. OTU & barcodes: ARMS and estimating coral reef biodiversity.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">5. Conclusions.</span><br />
<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: x-small;"><span class="Apple-style-span" style="line-height: 18px;"><br /></span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. Introduction: What is a species?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">What is biodiversity? (Review)</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Biodiversity = Number of taxa (species, genera).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">OTUs = operational taxonomic units</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Coral reefs are highly biodiverse, <0.2% of surface of Earth, >25% of marine species live there.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">What is a species?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">A species can be different, depending on who you talk to, or what meaning is implied.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Before we discuss species, we must be clear about what species concept we are discussing.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Three types are:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. taxonomic species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">A species with a scientific name.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Names are important for science & conservation.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Accuracy and authorship important.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Problems:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Naming species takes time & money.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Few experts.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. Biological species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">A species proven to reproduce only with itself.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Reproductive isolation.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Species concept important.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Problems:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Experiments take time & money.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Hybrids? Evolution is messy.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. OTU/barcode species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">A species defined by genetic differences.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Implies a threshold value.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Quick and easy.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Problems:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Sequencing species takes time & money.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Limited by previous knowledge.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Not always “true”, barcoding gap is problematic.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">It is estimated we have described 1~25% of the total marine species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Description of all species – possible?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">However, describing is important.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. Unknown species - What kind of undescribed species exist?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">We have no idea what awaits discovery.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. “Hidden” species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Hidden species may be hidden due to their cryptic nature, or due to researchers not being able to distinguish them from other, similar species. Usually small.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Often, there are large groups of “species complexes” that are hard to make sense of.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">C. Known but not described species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">We know this is a zoanthid. DNA has shown us how it is related to other zoanthids (=very unique).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">We also know it is undescribed, and only on Okinawa.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">It is waiting to be described.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Part 2: Taxonomic species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Commensal amphipods in Okinawa</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">White & Reimer 2011-2012</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Taxonomic species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Can be detected through observation of morphology or classic diagnostic characteristics. DNA?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Compare with previous taxonomic literature.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Only way to name a species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Leucothoidae (139 sp.) – one family of amphipods</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Anamixid clade (pronounced sexual dimorphism):</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• 22</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">Anamixis</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Stebbing, 1897</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• 4</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">Nepanamixis</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Thomas, 1997a</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• 13</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">Paranamixis</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Schellenberg, 1938</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Leucothoid clade</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">(minimal to moderate sexual dimorphism):</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• 98</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">Leucothoe</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Leach, 1814a</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• 2</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">Paraleucothoe</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Stebbing, 1899</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Ecologically unique</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• Endocommensal associates of sponges, ascidians, and bivalve mollusks</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• Extended parental care</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• Social system</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• Potential eusociality</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">•</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">These are completely unexamined in Okinawa!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Contain two morphotypes, leucomorphs and anamorphs, previously thought to be different families of amphipods! DNA barcoding confirmed same species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Materials and Methods</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• Collect in-situ directly from host, take whole host, or coral rubble</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• Traditional taxonomy</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• Digital Inking</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">• Molecular DNA sequencing</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Results</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">25 new species from Okinawa in 1.5 years. More diverse in Okinawa than the GBR.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Part 3: Biological species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Fish species complex in the Pacific (Leray et al. 2010)</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Biological species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Can be detected through observation of reproduction.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Also, reproductive experiments.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">But these require extensive field work. Recently, molecular analyses usual, using phylogeny.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Background – Genus</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">Dascyllus</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">: Complex has 4 species:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">D. trimaculatus</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">(E. Africa to Central Pacific): 3 spots</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">D. albisella</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">(Hawaii): white flanks</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">D. strasburgi</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">(Marquesas Islands): gray</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">D. auripinnis</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">(Line, Phoenix Islands): yellow fins</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Each species has its own ecology and preferred habitats.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Materials and Methods</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Specimens (n=563) from across the Indo-Pacific.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Microsatellite DNA data examined (data from previous research included).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Phylogenetic analyses and genotype assignment.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Results</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Previous research showed 5 clades, not 4 (Bernadi et al. 2003).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">This research showed 7 (!) groups of</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">Dascyllus</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">, not all with clear morphology.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Appears ancient history of Indo-Pacific combined with recent evolutionary events drives speciation.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Hybridization appears to be occuring.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">NOTE: unknown species are not yet valid species, or new species. They are undescribed species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">So…. Biological species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Results could lead to “finding” undescribed species or groups</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">This leads to…</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Taxonomic species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Describing a species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Only way to give a scientific name.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">New species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Part 4: OTU/barcode species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">ARMS and crustaceans</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Plaisance et al. 2011;</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Brainard et al. 2010</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Background:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Coral reef monitoring of other species asides from fish/corals.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Establish systematic and consistent metric to assess and monitor change.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">ARMS – manmade deployment devices to look at crustaceans/molluscs, etc., simulate dead coral heads.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Easy to build, 200USD each.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Rugged, look like plastic boxes/crates.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Prototypes tested in Northwestern Hawai’i. Seemed to work well.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Deployed worldwide, and retrieved. Then processed, samples preserved, DNA sequencing (DNA barcoding).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">So…. OTU/barcode species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Results could lead to “finding” undescribed species or groups</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">This leads to…</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Biological species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Results could lead to “finding” undescribed species or groups</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">This leads to…</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Taxonomic species</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Describing a species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Only way to give a scientific name.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">New species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">References cited:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. CP Meyer, G Paulay. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3(12) e422.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. KN White, JD Reimer – three papers (2011-2012). Commensal Leucothoidae in the Ryukyu Archipelago, Japan. ZooKeys (in press).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. M Leray, R Beldade, SJ Holbrook, RJ Schmitt, S Planes, G Bernadi. 2010. Allopatric divergence and speciation in coral reef fish: the three spot dascyllus,</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">Dascyllus trimaculatus</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">, species complex. Evolution 64-5: 1218-1230.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. L Plaisance, MJ Caley, R Brainard, N Knowlton. 2011. The diversity of coral reefs: what are we missing? PLoS One vol 6 issue 10 e25026.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">5. R. Brainard et al. 2009. Autonomous Reef Monitoring Structures (ARMS): a tool for monitoring indices of biodiversity in the Pacific Islands. Pacific Science InterCongress, March 4, 2009.</span>James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-67565097322872501502012-12-18T20:20:00.001-08:002012-12-18T20:20:43.417-08:00Additional classesHi everyone,<br />
<br />
After checking students' schedules, we have decided the additional dates for classes as follows:<br />
<br />
1. Tuesday, January 15th, 4th period (14:40-16:10).<br />
2. Thursday, January 24th, 5th period (16:30-18:00).<br />
<br />
Classrooms are not yet decided.<br />
<br />
One or two students' schedules do not fit some of these classes, so if you cannot attend, please get the notes from the blog or another student. As attendance does not count in your mark, as long as you have notes you should be able to study for the test!<br />
<br />
cheers,<br />
<br />
JDRJames Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-12055530600734237742012-12-17T00:55:00.004-08:002012-12-17T00:55:44.882-08:00November 28, 2012 class notes<br />
<b>Class notes for November 28, 2012</b><br />
<br />
<b>Recent Research: Symbiodinium introduction & diversity studies</b><br />
<div>
Outline:</div>
<div>
<div>
1. Review of <i>Symbiodinium</i> and coral bleaching.</div>
<div>
2. Bleaching in Thailand, 2010.</div>
<div>
3. <i>Symbiodinium</i> diversity.</div>
</div>
<div>
<br /></div>
<br />
<b>Part 1: Review of <i>Symbiodinium</i> and bleaching.</b><br />
• Dangers facing coral reefs:<br />
• Global warming is raising the temperature of the ocean; this kills corals - “coral bleaching”.<br />
• Also, as the oceans become more acidic, it is more difficult for corals to make their skeletons.<br />
• Perhaps 90% of coral reefs will be dead by 2050.<br />
• Diagram of iving tissue<br />
• Numbers of zooxanthellate genera over time, increase in ZX genera of corals.<br />
• More diverse than ever, showing benefits of symbioses.<br />
• Believed to have started approximately 60 million years ago.<br />
• Symbiodinium spp. in invertebrates holobiont=host+symbiont(s)<br />
• Corals and symbionts<br />
• Many shallow water corals get their energy from symbiotic zooxanthellae.<br />
• These small animals make it possible for corals to live in the warm oceans.<br />
• But, these symbionts are sensitive to hot ocean temperatures.<br />
• What turns the coral white?<br />
• As a stress response, corals expel the symbiotic zooxanthellae from their tissues<br />
• The coral tissue is clear, so you see the white limestone skeleton underneath<br />
• What can stress a coral?<br />
• High light or UV levels<br />
• Cold temperatures<br />
• Low salinity and high turbidity from coastal runoff events or heavy rain<br />
• Exposure to air during very low tides<br />
• Major: high water temperatures<br />
• Thermal stress<br />
• Corals live close to their thermal maximum limit<br />
• If water temperature gets 1 or 2°C higher than the summer average in many parts of the world, corals may get stressed and bleach<br />
• NOAA satellites measure global ocean temperature and thermal stress<br />
• How warm is warm?<br />
• How hot do you think the ocean has to get before corals start to bleach?<br />
<b>• GLOBAL WARMING</b><br />
• Glaciers and sea ice are melting<br />
• World map showing levels of coral bleaching. Source: ReefBase<br />
• Can corals recover?<br />
• Yes, if the stress doesn’t last too long<br />
• Some corals can eat more zooplankton to help survive the lack of zooxanthellae<br />
• Some species are more resistant to bleaching, and more able to recover<br />
• Can corals recover?<br />
• Corals may eventually regain color by repopulating their zooxanthellae<br />
• Algae may come from the water column<br />
• Or they may come from reproduction of the few cells that remain in the coral<br />
• Can corals recover?<br />
• Corals can begin to recover after a few weeks<br />
• Does bleaching kill corals?<br />
• Yes, if the stress is severe<br />
• Some of the polyps in a colony might die<br />
• If the bleaching is really severe, whole colonies might die<br />
• Bleaching in Puerto Rico killed an 800-year-old star coral colony in 2005<br />
• What else can stress do to corals?<br />
• Question: what is something that happens to people when they are highly stressed?<br />
• What else can stress do to corals?<br />
• Question: what is something that happens to people when they are highly stressed?<br />
• Bleaching and coral disease<br />
• Coral diseases are found around the world<br />
• High temperatures and bleaching can leave corals more vulnerable to disease<br />
• Can quickly kill part or all of the coral colony<br />
• Bleaching and bioerosion<br />
• We have seen that bleaching can kill part or all of a coral colony<br />
• Areas of dead coral are more vulnerable to bioerosion (when animals wear away the coral reef’s limestone structure)<br />
• Storms & coral bleaching<br />
• The same warm water that causes corals to bleach can also lead to strong storms.<br />
• Storms: a mixed blessing<br />
• Storms: a mixed blessing<br />
• Each passing hurricane in 2005 cooled the water in the Florida Keys.<br />
<br />
<b>Part 2: Coral bleaching images from Phuket, Thailand in 2010</b><br />
<br />
Corals (and many other coral reef invertebrates) are in symbiosis with <i>Symbiodinium</i> (zooxanthellae).<br />
This symbiosis allows these invertebrates to live in nutrient-deficient sub-tropical and tropical waters.<br />
Algal-animal symbioses are a successful strategy that has been repeated many times in evolution.<br />
<div>
<br /></div>
<div>
Weak point:</div>
<div>
<div>
Despite the success of this symbiosis, it has one very serious weak point:</div>
<div>
<i>Symbiodinium</i> are very sensitive to low and high temperatures.</div>
<div>
<18°C, and >30°C.</div>
</div>
<div>
Coral bleaching:</div>
<div>
<div>
When temperatures are abnormal for the holobiont, stress occurs.</div>
<div>
With this stress, thylakoids in <i>Symbiodinium</i> begin to break down; the symbiont begins to poison the host.</div>
<div>
Corals lose their symbionts, either through cell-death, or by expelling them.</div>
<div>
Hosts turn white = coral bleaching.</div>
</div>
<div>
<br /></div>
<div>
Predicting coral bleaching:</div>
<div>
<div>
The NOAA (USA) has spent much time on predicting bleaching.</div>
<div>
Can now predict bleaching very accurately.</div>
<div>
These tools available for free on the internet.</div>
</div>
<div>
<div>
SST=sea surface temperature</div>
<div>
DHW=degree heating weeks</div>
<div>
Daily max=expected average maximum SST for a certain day</div>
<div>
MMM=maximum monthly mean, average temperature of the hottest month</div>
</div>
<div>
SST anomolies, coral bleaching hot spots, degree heating weeks.</div>
<div>
<br /></div>
<br />
<br />
<b>Part 3: Investigating diversity of <i>Symbiodinium</i>: past to present.</b><br />
What are zooxanthellae?<br />
Algae that live in the coral polyp’s surface layer<br />
Algae get nutrients and a safe place to grow<br />
Corals get oxygen and help with waste removal<br />
Corals also get most of their food from the algae<br />
Symbiosis overview<br />
Genus <i>Symbiodinium</i><br />
Described in 1962 by H. Freudenthal.<br />
Within dinoflagellates.<br />
Was though there was one single species worldwide.<br />
<br />
Morphology & life cycle<br />
Host species<br />
Cnidaria (corals, jellyfish, anemone, zoanthids, octocorals).<br />
Mollusca (clams, snails).<br />
Platyhelminthes (flatworms).<br />
Porifera (sponges).<br />
Protista (forams).<br />
<br />
First genetic studies<br />
Rowan & Powers 1991.<br />
Utlized 18S ribosomal DNA.<br />
Sampled from corals & anemones.<br />
Found unexpected diversity!<br />
Recommended further genetic studies.<br />
<br />
Second wave of studies<br />
Used faster evolving DNA markers.<br />
Particularly ITS-rDNA.<br />
Even more diversity!<br />
Zooxanthellae clade<br />
DNA analyses<br />
Clade: A group composed of all the species descended from a single common ancestor<br />
Diversity<br />
Eight major clades known.<br />
Within each clade many subclades.<br />
Do not know what taxonomic level clades are equal to.<br />
Evolution and biogeography<br />
Many studies have catalogued diversity.<br />
Can now understand on many scales.<br />
Can predict evolution.<br />
Specific types<br />
Many subclades or types associate with similar hosts.<br />
Could be co-evolution.<br />
<br />
<i>Symbiodinium</i> in <i>Zoanthus sansibaricus</i><br />
We sampled the same species from 4 locations.<br />
Each host colony was shown to associate with one subclade of <i>Symbiodinium</i>.<br />
Subclade C1/C3 was common in the north, and subclade A1 was dominant in the south.<br />
C1/C3 has been shown to be a dominant Indo-Pacific “generalist”, with C15 common in <i>Porites</i> spp., and A1 a shallow-water specialist.<br />
<br />
In Okinawa, shallow and deep populations of<i> Z. sansibaricus</i>.<br />
Shallow colonies had <i>Symbiodinium</i> clade A1, or C1z.<br />
Deep colonies had different type; C1zd.<br />
Similar results seen in hard corals.<br />
Suggests many species of <i>Symbiodinium</i>.<br />
<div>
<br /></div>
<div>
Recent news!</div>
<div>
<div>
Types described using various DNA markers.</div>
<div>
Supported with morphological and ecological data.</div>
<div>
Suggests 1000s of species of <i>Symbiodinium</i>.</div>
<div>
Without names, these species cannot be protected.</div>
</div>
<div>
<br /></div>
<br />
<br />
Modes of transmission & flexibility<br />
2 major types; a) vertical and b) horizontal.<br />
Vertical should result in more co-evolution and less flexibility.<br />
Also, in horizontal, ZX from environment still rare.<br />
Changes in ZX<br />
over time?<br />
Changes have been seen over time in content of ZX within coral colonies!<br />
Particularly after bleaching events.<br />
ZX shuffling?<br />
<br />
Adaptive Bleaching Hypothesis (ABH).<br />
Very controversial, large conservation implications.<br />
Two ways this occurs.<br />
Diversity within colonies<br />
Same colony may have different ZX at different locations!<br />
Differences in types<br />
Since we know diversity, we can experiment with different conditions.<br />
Many ZX are easy to culture.<br />
Control light, temperature, nutrients, etc.<br />
<br />
Can also then experiment <i>in situ</i>.<br />
<i>Symbiodinium</i> spp. characters<br />
Believed to alternate between a free-living stage with flagella, and a non-motile stage with chlorophyll.<br />
Believed to sexually reproduce, although this has not been observed.<br />
Overall morphological condition can degrade based on non-optimal environmental conditions, in particular low (<15 data-blogger-escaped-and="and" data-blogger-escaped-c="c" data-blogger-escaped-high="high">30ºC) sustained ocean temperatures.
<br />
“Adaptive bleaching” hypothesis<br />
Bleaching may enable corals to adopt different classes of zooxanthellae, better suited for a new environment. By:
<br />
‘symbiont switching’ (a new clade from exogenous sources) or
<br />
‘symbiont shuffling’ (host contains multiple clades and a shift in dominance occurs).
<br />
Can we protect corals from bleaching?
<br />
<br />
Marine invertebrate - <i>Symbiodinium</i> spp. symbioses overview
<br />
Symbiodinium spp. found in many clonal cnidarians (and other invertebrates) in tropical and sub-tropical oceans. <i>Symbiodinium</i> are the main reason coral reefs exist and have large levels of diversity.
<br />
<i>Symbiodinium</i> is now divided into 9 “clades” labelled A-H (of unknown taxonomic level) with many “subclades” (designated by numbers) within each clade (see various works by Pochon et al., and LaJeunesse et al.)<br />
Host species’ association with various clades and subclades of <i>Symbiodinium</i> (often more than one) may be at least partially responsible for differences in bleaching patterns seen during bleaching events (i.e. ENSO event of 2001, etc.).<br />
Also, some host species have been shown to have flexible associations with <i>Symbiodinium</i> over biogeographical ranges (depth, latitude, etc.) or time (summer versus winter, etc.). This is part of the Adaptive Bleaching Hypothesis (ABH) (Buddemier and Fautin 2004; Baker 2001), and is very contentious.
<br />
Need to understand <i>Symbiodinium</i> diversity within zoanthids before any discussion of symbiotic zoanthid ecology can be conducted.
<br />
<br />
<b>References</b>:
<br />
<br />
1. Rowan & Powers. 1991. Molecular genetic identification of symbiotic dinoflagellates (zooxanthellae). Marine Ecology Progress Series 71: 65-73..<br />
2. Stat et al. 2006. The evolutionary history of <i>Symbiodinium</i> and scleractinian hosts - Symbiosis, diversity, and the effect of climate change. Plant Ecology, Evolution and Systematics 8: 23-43.<br />
3. LaJeunesse 2005. ‘Species’ radiations of symbiotic dinoflagellates in the Atlantic and Indo-Pacific since the Miocene-Pliocene transition. Molecular Biology and Evolution 22: 570-581.<br />
4. Pochon et al. 2004. Biogeographic partitioning and host specialization among foramineferan dinoflagellate symbionts (<i>Symbiodinium</i>; Dinophyta). Marine Biology 139: 17-27.<br />
5. Reimer et al. 2006. Latitudinal and intracolony ITS-rDNA sequence variation in the symbiotic dinoflagellate genus <i>Symbiodinium</i> (Dinophyceae) in <i>Zoanthus sansibaricus</i> (Anthozoa: Hexacorallia). Phycological Research 54: 122-132.<br />
6. Kamezaki et al. 2012. Different zooxanthellae types in populations of the zoanthid <i>Zoanthus sansibaricus</i> along depth gradients in Okinawa, Japan. Marine Biodiversity (online).<br />
7. LaJeunesse et al. 2012. A genetics-based description of <i>Symbiodinium minutum</i> sp. nov. and <i>S. psygmophilum</i> sp. nov. (Dinophyceae), two dinoflagellates symbiotic with Cnidaria. Journal of Phycology (in press).<br />
<div>
<br /></div>
<br />
<div>
<br /></div>
James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-30189740502137036082012-12-17T00:38:00.001-08:002012-12-17T00:38:10.386-08:00November 21, 2012 class notes<br />
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>November 21, 2012</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>Reverse taxonomy examples</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>Outline</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
1. Trouble-shooting: dangers of reverse taxonomy.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
2. Examples of reverse taxonomy from mammals (terrestrial, marine).</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
3. Atlantic and Pacific corals.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
4. Four species of COTS.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
5. Deep-sea zoanthids.</div>
<div>
<br /></div>
<br />
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>Part 1 - dangers of reverse taxonomy </b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
What is morphological convergence?</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
In response to similar selective pressures, evolutionarily distant lineages evolve in similar ways and end up resembling each other in appearance, function, or both. (wiki answers)</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
In other words, distinct lineages look similar morphologically.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Not to be confused with the “ghost” of molecular convergence.</div>
<div>
<br /></div>
<div>
Much more common than thought!</div>
<div>
<div>
Many recent phylogenetic studies have shown morphological convergence is widespread.</div>
<div>
Butterflies, birds, lizards, algae, trees, even zoanthids!</div>
<div>
Famous recent examples include Atlantic and Pacific corals.</div>
</div>
<div>
<br /></div>
<div>
Extinct-extant convergence: Similar “shapes” or body plans have appeared many times throughout the fossil record, and may even remind us of extant species.</div>
<div>
<br /></div>
<div>
Cryptospecies</div>
<div>
<div>
Many “undiscovered” large vertebrate species may yet await description (e.g. Amato et al. 1998; Dung et al. 1993).</div>
<div>
These are from the deep sea, remote regions, or are cryptic in other ways.</div>
<div>
One famous example is theorized to exist in mountain regions of the world.</div>
<div>
Rarely seen, but many clues (sightings, footprints, etc).</div>
</div>
<div>
<br /></div>
<div>
Giant unknown hominids?</div>
<div>
<div>
Many legends exist of “giant apes” or “hairy men”.</div>
<div>
Common in the Himalayas (yeti) and in western North America (sasquatch).</div>
<div>
Despite large size, very little physical evidence they exist.</div>
</div>
<div>
<br /></div>
<div>
Evolutionary history of Gigantopithids</div>
<div>
<div>
These cryptospecies may have evolved from extinct <i>Gigantopithelus</i> (Matthiesson 1979).</div>
<div>
Fossils of <i>Gigantopithelus</i> known from Asia, until 3K ybp.</div>
<div>
Possible sister lineage to humans.</div>
</div>
<div>
<br /></div>
<div>
Materials and Methods</div>
<div>
<div>
Trips made to remote regions of Nepal 1992-1995, within the Himalaya mountain range (Matthiessen & Laird 1992; 1995).</div>
<div>
Region home to the “ye-the” or “mehti”; yeti in English (described in Herge 1960; Matthiessen 1979).</div>
<div>
Extensive trekking, traps, and local guides utilized.</div>
<div>
Very little concrete evidence found, although highly likely to exist in the mysterious Lo Monthang valley. </div>
<div>
<br /></div>
<div>
Hair samples</div>
</div>
<div>
<div>
Hair found by local guides in Lo Monthang valley, conclusively identified by them as “mehti” hair.</div>
<div>
Hair deposited in local temple.</div>
<div>
In 2003, request made to Nepalese government to examine hair granted.</div>
</div>
<div>
<br /></div>
<div>
DNA analyses</div>
<div>
<div>
DNA well-preserved in hair. </div>
<div>
Used mt 12S rDNA, excellent mammal marker, with modified universal primers L1091 and H1478 (Kocher et al. 1989).</div>
<div>
Acquired sequences aligned with 15 known mammalian groups, including homonids, chimpanzees, gorillas, whales, bovine, armadillo, and Perissodactyla (horses, rhinoceros, and zebra) sequences (all GenBank).</div>
</div>
<div>
<div>
Resulting SOAP alignment (Loytynoja & Milinkovitch 2001) subjected to MP, NJ, and Bayes analyses (Felsenstein 1985) using PAUP v 4.0b4a (Swofford 1997).</div>
<div>
ML consensus tree, with KH tests (Kishino & Hasegawa 1989).</div>
<div>
<br /></div>
</div>
<div>
Results</div>
<div>
<div>
Yeti formed highly supported monophyly with ungulates (horses, zebra, donkey, well within Perissodactyla.</div>
<div>
Identical mt 12S rDNA to X9547 and U02581.</div>
<div>
Well removed from primates, and outgroups.</div>
</div>
<div>
<br /></div>
<div>
Conclusions:</div>
<div>
<div>
Despite “primate” appearance, the yeti is ungulate (=related to horses).</div>
<div>
Yeti have undergone extensive morphological convergence with primates despite being genetically distant.</div>
<div>
This idea was first proposed in Herge 1960!</div>
</div>
<div>
<br /></div>
<div>
Questions</div>
<div>
<div>
Do you believe the results? Why or why not?</div>
<div>
What else could cause these results?</div>
<div>
What can we learn from this?</div>
<div>
How can we prevent such things from happening?</div>
</div>
<div>
<br /></div>
<div>
<b>Part 2 - New species (marine & terrestrial)</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>2a. A 3rd species of elephant</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Background</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
African elephant traditionally one species with 2 major subspecies: <i>Loxodonta africana africana</i> and <i>L. africana cyclotis</i>.</div>
<div>
<div>
Recent research suggests may be separate species, or even 4 species.</div>
<div>
Different DNA markers, different results.</div>
<div>
In this study, used genomic results to analyze number of species.</div>
<div>
Samples from Mastodon, Mammoth, Asian Elephant, two populations of African Elephant.</div>
</div>
<div>
<br /></div>
<div>
Results</div>
<div>
<div>
Africa-Asia split 4.2-9.0 mya.</div>
<div>
Based on DNA, Forest & Savanna split 2.6-5.6 mya.</div>
<div>
Asian & Mammoth split 2.5-5.4 mya.</div>
</div>
<div>
<br /></div>
<div>
Conclusions:</div>
<div>
<div>
2 species of African elephant.</div>
<div>
Asian closely related to Mammoth!</div>
<div>
Assumptions need re-examination.</div>
</div>
<div>
<br /></div>
<br />
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>2b. Dalebout et al. 2002. A new species of beaked whale <span style="font-style: italic;">Mesoplodon perrini</span> sp. n. (Cetacea: Ziphiidae) discovered through mitochondrial DNA sequences. Marine Mammal Science 18: 577-608.</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b><br /></b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Introduction</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Beaked whales are rare, with cryptic lifestyles. Most never observed alive.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• 12 species described in last 100 years!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• <span style="font-style: italic;">Mesoplodon hectori</span> common in southeast Pacific.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Materials & Methods</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• 5 specimens of beaked whale stranded in California, 1977-1995.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Thought to be <span style="font-style: italic;">M. hectori</span> based on morphology.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Researchers then examined 2 mt DNA markers…</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Results</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Results surprisingly show five specimens not M. hectori.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• New species!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Re-examination shows morphological differences as well.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Discussion</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Authors suggest genetic voucher material for all taxa.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Also state there are likely 40 marine mammal species still unknown!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Cookiecutter sharks feed on <span style="font-style: italic;">M. perrini</span>.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Who knows what species await description?</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Recent news:</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
"This is good reminder," said Constantine, "of how large the oceans are, and of how little we know about them. "</div>
<div>
<div>
Kirsten Thompson, C. Scott Baker, Anton van Helden, Selina Patel, Craig Millar, Rochelle Constantine. 2012. The world’s rarest whale. Current Biology 22(21) pp. R905 - R906</div>
</div>
<div>
<br /></div>
<br />
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b><br /></b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>Part 3 Atlantic & Pacific corals</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Fukami et al. 2008. Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria). PLoS One 3:9: e3222</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Coral phylogeny has been in flux for 10+ years.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Perhaps corallimorphs within hard corals.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Here examine 127 species, 75 genera, 17 families.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Four markers; 2 nuclear, 2 mitochondrial.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Corals monophyletic.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• 11/16 families not monophyletic.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Corresponding morphological characters found.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Corallimorphs not part of stony corals.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Many Atlantic corals are very unique, and should be conserved.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Some clades vulnerable to extinction (II, V, VI, XV, XVIII+XX).</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Ability to conserve depends on knowing what to conserve.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Re-organize based on DNA, re-examine morphology.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Atlantic corals must be protected more strongly.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Basic ideas need to be re-examined (e.g. favids).</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>Part 4 - Crown-of-thorns</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Vogler et al. 2008. A threat to coral reefs multiplied? Four species of crown-of-thorns starfish. Biology Letters doi:1-.1098/rsbl.2008.0454</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• <span style="font-style: italic;">Acanthaster planci</span> outbreaks threaten coral reefs.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Causes of outbreaks not clear.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Species has long-lived larvae, but apparent population structure.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Here used COI sequences from 237 samples.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Four clades found, 8.8-10.6% divergent.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Diverged 1.95-3.65 mya.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Species show geographical partitioning. Due to sea level changes.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• All populations expanding.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Four species, SIO, NIO, Red Sea, and Pacific.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Outbreaks mainly seen in Pacific - could this be a species difference?</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
• Clearly more research needed, critical for coral reef management.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>Part 5. Deep-sea zoanthids</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Background:</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Until 2007, all described deep-sea zoanthids are placed in Epizoanthidae despite morphological and ecological differences.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
今まで、全ての深海スナギンチャクはヤドリスナギンチャク科に分類されていた。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
No deep-sea zoanthids formally described from the Pacific.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
太平洋の深海スナギンチャクは全く分類されていない。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
None described from limited environments.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
極限環境(化学合成環境)のスナギンチャクの報告はあるが、サンプルや論文も無い。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
However, data literature suggests deep sea zoanthids may be quite common - underreported? Theorized to be worldwide is distribution - almost always found when specifically searched for.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
おそらく、珍しくはない。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Potential new zoanthid?</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
During Shinkai 6500 dive #884 (June 2005), several unidentified zoanthid-like samples “accidentally” collected off Muroto, Nankai Trough, depth=approx. 3300 m.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
高知県の室戸の近くにある南海トラフで、2005年に間違えて、謎のスナギンチャクらしき生き物が採取された。水深は約3300m、冷水の極限環境。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Back checks of images show that the sample organism is apparently quite common at the dive site.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
画像をチェックすると、この生き物が非常に多い。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Lives on mudstone but not loose sediment.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
固い泥岩の上に存在、泥上には存在しない。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
No high-resolution in situ images exist.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
綺麗な画像が無い。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Only 12 polyps collected.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
ポリプは12個しか採取されなかった。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
External morphology</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Samples appeared to be zoanthid-like based on: sand encrustation and polyp shape. No tentacle data available.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
スナギンチャクと同様に、砂を取り込んでいる。ポリプが閉じている。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
However, samples have several unique features: free-living and inhabited a deep sea methane cold seep. Morphology and ecology do not fit with any known zoanthid families.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
単体性、極限環境の初めてのスナギンチャク。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Internal morphology</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
As expected, cross section using normal (wax-embedded) methods gave poor results.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
パラフィン切片での結果はあまりよくない。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Attempted to set sample in epoxy resin, cut a section, and polish to necessary thickness but failed.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
レジンでの切片も無理。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Another possibility is digestion of outer surface of polyp.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
フ酸での切片は可能だが、非常に危ない。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Could obtain mesentery count number from rough cross-sections (19-22).</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
状態が悪い切片で、約19〜22隔膜を確認できたが、形など観察できなかった。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
We examined nematocysts. These can differ between species but do not tell anything about relationship.</div>
<div>
<br /></div>
<div>
Phylogenetic results:</div>
<div>
<div>
Obtained mt COI, mt16S rDNA, and 5.8S rDNA sequences confirm samples are zoanthid, but divergent from all known zoanthid families.</div>
<div>
今回のサンプルはスナギンチャク目に入っているが、今まで知られているスナギンチャクと離れている。</div>
<div>
Particularly, divergent from all known groups of deep-sea zoanthids described.</div>
<div>
特に、今までの深海のスナギンチャクと違う。</div>
<div>
Bootstrap support for monophyly 100% (all methods, all markers).</div>
<div>
遺伝子解析の結果の確率が非常に高い。</div>
</div>
<div>
<div>
Based on external morphology and genetic results, these samples are a new family of zoanthid: Abyssoanthidae.</div>
<div>
形態、生態、遺伝子解析を含めて、今回のサンプルは新科、新属、新種。</div>
<div>
However, several questions remain regarding ecology and reproduction of this new family.</div>
<div>
今後、日本周辺の深海で調査を行う予定。</div>
<div>
<br /></div>
</div>
<div>
More species?</div>
<div>
<div>
Images suggest more specimens present in Japan Trench at 5600 m.</div>
<div>
In autumn 2007, we went to investigate and collect specimens.</div>
<div>
17 day cruise, 3 dives, on RV Yokosuka and the Shinkai 6500.</div>
</div>
<div>
<div>
Presence of zoanthids confirmed, many specimens collected.</div>
<div>
Also, collected an octocoral, also an undescribed species.</div>
<div>
Found on other benthos, found in limited environments.</div>
<div>
Below 1000m very few samples, these specimens are invaluable to science.</div>
<div>
Specimens were examined using morphology and DNA.</div>
</div>
<div>
<div>
Specimens collected were very similar in morphology to <i>A. nankaiensis</i>.</div>
<div>
DNA was slightly (1-2 base pairs/marker) different.</div>
<div>
DNA, environment (5600 vs 3300 m) different enough to describe a new species; <i>A. convallis</i>.</div>
</div>
<div>
<br /></div>
<br />
<br />
<br />
<div>
<br /></div>
<br />
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>Overall conclusions:</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
1. Genetics already impacting our understanding of diversity.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
2. Expect more surprises in the future.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
3. Massive revision of all coral reef organisms!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<b>References:</b></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
1. Milinkovitch MC, Caccone A, Amato G. 2004. Molecular phylogenetic analyses indicate extensive morphological convergence between “yeti” and primates. Mol Phylogenet. Evol. 31: 1-3</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
2. N Rohland, D Reich, S Mallick, M Meyer, RE Green, NJ Georgiadis, AL Roca, M Hofreiter. 2010. Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants. PLoS Biol v.8(12): PMC3006346</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
3. Dalebout et al. 2002. A new species of beaked whale <span style="font-style: italic;">Mesoplodon perrini</span> sp. n. (Cetacea: Ziphiidae) discovered through phylogenetic analyses of mitochondrial DNA sequences. Marine Mammal Science 18: 577-608.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
4.Thompson et al. 2012. The world’s rarest whale. Current Biology 22(21) pp. R905 - R906.</div>
<br />
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
5. Fukami et al. 2008. Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria). PLoS One 3:9: e3222.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
6. Vogler et al. 2008. A threat to coral reefs multiplied? Four species of crown-of-thorns starfish. Biology Letters doi:1-.1098/rsbl.2008.0454</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
7. Reimer et al. 2004-2010. Various papers on zoanthid phylogeny.</div>
<div>
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-8903148499260805032012-12-17T00:20:00.000-08:002012-12-17T00:21:44.711-08:00November 7 & 14, 2012 class notes (combined)<br />
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Class 2012.11.7 & 14 - Genetics (linked to biodiversity and conservation)</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Part 1 Review</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
1. Introduction to genetics, diversity and conservation.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Link between diversity and conservation:</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Species diversity (# of species) for many groups of animals and plants unknown - lack of taxonomy.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
分類学の研究が足りないせいで、色々な生物の集団の種類多様性(種の数)がほとんど知れていない状態。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
99.5% of species go extinct before we even describe them.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
99.5%の種類は、分類する前に絶滅になってしまう。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Without knowledge of species, how can we protect them?</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
種類の分類が無いと、保全ができない。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Therefore, taxonomy and diversity VERY important.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
分類学や多様性の理解が重要な研究。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
BUT…</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Not enough taxonomy specialists, training takes time, not good pay!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Many animals and plants are VERY hard to identify using traditional methods!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Remember that...</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Biodiversity = Number of taxa (species, genera), or ecosystem types, etc.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Biodiversity = bioresources.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Bioresources = long-term economic well-being.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Conserving biodiversity is important; we need to understand baseline biodiversity.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Many “neglected taxa” remain.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
History of measuring marine benthic biodiversity</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Marine biodiversity less understood than terrestrial.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Many marine ecosystems have high biodiversity; particularly coral reefs.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Early biodiversity work focused on hard corals, sponges, easy to preserve taxa.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Collectors did not enter the ecosystem or observe living specimens.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Type specimens in Europe or N. America; ICZN problematic.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Currently almost all marine benthos taxa have gaps.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
DNA can be used to differentiate cryptic species - example adult Astraptes spp.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
There are many new methods that have helped us understand diversity:</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
a. SCUBA - brings scientists into marine environment</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
b. deep-sea subs and ROVS - same as SCUBA but deeper</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
c. DNA - allows us to confirm without (hopefully) bias what relations exist between organisms.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Part 2 - Genetic diversity - variety of alleles or genotypes in a group being investigated.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Overview: quick explanation of evolution. Species gradually diverge; develop unique traits. Some groups disappear, others continue to evolve. Adaptations always needed.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
In order to understand phylogeny we must understand evolution:</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
The modern synthesis of evolution is the combination of Darwin's and Mendel's theories.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
The theory underlying the modern synthesis has three major aspects:</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
The common descent of all organisms from a single ancestor.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
全ての生き物は共通の祖先から進化した。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
The origin of novel traits in a lineage.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
それぞれのグループはそれぞれの特徴を持つ。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Changes cause some traits to persist while others perish.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
様々な変化によって、あるグループは生き残り、あるグループは絶滅する。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
DNA and phylogenetics</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
All cells contain DNA - the code or blueprint of life.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
全ての細胞には遺伝子が入っている。遺伝子は生き物の設計図。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
This code has only four different "letters": A, G, C, T.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
遺伝子は4つのコードしかない。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Usual length 1,000,000 to 100,000,000,000 base pairs.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
生き物のひとつの細胞にある遺伝子の長さは,000,000 to 100,000,000,000 。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Genome projects read everything in one organism, but takes time and expensive.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
全ての遺伝子を読むことは時間とお金の無駄。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Many studies use one or a few markers to investigate relations.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
遺伝子の短い部分だけでも系統関係が解析できる。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
By collecting the same marker from different samples and then analyzing them, we can make a tree.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
いくつかのサンプルから同じマーカーを読んで、並べてから、解析し系統樹を作る。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
It is thought/hoped a tree is similar to how evolution occurred.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
系統樹から進化が見えると思われる。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
DNA may be a way to have non-specialists identify species quickly!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
So, DNA tree = evolutionary tree (or so we hope)</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Genetic diversity is required to adapt to changing environments (ex: Hawaiian honeycreeprs). Environments are ALWAYS changing, never static. Many methods to measure genetic diversity. Large populations usually have high diversity; small populations are a concern.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Diveristy needed, give examples we have seen - industrial melanism. Also failures to adapt - chestnut trees and Okinawan pines.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Low genetic diversity also leads to less reproductive success, more inbreeding. Ex: European royal families! Maintaining different populations important.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
How do we measure genetic diversity?</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
1. quantative measurement - morphology. size, shape, height, weight, etc. But not due only to genes, also environment and expression. Difficult to assess. Can be done in absence of other methods, cheap.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
2. deleterious alleles - results from inbreeding, i.e. flies. But not good for conservation!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
3. proteins - started in 1960s, slight changes in sizes form species or individuals. Uses electrophoresis. Need blood or organs, invasive.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
4. DNA - many methods, always new developments. We will discuss</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
c. Microsatellites - used for population studies; repeats of DNA. Development time is considerable.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
In a cell, two major types of DNA we will study:</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
a. nuclear DNA - fast evolving in Cnidaria, slower in other animals - very general rule. More later.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
他の動物と違い、刺胞動物で進化が早い</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
b. mitochondrial DNA - slow in Cnidaria, fast in other animals. Again generalization.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
他の動物と違い、刺胞動物で進化が遅い。</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Example DNA markers:</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
COI, cytochrome oxidase subunit 1 - mt DNA, used for many studies, much data available.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
16S rDNA - mt DNA, useful in zoanthids! some indels, especially V5 region.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
More on these next week!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Can use DNA to identify species new and old.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
5. Chromosomes - often clear differences between species. But no genetic distance or often no idea of relationships between species.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Endangered species have low genetic diversity, due to bottlenecks and reduced populations. Shown for many species (ex. nene).</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Variation over space and time - higher dispersal means less variation within species, lower dispersal means more variation. Give example of humans. Large populations more stable than small populations which lose genetic diversity quickly.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Part 3- How genetics can be used in conservation.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
A. Minimizing inbreeding and loss of genetic diversity e.g. Florida panther with outside popn individuals introduced into gene pool, results seen to alleviate inbreeding.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
B. Identifying populations of concern.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Example: Asiatic lions in Gir Forest, India, shown to be genetically distinct from other lions, with low genetic diversity.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Steps then taken to protect this population. Also, rare "pine" tree from Aus, with seemingly identical population.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
C. Resolving population structure.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Example: If a species has many isolated populations, can examine if translocation is needed.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
For example wolves in the Alps.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
D. Resolving taxonomic uncertainty.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Particularly true for marine species, invertebrates, plants.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Many examples, including: sea stars, whales, zoanthids, tuatara.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Talked about tuatara and Antarctic minke whale.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
E. Defining management units within species.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Often different populations within species have different lifestyles, habits, or ranges that should be managed separately.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
E.g. salmon and different populations with different lifestyles that need different management styles.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
F. Detecting hybridization.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Can be done with mt DNA.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Some species in danger of disappearing due to this; examples include the Ethiopian wolf.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
G. Non-intrusive sampling.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Very useful for reclusive or endangered animals.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Can be done with feces, hair, or even food.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
H. Choosing sites for re-introduction of species.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Recent fossils or museum specimens can indicate where species used to be.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Example is the northern hairy-nosed wombat.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
I. Choosing the best population to use in re-introductions.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Often island populations considered valuable resource; but in case of Barrow Island wallabies, low genetic variability. This population should not be used for re-introduction plans.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
J. Forensics.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Identifying what came from where.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Example 1: Research has shown 2-20% of whale meat sold in Japan is not the whale it is advertised to be, but protected species.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Example 2: Over 50% of fish in several restaurants were not as advertised!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
K. Understanding species biology.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Again, use of mt DNA very useful in understanding reproduction due to maternal inheritance.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Also, comparing and contrasting with nuclear DNA data can indicate potential reticulate evolution.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Can determine sexes of hard to identify species.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Parenthood also determinable. e.g. monitor lizard "virgin" births.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Part 4 - Lionfish invading the Atlantic</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Lionfish known from the Indo-Pacific.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Mainly eat reef fish, and often larvae or juveniles.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Popular in the aquarium trade despite poison.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Marine fish introductions less common.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Most introductions due to purposeful introduction for fisheries, or released aquarium fish.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Success often investigated.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Whitfield et al. (2002) document several sightings (n=19) of <span style="font-style: italic;">Pterois volitans</span> along E. Atlantic.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Four specimens collected, numerous juveniles sighted, two collected.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
First introduction of Pacific fish to Atlantic.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Likely limited by cold waters, but surviving.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Can spread to Bermuda and Caribbean.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Similar fish in this region overfished, niche is available perhaps!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Introduction?</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Introduction method; 2 possibilities.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Ballast water possible, but no reports thus far.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Aquaria very likely. Specimens known to have been released occasionally.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Morphology appears to be typical of aquaria types.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Effects?</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
No fish in region used to lionfish.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
No predators.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Need genetic and temperature studies.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Modeling needed.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Spreading populations</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Since sightings in 2000, lionfish have spread.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Now known (Snyder&Burgess 2006) from Bahamas.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Apparently spreading throughout Caribbean.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Easy to document spread.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Genetic studies</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Since Whitfield et al (2002), more studies.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Hamner et al. (2007) used mt DNA to examine specimens.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Two markers (cyt B, 16S rDNA) previously used on lionfish in native ranges.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Found two species of lionfish; <span style="font-style: italic;">P. volitans</span> (93%) and<span style="font-style: italic;"> P. miles</span> (7%).</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Very reduced genetic diversity!</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Minimum-spanning network analyses - <span style="font-style: italic;">P. volitans</span></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Atlantic specimens likely from Indonesia.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<span style="font-style: italic;">P. miles</span> source unknown.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Reduced genetic diversity clear.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Founder effect! Minimum of 3<span style="font-style: italic;"> P. volitans</span> and 1 <span style="font-style: italic;">P. miles</span> established populations.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Invasions may be rapid and irreversible.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
Education needed.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
<br /></div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
References:</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
1. Corals of the World. JEN Veron. 2000. AIMS, Melbourne. Volume 1.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
2. Introduction to Conservation Genetics. R Frankham et al. 2002. Cambridge. Ch. 3</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
3. Molecular markers, selection and natural history. 2nd edition. J Avise. 2004. Ch.4</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
4. Whitfield et al. 2002. Biological invasion of the Indo-Pacific lionfish <span style="font-style: italic;">Pterois volitans</span> along the Atlantic coast of North America. Mar Ecol Prog Ser 235: 289-297.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
5. Snyder & Burgess. 2007. The Indo-Pacific red lionfish, <span style="font-style: italic;">Pterois volitans</span> (Pisces: Scorpaenidae), new to Bahamian ichthyofauna. Coral Reefs 26: 175.</div>
<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;">
6. Hamner et al. 2007. Mitochondrial cytochrome b analysis reveals two invasive lionfish species with strong founder effects in the western Atlantic. J Fish Biol 71: 214-222.</div>
James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-12833573566386706962012-12-17T00:10:00.001-08:002012-12-17T00:21:34.135-08:00October 31, 2012 class notes<span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-weight: bold;">Coral Reef Diversity and Conservation<br />October 31, 2012<br />Introduction to the Coral Reef Ecosystems and Biodiversity</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Introduction to Coral Reefs:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Outline:</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. Coral reefs (large scale)</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. Coral (the animal)</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. Biodiversity</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. Example study of human influences on coral reef (Sandin et al. 2008)</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. Coral reefs (large scale)</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">a. What are coral reefs? How do they form?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Biggest structures made by living organisms. GBR is 1000s of km long.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Thus we may think they are tough and permanent, but they are not, and only top thin layer is generally alive.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Existed before hard corals existed, different groups have taken turns making reefs.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Modern reefs due to symbiosis between coral and zooxanthellae, can get nutrients from water, but limited to warm clear shallow water (more on this later in another class), where they compete with macroalgae (more later).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Reefs can be geological structures, and living ecosystems.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">For geology, reefs affected by oceans going up and down, changes in temp and current. Shorter scales, typhoons, tsunamis, crown-of-thorns, etc.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Even shorter; bleaching, fishing, dynamite, coral reef trade, shellfish, etc.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Recently sea level has not changed so much, resulting in reefs today, but past there were many changes. Underwater cave example even.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Many reefs are like forests, tear them down and build them up.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Anyone been diving? Different levels of shelves are often indicators of past sea levels.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">b. Different types of coral reefs</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Starting with Darwin, many people have attempted to classify reefs into types. Humans like to classify.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Can be classified broadly into 3 types, as Darwin did. Rainwater, pounding of waves, and coralline algae make limestone from dead corals. Often reef edges have no corals, but much coralline algae. Also rubble, which may become reef in the future. Usually brought here by waves.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1: Fringing reefs: close to coastlines, may include rocks and other things besides dead coral. Briefly describe picture. Lagoons often muddy, corals on seaward edge, much variation in communities. Often lagoons may have low species diversity, while reef slopes often have highest diversity. Explain parts of the reef. Lagoon, edge,slope, channel.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2: Barrier reefs: Basically fringing reefs but further from shore, due to changes in sea level and time etc. Made almost entirely of carbonate. Often have channels for massive currents to flow through. May be a barrier reef followed by a fringing reef.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3:Atoll: walls of a reef around a lagoon, from a sunken island. Darwin first thought of this.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Many grades between these three types. Also, platform reefs that do not fit any of the classes above. Mention deep sea reefs too.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">c. Geological history of coral reefs, currents etc.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Now: Reefs found in Pacific, Atlantic, and Indian. Reefs need to be in areas over 18C, this is a good temperature for ZX, for coralline algae. Reefs are not found in areas with poor visibility, with little wave action, although corals may be found there. Need also to out-compete algae.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">There is little correlation between coral species numbers and reefs, as many reefs are built by just a few species. But there is a link between reefs and overall biological diversity (more on this later).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">History: known from 2 billion years ago. Explain these using timelines.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">First reefs built by stromatolites (blue green algae mounds that can take up sediment), then archaeocyaths (like sponges), then corals (not modern ones) along with sponges, bryozoans.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Probably in this period the first endosymbiotic symbioses evolved.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Two types of corals: Rugose and Tabulate, but died when dinosaurs did. After this no reefs for a long time.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Modern corals appeared in Triassic, have dominated reef building since then. Show maps? Show some old extinct reefs.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">In mid-cretaceous, rudist bivalves dominated, probably symbiotic, and then corals came back.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">At end of dinosaurs 1/3 of families, 70% of genera became extinct. All species changed!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">More recent: Diversity levels have recovered. More diversity with zooxanthellate genera. Results of land shifting and old distributions show that Atlantic genera are much older than Pacific. This does not mean evolution was faster, based on previous patterns and the Tethys Sea.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Closure of Panama very important. No species of corals and few genera shared between Indo-Pacific and Atlantic. Even if many animals look the same, very few shared!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. Coral (the animal)</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">a. Corals are part of</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Cnidaria - animals that have one hole that serves as both mouth and anus. This is surrounded by tentacles. All Cnidaria and only cnidarians have nematocysts, defense and feeding. Two main shapes, polyp and medusa. Life cycle alternates between these two shapes; main for corals is polyps, main for jellyfish is medusae.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Anthozoa = includes octocorals and hexacorals.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Hexacorallia = includes corals, anemones, zoanthids, corallimorphs, antipatharians and cerianthids. Have mesenteries in multiples of 6.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Corals - may be colonial or solitary, zooxanthellate or azooxanthellate. Zooxanthellate colonial species responsible for making coral reefs. Polyps (living tissue) surrounded by calcium carbonate skeleton. Classification traditionally uses skeletal characteristics; color and size also used. Polyps include a mouth and oral disk surrounded by tentacles, as well as zooxanthellae (</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><span style="font-style: italic;">Symbiodinium</span></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">spp.; abbreviated here as ZX=zooxanthellae).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Skeletons have much microstructure, important for many other animals as homes, especially when coral dead. Refuge from predators etc. Many types of corals - show pictures of these.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Also, zoanthids - related order to corals. Colonial like corals, soft like anemones. Many species have ZX. Very variable morphology even within species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">b. When understanding coral or other cnidarians on the reef, please remember that the holobiont is important.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Holobiont = host (animal) + ZX + bacteria, viruses, etc. Host may be same species, but if ZX are different, this has implications for biology and ecology of holobiont.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">ZX are dinoflagellates with chlorophyll. Live inside host, give energy from sunlight to host.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">ZX look similar, thought to be one species, but DNA etc. have revealed diversity, now 8 clades (A to H). Most ZX sensitive to high ocean temperatures. Usually 30C is considered a threshold. Different clades or subclades may have different physiology. ZX thylakoids degrade at hot temperatures, causing coral bleaching. Also can happen at low (<15C).</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Research example: Zoanthus sansibaricus at different locations in Japan has different ZX clades!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">c. Dangers facing coral reefs: Bleaching, acidification (will discuss this more in another class taught by Kurihara-sensei). Perhaps 90% of reefs dead by 2050, NOAA says 60% by 2030.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">d. Species diversity for many organisms unknown. 99.5% of species go extinct before we identify them. Without knowledge of species how do we protect them? Taxonomy and diversity study important. but... training takes time, pay is poor, and many organisms VERY hard to identify in traditional methods.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. Biodiversity;</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">a. Less than 0.2% of the earth, 25% or more of the ocean’s species! 10% of fish caught. Protect land as breakwaters, and valuable for tourism. All of this despite low nutrients and compounds in the surrounding water.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"> </span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Corals make very complex structures thanks to their skeletons. Greatly increase amount of habitable areas, or niches, for many different species. Explain about specialized animals, use zoanthids and shogun ebi as examples.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Much problem trying to calculate actual surface area. For macroorganisms, factors of at least 15 (Dahl 1973). Much greater for microorganisms. And this is on the surface alone!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">b. Diversity? How to measure it?</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Biodiversity=number of species or genera, OTUs (operational taxonomic units)</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Coral reefs <0.2% of the earth's surface, 25-50% of marine species.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Reefs increase surface area, 15X for large animals, more for smaller. More niches = more specialized animals.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Discuss before scuba and ideas at that time</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">First corals where collected in 1700s when scientific interest began, and first cataloguing. Increased greatly in 1800 and early 1900s. Museums and names.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Corals were particularly easy, as they could be preserved. So, along with fish and sea mammals and macroalage, very extensively documented.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Problems: no observation of living things in situ, no idea of variance, differ from place to place, so many incorrect names.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">But, according to ICZN, these names MUST be correct, so we have continued on with bad ideas.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Other animals were largely ignored until 1800s or 1900s, such as anemones, zoanthids, corallimorphs, etc.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Many understudied groups are finally getting reexamined today, along with corals!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">"New" techniques: SCUBA, submersibles, molecular techniques, have allowed a re-examination of biodiversity.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Often, "reverse" taxonomy, using DNA to identify specimens of interest, then going back to look at morphology.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. Wrap-up using Sandin et al. (2008): Just how much biomass was on reefs before humans? What is a healthy reef? Line Islands study.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Recent papers, including the one from which handout came from (Sandin et al. 2008), show that the biomass of coral reefs may be inverted. Healthy reefs have 85% of fish biomass in sharks!! Go over paper quickly.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">This has sent researchers back to old papers and accounts.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Discuss old papers where so many sea turtles</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Early Atlantic explorers running aground on sea turtles.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Numerous shark stories of huge numbers of sharks.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Even in Okinawa, giant clams over 100 kg. The sea is richer than we can imagine in untouched places, but we have never seen or almost never will see. We are missing so-called “baseline” data, and now a race to get some!</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Show images from Bonotsu 2011 and destroyed coral reef.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Emphasize the link between conservation and biodiversity.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">VI. Recommended reading (bold in particular):</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">1. SA Sandin et al. 2008. Baselines and Degradation of Coral Reefs in the Northern Line Islands. PloS One 3 (2) e1548:1-11.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">2. EA Dinsdale et al. 2008. Microbial Ecology of Four Coral Atolls in the Northern Line Islands. PloS One 3 (2) e1584: 1-17.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">3. N Knowlton, JBC Jackson. 2008. Shifting Baselines, Local Impacts, and Global Change on Coral Reefs. PloS Biology 6 (2) e54:215-220.</span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span><span class="Apple-style-span" style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">4. Corals of the World – JEN Veron. 2000. Australian Institute of Marine Science. Melbourne.</span>James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-35524171525820408462012-12-17T00:05:00.001-08:002012-12-17T00:12:12.523-08:00Revised scheduleHello everyone:<br />
<br />
Here is a revised schedule for the next couple of months. <b>Note we will also add 2 classes at some point!</b><br />
<br />
<br />
<table border="0" cellpadding="0" cellspacing="0" style="border-collapse: collapse; font-family: 'Trebuchet MS', Trebuchet, sans-serif; font-size: 13px; line-height: 18px; width: 516px;"><tbody>
<tr height="27" style="height: 27.19pt;"><td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>19 Dec</b></span></div>
</td><td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span class="Apple-style-span" style="font-family: Calibri;"><span class="Apple-style-span" style="font-size: 21px; line-height: normal;"><b>Discovering New Species on Coral Reefs</b></span></span></div>
</td></tr>
<tr height="27" style="height: 27.19pt;"><td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-style: normal; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>26 Dec</b></span></div>
</td><td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>No class</b></span></div>
</td></tr>
<tr height="27" style="height: 27.19pt;"><td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>9 Jan</b></span></div>
</td><td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>保全学についての研究紹介 (GBR)</b></span></div>
</td></tr>
<tr height="30" style="height: 29.66pt;"><td class="oa3" height="30" style="height: 29.66pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>16 Jan</b></span></div>
</td><td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>DNA Barcoding and </b></span><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>CoMLの紹介</b></span></div>
</td></tr>
<tr height="30" style="height: 29.66pt;"><td class="oa3" height="30" style="height: 29.66pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>23 Jan</b></span></div>
</td><td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">Project</span></b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">発表</span></div>
</td></tr>
<tr height="27" style="height: 27.19pt;"><td class="oa6" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; text-align: justify; text-indent: 0in; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<h3 style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; position: relative;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>30 Jan</b></span></h3>
</div>
</td><td class="oa7" style="width: 424pt;" width="424"><div style="direction: ltr; margin-bottom: 0pt; margin-left: 0in; margin-top: 0pt; text-align: left; unicode-bidi: embed; word-break: normal;">
<h3 style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; position: relative;">
<span style="font-family: Calibri; font-size: 18pt;"><b>Final test</b></span></h3>
</div>
</td></tr>
</tbody></table>
<br />
Classes to be added:<br />
<span class="Apple-style-span" style="border-collapse: collapse; font-family: Calibri; font-size: 21px;"><b>網状進化の研究紹介</b></span><br />
<span class="Apple-style-span" style="border-collapse: collapse; font-family: 'Trebuchet MS', Trebuchet, sans-serif; font-size: 13px;"><b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">サンゴ礁生態系についての研究紹介III</span></b></span><br />
<br />James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-67953930272018985342012-11-05T00:07:00.003-08:002012-11-05T00:07:39.760-08:00October 24, 2012 class notes
<!--[if gte mso 9]><xml>
<o:DocumentProperties>
<o:Revision>0</o:Revision>
<o:TotalTime>0</o:TotalTime>
<o:Pages>1</o:Pages>
<o:Words>638</o:Words>
<o:Characters>3457</o:Characters>
<o:Company>University of the Ryukyus</o:Company>
<o:Lines>65</o:Lines>
<o:Paragraphs>28</o:Paragraphs>
<o:CharactersWithSpaces>4067</o:CharactersWithSpaces>
<o:Version>14.0</o:Version>
</o:DocumentProperties>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]-->
<!--[if gte mso 9]><xml>
<w:WordDocument>
<w:View>Normal</w:View>
<w:Zoom>0</w:Zoom>
<w:TrackMoves/>
<w:TrackFormatting/>
<w:PunctuationKerning/>
<w:DrawingGridVerticalSpacing>10 pt</w:DrawingGridVerticalSpacing>
<w:DisplayHorizontalDrawingGridEvery>0</w:DisplayHorizontalDrawingGridEvery>
<w:DisplayVerticalDrawingGridEvery>2</w:DisplayVerticalDrawingGridEvery>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:DoNotPromoteQF/>
<w:LidThemeOther>EN-US</w:LidThemeOther>
<w:LidThemeAsian>JA</w:LidThemeAsian>
<w:LidThemeComplexScript>X-NONE</w:LidThemeComplexScript>
<w:Compatibility>
<w:SpaceForUL/>
<w:BalanceSingleByteDoubleByteWidth/>
<w:DoNotLeaveBackslashAlone/>
<w:ULTrailSpace/>
<w:DoNotExpandShiftReturn/>
<w:AdjustLineHeightInTable/>
<w:BreakWrappedTables/>
<w:SnapToGridInCell/>
<w:WrapTextWithPunct/>
<w:UseAsianBreakRules/>
<w:DontGrowAutofit/>
<w:SplitPgBreakAndParaMark/>
<w:EnableOpenTypeKerning/>
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
<w:UseFELayout/>
</w:Compatibility>
<w:NoLineBreaksAfter Lang="JA">$([\{£¥‘“〈《「『【〔$([{「£¥</w:NoLineBreaksAfter>
<w:NoLineBreaksBefore Lang="JA">!%),.:;?]}¢°’”‰′″℃、。々〉》」』】〕゛゜ゝゞ・ヽヾ!%),.:;?]}。」、・゙゚¢</w:NoLineBreaksBefore>
<m:mathPr>
<m:mathFont m:val="Cambria Math"/>
<m:brkBin m:val="before"/>
<m:brkBinSub m:val="--"/>
<m:smallFrac m:val="off"/>
<m:dispDef/>
<m:lMargin m:val="0"/>
<m:rMargin m:val="0"/>
<m:defJc m:val="centerGroup"/>
<m:wrapIndent m:val="1440"/>
<m:intLim m:val="subSup"/>
<m:naryLim m:val="undOvr"/>
</m:mathPr></w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" DefUnhideWhenUsed="true"
DefSemiHidden="true" DefQFormat="false" DefPriority="99"
LatentStyleCount="276">
<w:LsdException Locked="false" Priority="0" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Normal"/>
<w:LsdException Locked="false" Priority="9" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="heading 1"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 2"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 3"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 4"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 5"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 6"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 7"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 8"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 9"/>
<w:LsdException Locked="false" Priority="39" Name="toc 1"/>
<w:LsdException Locked="false" Priority="39" Name="toc 2"/>
<w:LsdException Locked="false" Priority="39" Name="toc 3"/>
<w:LsdException Locked="false" Priority="39" Name="toc 4"/>
<w:LsdException Locked="false" Priority="39" Name="toc 5"/>
<w:LsdException Locked="false" Priority="39" Name="toc 6"/>
<w:LsdException Locked="false" Priority="39" Name="toc 7"/>
<w:LsdException Locked="false" Priority="39" Name="toc 8"/>
<w:LsdException Locked="false" Priority="39" Name="toc 9"/>
<w:LsdException Locked="false" Priority="35" QFormat="true" Name="caption"/>
<w:LsdException Locked="false" Priority="10" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Title"/>
<w:LsdException Locked="false" Priority="1" Name="Default Paragraph Font"/>
<w:LsdException Locked="false" Priority="11" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtitle"/>
<w:LsdException Locked="false" Priority="22" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" Priority="59" SemiHidden="false"
UnhideWhenUsed="false" Name="Table Grid"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Placeholder Text"/>
<w:LsdException Locked="false" Priority="1" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="No Spacing"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Revision"/>
<w:LsdException Locked="false" Priority="34" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="List Paragraph"/>
<w:LsdException Locked="false" Priority="29" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Quote"/>
<w:LsdException Locked="false" Priority="30" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Quote"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 1"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 1"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 1"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 1"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 1"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 1"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 1"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 2"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 2"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 2"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 2"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 2"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 2"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 2"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 2"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 2"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 2"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 2"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 3"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 3"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 3"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 3"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 3"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 3"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 3"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 3"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 3"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 3"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 3"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 3"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 3"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 4"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 4"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 4"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 4"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 4"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 4"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 4"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 4"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 4"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 4"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 4"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 4"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 4"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 4"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 5"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 5"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 5"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 5"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 5"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 5"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 5"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 5"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 5"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 5"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 5"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 5"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 5"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 5"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 6"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 6"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 6"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 6"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 6"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/>
<w:LsdException Locked="false" Priority="19" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/>
<w:LsdException Locked="false" Priority="21" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/>
<w:LsdException Locked="false" Priority="31" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/>
<w:LsdException Locked="false" Priority="32" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/>
<w:LsdException Locked="false" Priority="33" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Book Title"/>
<w:LsdException Locked="false" Priority="37" Name="Bibliography"/>
<w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/>
</w:LatentStyles>
</xml><![endif]-->
<!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:標準の表;
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-priority:99;
mso-style-parent:"";
mso-padding-alt:0mm 5.4pt 0mm 5.4pt;
mso-para-margin:0mm;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:12.0pt;
font-family:Century;
mso-ascii-font-family:Century;
mso-ascii-theme-font:minor-latin;
mso-hansi-font-family:Century;
mso-hansi-theme-font:minor-latin;
mso-font-kerning:1.0pt;}
</style>
<![endif]-->
<!--StartFragment-->
<br />
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: Cambria;">Class notes 2012.10.24<o:p></o:p></span></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: Cambria;">Outline<o:p></o:p></span></b></div>
<ol start="1" style="margin-top: 0mm;" type="1">
<li class="MsoNormal" style="mso-list: l6 level1 lfo1; tab-stops: list 36.0pt;"><span style="font-family: Cambria;">Classification & taxonomy<o:p></o:p></span></li>
<li class="MsoNormal" style="mso-list: l6 level1 lfo1; tab-stops: list 36.0pt;"><span style="font-family: Cambria;">Taxonomy today<o:p></o:p></span></li>
<li class="MsoNormal" style="mso-list: l6 level1 lfo1; tab-stops: list 36.0pt;"><span style="font-family: Cambria;">Reminder<o:p></o:p></span></li>
<li class="MsoNormal" style="mso-list: l6 level1 lfo1; tab-stops: list 36.0pt;"><span style="font-family: Cambria;">Activity!<o:p></o:p></span></li>
</ol>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: Cambria;">1. Classification & taxonomy<o:p></o:p></span></b></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">What is classification?<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Classification is the
grouping of things according to characteristics<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">The science of classifying
organisms is known as <u>taxonomy</u><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Early classification
systems:<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l5 level1 lfo2; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Aristotle
grouped animals according to the way they moved <o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l5 level1 lfo2; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">John Ray
(1627-1705) was the first to define the term “species” <o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Binomial classification:<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Started with Linneaus (1707-1778)<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-left: 72.0pt; mso-list: l0 level2 lfo4; tab-stops: list 72.0pt; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Times; mso-bidi-font-family: Times; mso-fareast-font-family: Times;"><span style="mso-list: Ignore;">•<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria; mso-bidi-font-weight: bold;">a two name system for writing scientific names.</span><span style="font-family: Cambria;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-left: 72.0pt; mso-list: l0 level2 lfo4; tab-stops: list 72.0pt; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Times; mso-bidi-font-family: Times; mso-fareast-font-family: Times;"><span style="mso-list: Ignore;">•<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">The <span style="mso-bidi-font-weight: bold;">genus name is written first (always Capitalized).</span><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-left: 72.0pt; mso-list: l0 level2 lfo4; tab-stops: list 72.0pt; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Times; mso-bidi-font-family: Times; mso-fareast-font-family: Times;"><span style="mso-list: Ignore;">•<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">The <span style="mso-bidi-font-weight: bold;">species name is written second (never
capitalized).</span><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-left: 72.0pt; mso-list: l0 level2 lfo4; tab-stops: list 72.0pt; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Times; mso-bidi-font-family: Times; mso-fareast-font-family: Times;"><span style="mso-list: Ignore;">•<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Both words are
italicized if typed or underlined if hand written. <o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria; mso-bidi-font-weight: bold;">Example:<i><span style="mso-spacerun: yes;"> </span>Felis concolor or F. concolor</i></span><span style="font-family: Cambria;"><o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l8 level1 lfo5; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">"Formal"
scientific names should have a third part, the authority. <br />
The authority is <u>not</u> italicized or underlined. <o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l8 level1 lfo5; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">The authority
is written as an abbreviation of the last name of the person responsible for
naming the organism. Since Carolus Linnaeus was the first person to name many
plants, the L. for Linnaeus is very common in plant scientific names. <o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Examples: <i>Quercus alba</i>
L.<o:p></o:p></span></div>
<div class="MsoNormal">
<i><span style="font-family: Cambria;">Abyssoanthus convalis </span></i><span style="font-family: Cambria;">Reimer & Sinniger, 2009<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Hierarchical
Classification <o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l7 level1 lfo3; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Based on
species. Classification goes down, but the basis is “bottom up”.<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">7 hierarchies in system:<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Kingdom<span style="mso-tab-count: 3;"> </span>very broad<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Phylum (Division)<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Class<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Order <o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Family<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Genus<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Species<span style="mso-tab-count: 3;"> </span>very specific<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">The International Code of
Zoological Nomenclature (ICZN) specifically governs the family-genus-species
level.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Points to remember:<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l7 level1 lfo3; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">We only know
about a fraction of the organisms that exist or have existed on Earth.<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l7 level1 lfo3; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Taxonomists give
a unique scientific name to each species they know about whether it’s alive today
or extinct.<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l7 level1 lfo3; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">The scientific
name usually comes from one of two “dead”<span style="mso-spacerun: yes;">
</span>languages – Latin or ancient Greek. <o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l7 level1 lfo3; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Scientific
names are used to avoid problems with common names. Examples: American mountain
lion, and “chinu/kurodai”.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: Cambria;"><b>2. Taxonomy today<o:p></o:p></b></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Linnaeus vs. Today<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l1 level1 lfo6; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Linnaeus
grouped plants and animals based on reproductive characteristics <o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l1 level1 lfo6; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Now we group
plants and animals based on phylogeny<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l1 level1 lfo6; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Phylogeny=Evolutionary
history, or how the plants and animals are related. <o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l1 level1 lfo6; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">We use
genetics to figure out how plants and animals are related. <o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 24.0pt; mso-list: l1 level1 lfo6; mso-para-margin-left: 0gd; text-indent: -24.0pt;">
<!--[if !supportLists]--><span style="font-family: Wingdings; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">l<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">In Linnaeus’s
day, scientists did not know what evolution was or what DNA and genetics was. <o:p></o:p></span></div>
<div class="MsoNormal">
<i><u><span style="font-family: Cambria;">Phylogeny</span></u></i><u><span style="font-family: Cambria;">,</span></u><span style="font-family: Cambria;"> the
evolutionary history of an organism, is the cornerstone of a branch of biology
called systematic taxonomy. <o:p></o:p></span></div>
<div class="MsoNormal">
<i><u><span style="font-family: Cambria;">Systematics</span></u></i><span style="font-family: Cambria;">, as systematic taxonomy is commonly called, is the
study of the evolution of biological diversity. <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-left: 36.0pt; mso-list: l4 level1 lfo7; tab-stops: list 36.0pt; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Arial; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;">•<span style="font: 7.0pt "Times New Roman";"> </span></span></span><!--[endif]--><span style="font-family: Cambria;">A phylogenetic tree is a shows a<i> <u>hypothesi</u>s
</i>about the evolutionary relationships thought to exist among groups of
organisms. <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-left: 36.0pt; mso-list: l4 level1 lfo7; tab-stops: list 36.0pt; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Arial; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;">•<span style="font: 7.0pt "Times New Roman";"> </span></span></span><!--[endif]--><span style="font-family: Cambria;">Trees may or may not show the actual evolutionary
history of organisms. <o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Phylogenetic trees are
usually based on a combination of these lines of evidence: <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-left: 72.0pt; mso-list: l2 level2 lfo8; tab-stops: list 72.0pt; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Arial; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;">•<span style="font: 7.0pt "Times New Roman";"> </span></span></span><!--[endif]--><span style="font-family: Cambria;">Fossil record<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-left: 72.0pt; mso-list: l2 level2 lfo8; tab-stops: list 72.0pt; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Arial; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;">•<span style="font: 7.0pt "Times New Roman";"> </span></span></span><!--[endif]--><span style="font-family: Cambria;">Morphology<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-left: 72.0pt; mso-list: l2 level2 lfo8; tab-stops: list 72.0pt; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Arial; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;">•<span style="font: 7.0pt "Times New Roman";"> </span></span></span><!--[endif]--><span style="font-family: Cambria;">Embryological patterns of development<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-left: 72.0pt; mso-list: l2 level2 lfo8; tab-stops: list 72.0pt; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Arial; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;">•<span style="font: 7.0pt "Times New Roman";"> </span></span></span><!--[endif]--><span style="font-family: Cambria;">Genetic information<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Brief discussion on:<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 18.0pt; mso-list: l3 level1 lfo9; mso-para-margin-left: 0gd; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Cambria; mso-bidi-font-family: Cambria; mso-fareast-font-family: Cambria;"><span style="mso-list: Ignore;">1.<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Adaptive
radiation – and modification of homologous structures.<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 18.0pt; mso-list: l3 level1 lfo9; mso-para-margin-left: 0gd; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Cambria; mso-bidi-font-family: Cambria; mso-fareast-font-family: Cambria;"><span style="mso-list: Ignore;">2.<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Convergent evolution
– evolving similar adaptations as organisms inhabit similar niches or play
similar ecological roles. Analogous structures – traits that morphologically
and functionality even though they do not have a common ancestor (organism, or
tissue, etc.).<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 18.0pt; mso-list: l3 level1 lfo9; mso-para-margin-left: 0gd; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Cambria; mso-bidi-font-family: Cambria; mso-fareast-font-family: Cambria;"><span style="mso-list: Ignore;">3.<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Homology,
parallelism, convergence, analogy.<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 18.0pt; mso-list: l3 level1 lfo9; mso-para-margin-left: 0gd; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Cambria; mso-bidi-font-family: Cambria; mso-fareast-font-family: Cambria;"><span style="mso-list: Ignore;">4.<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria; mso-bidi-font-weight: bold;">A phylogenetic tree based on a cladistic analysis is called a cladogram. </span><span style="font-family: Cambria;"><o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 18.0pt; mso-list: l3 level1 lfo9; mso-para-margin-left: 0gd; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Cambria; mso-bidi-font-family: Cambria; mso-fareast-font-family: Cambria;"><span style="mso-list: Ignore;">5.<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">Dichotomous
key: A key is a device for easily and quickly identifying:<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 84.0pt; mso-list: l9 level1 lfo10; mso-para-margin-left: 0gd; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Cambria; mso-bidi-font-family: Cambria; mso-fareast-font-family: Cambria;"><span style="mso-list: Ignore;">a.<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">an unknown
organism.<o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 84.0pt; mso-list: l9 level1 lfo10; mso-para-margin-left: 0gd; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Cambria; mso-bidi-font-family: Cambria; mso-fareast-font-family: Cambria;"><span style="mso-list: Ignore;">b.<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">The
dichotomous key is the most widely used type in biological sciences. <o:p></o:p></span></div>
<div class="MsoListParagraph" style="margin-left: 84.0pt; mso-list: l9 level1 lfo10; mso-para-margin-left: 0gd; text-indent: -18.0pt;">
<!--[if !supportLists]--><span style="font-family: Cambria; mso-bidi-font-family: Cambria; mso-fareast-font-family: Cambria;"><span style="mso-list: Ignore;">c.<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="font-family: Cambria;">The user is
presented with a sequence of<span style="mso-spacerun: yes;"> </span>choices
between two statements, couplets, based on characteristics of the organism. By
always making the correct choice, the name of the organism will be revealed.<o:p></o:p></span></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;"><span style="font-family: Cambria;">3. Reminder<o:p></o:p></span></b></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">In this class we will be
discussing a small fraction of total diversity of life. Show a domain of life
tree.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: Cambria;"><b>4. Activity:<o:p></o:p></b></span></div>
<div class="MsoNormal">
<span style="font-family: Cambria;">Classification of
organisms based on diagnostic characteristics, and group discussion to show how
ICZN and decisions work in taxonomy. Discuss areas for mistakes and problems.<o:p></o:p></span></div>
<!--EndFragment-->James Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-58119316347501157552012-10-10T06:27:00.002-07:002012-12-17T00:12:40.489-08:00Class scheduleClass schedule<br />
<br />
<!--StartFragment-->
<br />
<table border="0" cellpadding="0" cellspacing="0" style="border-collapse: collapse; mso-yfti-tbllook: 1536; width: 516px;">
<colgroup><col style="mso-width-source: userset; width: 92pt;" width="92"></col>
<col style="mso-width-source: userset; width: 424pt;" width="424"></col>
</colgroup><tbody>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa1" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>10 Oct</b></span></div>
</td>
<td class="oa2" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">登</span></b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">録調整と説明</span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-style: normal; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>17 Oct</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-style: normal; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>No class (Happy Monday)</b></span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>24 Oct</b></span></div>
</td>
<td class="oa5" style="width: 424pt;" width="424"><div style="direction: ltr; margin-bottom: 0pt; margin-left: 0in; margin-top: 0pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: left; unicode-bidi: embed; word-break: normal;">
<b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">Logical</span></b><span style="font-family: Calibri; font-size: 18.0pt; language: en-US; mso-ascii-font-family: Calibri; mso-color-index: 1; mso-font-kerning: 12.0pt; mso-style-textfill-fill-alpha: 100.0%; mso-style-textfill-fill-color: black; mso-style-textfill-fill-themecolor: text1; mso-style-textfill-type: solid; text-combine: letters;">
thinking/debate</span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>31 Oct</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">サンゴ</span></b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">礁生態系の紹介</span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>7 Nov</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">遺</span></b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">伝学の紹介</span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>14 Nov</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>系統樹の説明</b></span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-style: normal; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>21 Nov</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>サンゴ礁生態系についての研究紹介I</b></span></div>
</td>
</tr>
<tr height="51" style="height: 50.92pt; mso-height-source: userset;">
<td class="oa3" height="51" style="height: 50.92pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>28 Nov</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">サンゴ礁生態系についての研究紹介II</span></b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"> &</span><b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">Project</span></b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">発表</span><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">の説明</span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>5 Dec</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt;"><b>未記載種の発見</b></span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>12 Dec</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<b><span style="font-family: Calibri; font-size: 16pt;">No class</span></b><span style="font-family: Calibri; font-size: 16pt; vertical-align: baseline;"> (Palau)</span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>19 Dec</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>網状進化の研究紹介</b></span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-style: normal; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>26 Dec</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>To be announced</b></span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa3" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>9 Jan</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0pt; mso-line-break-override: none; mso-vertical-align-alt: auto; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>保全学についての研究紹介 (GBR)</b></span></div>
</td>
</tr>
<tr height="30" style="height: 29.66pt; mso-height-source: userset;">
<td class="oa3" height="30" style="height: 29.66pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>16 Jan</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">Project</span></b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">発表</span></div>
</td>
</tr>
<tr height="30" style="height: 29.66pt; mso-height-source: userset;">
<td class="oa3" height="30" style="height: 29.66pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>23 Jan</b></span></div>
</td>
<td class="oa4" style="width: 424pt;" width="424"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">DNA Barcoding and </span></b><span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;">CoMLの紹介</span></div>
</td>
</tr>
<tr height="27" style="height: 27.19pt; mso-height-source: userset;">
<td class="oa6" height="27" style="height: 27.19pt; width: 92pt;" width="92"><div style="direction: ltr; line-height: normal; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 3.84pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: justify; text-indent: 0in; text-justify: inter-ideograph; unicode-bidi: embed; vertical-align: baseline; word-break: normal;">
<h3>
<span style="font-family: Calibri; font-size: 16pt; font-variant: normal; text-transform: none; vertical-align: baseline;"><b>30 Jan</b></span></h3>
</div>
</td>
<td class="oa7" style="width: 424pt;" width="424"><div style="direction: ltr; margin-bottom: 0pt; margin-left: 0in; margin-top: 0pt; mso-line-break-override: none; punctuation-wrap: hanging; text-align: left; unicode-bidi: embed; word-break: normal;">
<h3>
<span style="font-family: Calibri; font-size: 18pt;"><b>Final test</b></span></h3>
</div>
</td>
</tr>
</tbody></table>
<br />
<!--EndFragment--><br />
cheers,<br />
JDRJames Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0tag:blogger.com,1999:blog-1016460519636042877.post-39508898101042412342012-10-09T08:56:00.000-07:002012-10-09T08:58:48.758-07:00Welcome to the 2012 class!Coral Reef Biodiversity and Conservation<br />
Instructor and Class Information<br />
Time & Place: Science 327, Weds 8:30-10:00<br />
Instructor: James Reimer<br />
Office: Science 353<br />
URL: http://ryukyucoral2012.blogspot.com/<br />
Office hours: Anytime except Wednesdays<br />
<br />
Content:<br />
1. Use mainly marine invertebrate examples.<br />
2. Explore how to understand diversity, using modern techniques.<br />
3. Explore conservation and issues with coral reefs.
4. Basics of climate change and human impact on reefs.<br />
<br />
Goals:<br />
1. Understand why coral reefs have high importance and diversity.<br />
2. Understand new coral reef research.<br />
3. Understand basic DNA techniques (and others) and how to use them in conservation.<br />
4. Understand the threats coral reefs face from anthropogenic and climate change problems.<br />
5. Have fun!<br />
<br />
Evaluation:<br />
1. Mid-term presentation (in groups of 2-3 people): 60%.<br />
2. Final test: 40%<br />
You must pass both in order to pass the class.<br />
<br />
Text, reading, references:<br />
1. Nothing necessary, but you will do better by reading suggested readings.<br />
2. I may take questions from suggested readings.<br />
3. Posted on blog and at end of each class.<br />
<br />
Rules:<br />
1. No attendance taken.<br />
2. No copying or cheating.<br />
3. Drinks and food in class OK, but be respectful.<br />
4. Questions anytime OK.<br />
5. Take notes!<br />
<br />
Cheers,
JDRJames Reimerhttp://www.blogger.com/profile/14727875082126815355noreply@blogger.com0