Oral presentations today - 10 groups gave presentations.
Overall impressions: Very unique - and realistic. Should be interesting seeing the marks and reports!
お疲れさま to everyone!
Wednesday, January 23, 2013
January 16, 2013 class notes
Outline
1. Introduction: Problems facing taxonomy and diversity.
2. Accelerating “taxonomy”: DNA barcoding.
3. Promoting taxonomy: Census of Marine Life.
4. Images from one CoML Project (Creefs).
1. Introduction: Problems facing taxonomy and diversity.
Problems facing taxonomy 1
Too many species! Diversity confounds our best efforts to examine it.
Keep finding new species.
Extinction rates increasing.
Problems facing taxonomy 2
Not enough taxonomists.
Pay poor, work long.
Everyone says “important” but not considered essential.
Many groups have no active workers.
Potential solutions 1
Increasing technology and information available.
Global information systems.
Molecular experiment techniques.
Potential solutions 2
Increasing international research collaboration.
Growing awareness of biodiversity and importance.
2. Accelerating “taxonomy”: DNA barcoding.
What is “DNA barcoding”?
遺伝子バーコードというのは？
A DNA barcode is a short sequence, taken from standardized portions of the genome,used to identify species.
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。
If a genome project is deep and narrow, DNA barcoding is broad and shallow.
Genome projectは深くて、狭いが、遺伝子バーコードは浅くて、広い。
Requirements of a DNA barcoding marker
A sequence/marker used to barcode should:
be easy to amplify
not possess paralogues
have conserved regions to design primers efficiently for a broad taxonomic sampling
be variable enough to distinguish species
but conserved enough within species
Choosing the correct DNA marker is critical.
Point:
Barcoding does not aim to solve phylogeny!
Reasons for DNA barcoding
1. Works with fragments.
2. Works with all stages of life: Can link male/females. Different stages of same organism. E.g. Amphipods (White & Reimer 2012)
3. Cryptic species detection. E.g. Astraptes
4. Reduces ambiguity (set DNA code).
5. Makes expertise go further.
6. Democratizes access to data. E.g. Barcode of Life project
7. Opens the way for handheld barcoders.
8. Finds new diversity.
9. Demonstrates value of museum collections. Sequencing of collections vital.
10. Speeds up discovery of new species.
Additional strong point
Does not need expert knowledge.
Weak points
1. DNA (specifically COI) does not always work for each group of organisms.
2. Handheld technology has not succeeded, despite many advances.
3. Different taxa have different DNA protocols, so standardization is difficult.
4. The “barcoding gap”
Barcoding implies that the level of DNA divergence between and within species is different.
But evolution not neat - hybrids, incomplete lineage sorting, etc.
This gap is not always present – so taxonomy comes back to “judgement”.
Results
DNA barcoding proposed in 2003 as a “solution” to taxonomy.
Two large projects: Barcode of Life and Ocean Genome Legacy.
Encyclopedia of Life on the internet.
Common method of identification.
Gaining acceptance as a practical method to obtain much data.
But has not solved taxonomy, instead a new approach or “sub-field”.
For zoanthids (and corals), > 1 DNA marker is needed.
mt DNA evolves very slowly.
Still, better than no experts at all!
3. Promoting taxonomy: Census of Marine Life.
Scientific Framework
What has lived in the oceans?
What does live in the oceans?
What will live in the oceans?
The Census consisted of four major component programs organized around these questions.
1. Investigating the Past
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.
Teams of fisheries scientists, historians, economists and others conducted case studies in southern Africa, Australia, and approximately a dozen other regions.
Together, these case studies created the first reliable picture of life in the oceans before fishing.
The long historical records of marine populations help distinguish the contributions of natural fluctuations in the environment from the effects of human activities.
2. Assessing the Present
The largest component of the Census involved investigating what now lives in the world's oceans through 14 field projects.
Each sampled important kinds of biota in one of six realms of the global oceans using a range of technologies.
This included CReefs.
3. Forecasting the Future
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).
Integrating data from many different sources and creating new statistical and analytical tools to predict marine populations and composition of ecosystems in the future
4. Living Legacy
Such a global initiative required a state-of-the-art data assimilation framework, and this is:Ocean Biogeographic Information System (OBIS).
Numbers
2,700 scientists
80+ nations
540 expeditions
US$ 650 million
2,600+ scientific publications
6,000+ potential new species
30 million distribution records and counting
4. Example: CReefs:
Heron Island Trip
November 8th – December 1st, 2010
Census of Coral Reef Ecosystems (www.creefs.org), part of Census of Marine Life (CoML – www.coml.org).
Large international effort to understand biodiversity, use data for conservation.
Many researchers from different institutions, focused on different taxa, many “ignored”.
I focused on zoanthids (of course)!
Location:
Heron Island
Many seabirds nest here. Always noisy, and dangerous to walk without a hat!
Rails also live on the island.
The island is an important nesting site for green and loggerhead sea turtles.
Heron Island Research Station is run by the University of Queensland. Most of the station is very new.
There are excellent facilities for experiments, sample collection, and analyses, indoors and outside.
Scientists from all over the world, most based in Australia, but others from USA, Japan, Iceland, etc.
Most scientists had much field experience, and were good divers. Many also had boat licenses and first aid training.
There were also dive officers, who acted as boat captains, guides, diving assistants, etc.
Outreach included a professional photographer, and a professional blogger with stories and images posted every day.
A professional chef ensured everyone was well-fed. The food was amazing!
Every night at dinner, based on everyone’s ideas, weather conditions, and tides, the next day’s schedule was decided.
Boats were launched from the harbor, 3-10 people per boat. Often boats were out for over 7 hours.
Diving was always done under the buddy system, with very strict guidelines on diving protocol.
Special permits were obtained to allow specimen collection. Work underwater was intense and focused.
I was able to collect 270 specimens in 33 dives. Other groups collected up to >2000 specimens!
Samples were also collected on reef walks, and by snorkeling. Other groups used ARMS and the “carpet of death”.
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.
Another potential new species of zoanthid.
Many people also collected for other groups.
Back in the lab, data were collected, and specimens numbered. All data were given to the CReefs data manager as well.
All sites were assigned numbers, and all had GPS coordinates. 130 sites were visited in 3 weeks!
Samples will be shipped to institutions all over the world and analyzed further.
Of course, work was not 24 hours a day…
Sunset drinks were the one time of day when everyone would relax and take a break.
And the sunsets were amazing…
References cited:
1. CP Meyer, G Paulay. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3(12) e422.
2. Consortium for Barcoding of Life homepage.
3. Census of Marine Life homepage.
4. OBIS homepage.
1. Introduction: Problems facing taxonomy and diversity.
2. Accelerating “taxonomy”: DNA barcoding.
3. Promoting taxonomy: Census of Marine Life.
4. Images from one CoML Project (Creefs).
1. Introduction: Problems facing taxonomy and diversity.
Problems facing taxonomy 1
Too many species! Diversity confounds our best efforts to examine it.
Keep finding new species.
Extinction rates increasing.
Problems facing taxonomy 2
Not enough taxonomists.
Pay poor, work long.
Everyone says “important” but not considered essential.
Many groups have no active workers.
Potential solutions 1
Increasing technology and information available.
Global information systems.
Molecular experiment techniques.
Potential solutions 2
Increasing international research collaboration.
Growing awareness of biodiversity and importance.
2. Accelerating “taxonomy”: DNA barcoding.
What is “DNA barcoding”?
遺伝子バーコードというのは？
A DNA barcode is a short sequence, taken from standardized portions of the genome,used to identify species.
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。
If a genome project is deep and narrow, DNA barcoding is broad and shallow.
Genome projectは深くて、狭いが、遺伝子バーコードは浅くて、広い。
Requirements of a DNA barcoding marker
A sequence/marker used to barcode should:
be easy to amplify
not possess paralogues
have conserved regions to design primers efficiently for a broad taxonomic sampling
be variable enough to distinguish species
but conserved enough within species
Choosing the correct DNA marker is critical.
Point:
Barcoding does not aim to solve phylogeny!
Reasons for DNA barcoding
1. Works with fragments.
2. Works with all stages of life: Can link male/females. Different stages of same organism. E.g. Amphipods (White & Reimer 2012)
3. Cryptic species detection. E.g. Astraptes
4. Reduces ambiguity (set DNA code).
5. Makes expertise go further.
6. Democratizes access to data. E.g. Barcode of Life project
7. Opens the way for handheld barcoders.
8. Finds new diversity.
9. Demonstrates value of museum collections. Sequencing of collections vital.
10. Speeds up discovery of new species.
Additional strong point
Does not need expert knowledge.
Weak points
1. DNA (specifically COI) does not always work for each group of organisms.
2. Handheld technology has not succeeded, despite many advances.
3. Different taxa have different DNA protocols, so standardization is difficult.
4. The “barcoding gap”
Barcoding implies that the level of DNA divergence between and within species is different.
But evolution not neat - hybrids, incomplete lineage sorting, etc.
This gap is not always present – so taxonomy comes back to “judgement”.
Results
DNA barcoding proposed in 2003 as a “solution” to taxonomy.
Two large projects: Barcode of Life and Ocean Genome Legacy.
Encyclopedia of Life on the internet.
Common method of identification.
Gaining acceptance as a practical method to obtain much data.
But has not solved taxonomy, instead a new approach or “sub-field”.
For zoanthids (and corals), > 1 DNA marker is needed.
mt DNA evolves very slowly.
Still, better than no experts at all!
3. Promoting taxonomy: Census of Marine Life.
Scientific Framework
What has lived in the oceans?
What does live in the oceans?
What will live in the oceans?
The Census consisted of four major component programs organized around these questions.
1. Investigating the Past
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.
Teams of fisheries scientists, historians, economists and others conducted case studies in southern Africa, Australia, and approximately a dozen other regions.
Together, these case studies created the first reliable picture of life in the oceans before fishing.
The long historical records of marine populations help distinguish the contributions of natural fluctuations in the environment from the effects of human activities.
2. Assessing the Present
The largest component of the Census involved investigating what now lives in the world's oceans through 14 field projects.
Each sampled important kinds of biota in one of six realms of the global oceans using a range of technologies.
This included CReefs.
3. Forecasting the Future
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).
Integrating data from many different sources and creating new statistical and analytical tools to predict marine populations and composition of ecosystems in the future
4. Living Legacy
Such a global initiative required a state-of-the-art data assimilation framework, and this is:Ocean Biogeographic Information System (OBIS).
Numbers
2,700 scientists
80+ nations
540 expeditions
US$ 650 million
2,600+ scientific publications
6,000+ potential new species
30 million distribution records and counting
4. Example: CReefs:
Heron Island Trip
November 8th – December 1st, 2010
Census of Coral Reef Ecosystems (www.creefs.org), part of Census of Marine Life (CoML – www.coml.org).
Large international effort to understand biodiversity, use data for conservation.
Many researchers from different institutions, focused on different taxa, many “ignored”.
I focused on zoanthids (of course)!
Location:
Heron Island
Many seabirds nest here. Always noisy, and dangerous to walk without a hat!
Rails also live on the island.
The island is an important nesting site for green and loggerhead sea turtles.
Heron Island Research Station is run by the University of Queensland. Most of the station is very new.
There are excellent facilities for experiments, sample collection, and analyses, indoors and outside.
Scientists from all over the world, most based in Australia, but others from USA, Japan, Iceland, etc.
Most scientists had much field experience, and were good divers. Many also had boat licenses and first aid training.
There were also dive officers, who acted as boat captains, guides, diving assistants, etc.
Outreach included a professional photographer, and a professional blogger with stories and images posted every day.
A professional chef ensured everyone was well-fed. The food was amazing!
Every night at dinner, based on everyone’s ideas, weather conditions, and tides, the next day’s schedule was decided.
Boats were launched from the harbor, 3-10 people per boat. Often boats were out for over 7 hours.
Diving was always done under the buddy system, with very strict guidelines on diving protocol.
Special permits were obtained to allow specimen collection. Work underwater was intense and focused.
I was able to collect 270 specimens in 33 dives. Other groups collected up to >2000 specimens!
Samples were also collected on reef walks, and by snorkeling. Other groups used ARMS and the “carpet of death”.
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.
Another potential new species of zoanthid.
Many people also collected for other groups.
Back in the lab, data were collected, and specimens numbered. All data were given to the CReefs data manager as well.
All sites were assigned numbers, and all had GPS coordinates. 130 sites were visited in 3 weeks!
Samples will be shipped to institutions all over the world and analyzed further.
Of course, work was not 24 hours a day…
Sunset drinks were the one time of day when everyone would relax and take a break.
And the sunsets were amazing…
References cited:
1. CP Meyer, G Paulay. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3(12) e422.
2. Consortium for Barcoding of Life homepage.
3. Census of Marine Life homepage.
4. OBIS homepage.
January 15, 2013 class notes
January 15th class notes
Outline:
1. Community conservation in the Philippines.
2. Conservation History on the Great Barrier Reef
3. The future
4. Conclusions
Part 1
Community conservation in the Philippines.
History
Philippines consist of 7000+ islands.
Centuries have used reefs for livelihood.
Since 1970s, threatened by over-exploitation and destructive fishing methods.
Conservation started in 1974. Many projects failed.
Politics tied to conservation.
Local governments have authority but not knowledge or budget.
To be successful, combination of local and national people.
Within local group, must include users of reef; fishermen, resort owners, coastal residents, scuba divers.
Start of conservation
MDCP started in 1986 on three islands (62-166 households); Apo, Pamilacan, Balicasag.
All had less fish catch, increasing destruction and poverty.
MCDP plan
Marine reserves with buffer areas to increase number and diversity fish.
Development of local knowledge and alternative work.
Community center.
Outreach and replication program.
MCDP steps
Integration into community.
Education - marine ecology and resource management.
Group building, formalizing, strengthening.
Results
Apo & Pamilacan remain strong.
Balicasag protection groups somewhat weakened due to large PTA resort and less local “ownership”.
PTA has good points too.
All islands have stronger municipal laws now.
Results
Local fisherman believe sanctuary has helped.
Comparison of 1985-86 data with 1992 shows increases in fish, stable coral cover.
Conclusions
MPAs work on small islands by preventing destructive fishing and making locals understand value of conservation.
Small islands easier to implement plans.
Immediate benefits must be seen.
Baseline data necessary.
Local fishermen help with MPA location decisions.
Conclusions
Locals must understand how problem and answer related.
Management groups must have respected members.
Link with all potentially helpful groups.
All plans vulnerable to politics and outside groups.
Part 2 - Conservation History on the Great Barrier Reef:
The Great Barrier Reef = GBR
Great Barrier Reef Marine Park
Outline
Background
Why was rezoning of GBR necessary?
Representative Areas Program (RAP) (only part of solution)
Phase 1 and 2
Final zoning plan
Implementation phase
Monitoring
Other actions
Reef Water Quality Plan
Reducing fishing and policing
The Great Barrier Reef = GBR
345,000 km2
> 2000 km long
2900 separate reefs
> 900 islands
Formation of the Park
Late 1960’s – early 1970’s—much agitation for a park, reinforced by plans to mine Ellison Reef (off Innisfail)
Politicians promised that the GBR should be protected as a Park
Park established in 1975, under Great Barrier Reef Marine Park Act (Federal Parliament Act)
Implementation
Park boundaries are non-negotiable, can only be changed by Act of Parliament
No mining within the Park
Development & implementation of zoning plans is a Federal responsibility
Day to day management is the responsibility of Queensland Parks & Wildlife Service
Zoning Plans
First areas to be zoned Capricorn and Bunker, finished in 1977
Subsequently the other regions were zoned
Zoning plans reviewed at regular intervals, with public participation, and plans changed over time and even the type of zones changed
GBRMPA
Based in Townsville
Responsible to Minister for Science
Issues permits and licences, including those for scientific research
GBR declared World Heritage Area in 1981— such listing requires regular report card to ensure the reef is being maintained
During the 1990’s
Increasing use of the reef by tourists
Increased scientific knowledge of the reef
Increasing awareness of the connectivity of reefs (mass spawning)
Increasing evidence of decline of some habitats, especially inshore
The Great Barrier Reef Is ‘Under Pressure’
Downstream effects of land use (water quality issues)
Coral bleaching
Coastal developments
Increasing fishing effort and impacts
Shipping & pollution incidents
Increasing tourism and recreation
Trends in Regional Biodiversity Are Negative
Fishing effort increasing substantially in intensity & spatial extent (coral trout fishery—effort x2 since 1995; shark catch x5 since 1991)
Turtles–all 6 species threatened; 2 are endangered (Loggerhead and Olive Ridley)
Dugong population south of Cooktown has declined >90% since mid-1980’s
Humpbacks listed as vulnerable; other cetaceans (Irrawaddy & Indo-Pacific hump-backed dolphins) listed as rare
Trends for most species unknown
GBR Is Not Isolated From World Trends
10% of world’s reefs destroyed or severely degraded
58% of world’s reefs potentially threatened
70% reefs already degraded in Indonesia & Philippines
On current trends 70% of the world’s reefs will have gone in 40 years
Minimising the
‘Pressures’
Downstream effects of land use ==> Reef Water Quality Action Plan (results not immediate)
Coastal developments ==> Aquaculture Regs; GBRMP permit requirements
Increasing fishing effort and impacts ==> Queensland FS fisheries management plans (ECTMP, Reef Line)
Minimising the
‘Pressures’
Shipping & pollution incidents ==> Australia Marine Shipping Authority shipping review, compulsory pilotage, mandatory reporting, etc
Increasing tourism and recreation ==> PoMs; new tourism framework
Threatened species ==> new policies; species recovery plans; seasonal closures, RAP
Protecting biodiversity ==> RAP
Why was rezoning of the GBR necessary?
Queenslanders depend on the GBR
Important for economy—tourism, commercial fishing, recreational fishing, shipping
Important for Traditional Owners—connection with Sea Country
Important for communities—relaxation, lifestyles
>90% Australians (including Queenslanders) wanted more no-take zones
Important for building knowledge—education, research
Better protection = insurance for all these values
Connectivity in the GBR
An overview of RAP
Representative examples of the entire diversity of habitats protected
RAP reviewed the existing zoning of the Marine Park
RAP attempted to minimise negative impacts for users and stakeholders while aiming to achieve protection of biodiversity
RAP has meant an increase in Green Zones to protect biodiversity
RAP is a crucial part of the solution to a complex problem
Other Issues Addressed During Rezoning
Some current zoning plans had been in existence for 16 years
Ensured consistent zone names and zone provisions throughout GBR
Coastal areas zoned for first time
Clearer delineation of zone boundaries (GPS co-ordinates)
Developing the Zoning Plan
The Zoning Plan was developed using environmental, economic, and social information
Clear Principles on how to use the environmental and social information were followed
These principles were set out in the first round of community participation (CP1)
Environmental Information
Bioregions
Bioregions were mapped between 1999 and 2002 using expert knowledge and best available data and methods
30 reef bioregions 40 non-reef bioregions
Many bioregions previously lacked adequate protection
At least 20% of each bioregion included in a no-take zone
The GBR Marine Park
Non reef bioregions
Environmental Information
Other key issues:
Special and unique places
Critical habitats such as turtle nesting sites
Deep & shallow water sea-grass, fish spawning sites etc.
Special and unique places
Critical turtle nesting areas
Environmental Information
Biophysical Principles guided selection and use of environmental information
The Principles :
were developed by independent reef scientists
published in CP1
said that at least 20% of each bioregion had to be in no-take zones
No-take zones must be
large
arranged to form viable network, allowing connectivity, provides insurance policy
Social & Economic Information
Sources:
Recreational fishing diaries, and tag and release records
Commercial fishing log-books
The location of boat-ramps and coastal developments
Historic ship-wrecks
Visitor use data
Over 10,000 submissions received in Phase 1 & >21,000 in Phase 2
All submissions read to identify community issues
All submissions were taken into account
Recreational fishing sites
Commercial fishing values
Using Social Information
Social, Economic, Cultural and Management Principles were:
developed by an independent panel of experts
published in Community Phase 1
The SEC Principles attempted to
minimise impact on existing users of the Marine Park
be fair—ie not impacting on one group or community more than another
but needed a Zoning plan easy to enforce
Previous Zoning
Previous Zoning, plus Trawl Plans
New green zones—environmental data only
Green zones—using economic data too
Green zones—revising boundaries
The Plan
What Does This Plan Do?
Provides strong, medium and long-term protection for future generations
Green zones mean more and bigger fish
Green zone spill-over, better fishing for reef communities
Natural values which attracts tourists and $ will be maintained
Protects at least 20% of each bioregion, special and unique areas, important habitats, and nesting areas—over 33% achieved
Phases of RAP
Classification (map biodiversity)
Reviewed existing protection
informal consultation with user groups
formal Community Participation phase 1
Identification of possible network options
Selection of most acceptable network
Draft zoning plan
formal Community Participation phase 2 (over 21,000 submissions)
Ministerial & parliamentary approval March 2004
Implemented July 1st 2004
Representative Areas Program
A new and effective network of ‘no-take’ areas representative of all bioregions helps to:
maintain biological diversity
maintain ecological processes and systems
provide an ecological safety margin, and if necessary, enable species and habitats to recover
ensure viable and sustainable industries
Current Status
Distribution of information and many maps to fishers, tourist operators, dive, boat and bait shops
Revised maps at boat ramps
Sorting out current permits in relation to new zoning, research stations issuing permits
Working with GPS manufacturers to incorporate zoning plans into charts, some available
Website available to download zoning plans for particular areas of interest
Related Activities
Reef Water Quality Protection Plan-implemented
Fisheries related: Reduction of number of fishing boats
Reduction in areas where trawling allowed
compensation being paid
Increased surveillance, penalties imposed
Dugong protected areas and reduce netting areas
Qld zoned adjacent coastal parks
Recognition of RAP
Authority awarded a Eureka Prize for Biodiversity Research and Banksia Environmental Award
WWF Australia acknowledges its importance for conserving biodiversity
Recognition overseas of importance of this approach to marine park management
Best practise
Relevance to Other Areas
Zoning with scientific basis
Problems facing the GBR faced by all reefal areas
Methods for zoning multi-use parks relevant to all areas in Australia and elsewhere
Such community involvement results in ownership and stewardship of the reef– schools adopting reefs, communities becoming effective policers
Other Management Strategies
Reef Water Quality Protection Plan
being implemented but ongoing and results will take years to be apparent
Reduction in number of fishing licences, compensation being paid
Increasing policing and enforcement
Global warming— the big question
increased rates of bleaching
increased cyclones activity
What is the long term future for the GBR?
Part 3 - Looking towards the future (De'ath et al. 2012)
~50% of coral lost in GBR in last 27 years!!
Loss due to:
Storms (48%)
COTS (42%)
Bleaching (10%)
So, is conservation really working?
What can be done to stop this loss?
Focus on COTS possible.
Conclusions (1):
1. Increased connections in the world are increasing biological invasions.
2. Invasions can be rapid and irreversible.
3. Large scale management often needed, and international cooperation.
4. Coral reef biodiversity patterns different from land; different management needed.
Conclusions (2):
1. Coral reefs are linked to other ecosystems, both marine and on land.
2. Conservation plans must protect linked areas and ecosystems, and not “islands”.
3. Protected areas should be decided based on endemism, geographic features, neighboring ecosystems, etc.
4. Successful conservation involves all levels of people, but most important are locals.
5. Without demonstration of monetary value, coral reef protection very vulnerable to politics.
6. In the future, more conservation plans will be implemented.
7. The gap between well protected areas and those not protected will widen.
8. Very few non-protected reefs will survive.
We must do MORE!
Conclusions (Okinawa)
Points to consider for Okinawa/Ryukyu Islands:
Only three major governments (National, 2 Prefectural).
However, management is very ambiguous.
Local fisheries have strong power; no no-take zones anywhere in Japan, aquaculture common.
Competing interests within national government have different agendas (Construction, Environment).
National laws for parks weak.
Okinawa Prefecture likely has strong wishes, but needs money from National government.
However, management is very ambiguous.
Local fisheries have strong power; no no-take zones anywhere in Japan, aquaculture common.
Competing interests within national government have different agendas (Construction, Environment).
National laws for parks weak.
Okinawa Prefecture likely has strong wishes, but needs money from National government.
References cited:
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.
2. GBRMPA Conservation Plan. 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
January 9, 2013 class notes
Outline
Part 2: Common coral reef diseasesIntroduction to
coral reef diseases
• Bacteria observed in corals in early 1900s.
• Diseases noticed in 1970s, seemingly increasing over last 30 years.
• 34 mass events, affecting sponges, seagrasses, cetaceans, urchins, fish, molluscs, corals.
• Have changed composition of reefs.
Diseases affecting Scleractinia
• Many diseases named, but very little known.
• Most pathogens still unknown.
• Most common in Atlantic (Green & Bruckner).
• Not to be confused with coral bleaching.
Green & Bruckner 2000
Black Band Disease (BBD) Caused by numerous cyanobacteria (500 spp.) as a microbial mat.
Mat makes the colored band.
First observed in 1973.
Moves 3mm to 1cm/day.
Found in 42 spp. of coral.
Kuta & Richardson 2002
• BBD correlates strongly with depth, temperature, nitrites.
• Also correlates with diversity and orthophosphate.
White band disease: Pathogen unknown, may be bacteria. Noticed in 1981.
Tissue loss from base to tip.
Affects two species, Acropora cervicornis and A. palmata.
Moves 3mm to 1cm/day.
• WBD has drastically altered Caribbean reefs.
• Shifts in coral species.
• Loss of overall coral cover; algae increasing.
• Both species now “threatened”.
• Losses of over 98% of A. cervicornis. Locally extinct.
White plague: Affects many species, but no acroporoids.
Caused by Aurantimonas bacteria.
First observed in 1977.
Aspergillosis: Caused by terrestrial fungi.
Affect mainly Atlantic gorgonians.
Also affects waterfowl.
Noted in 1997.
Tumors: Similar to cancer.
Affects mainly A. palmata.
Irregular growth, no zooxanthellae.
Noted in 1960s and 1970s.
Other diseases: Many other diseases.
Mostly known from Atlantic.
Yellow band disease, yellow spot disease, white pox disease, brown band disease.
Most noted for first time in last 20 years.
Pathogens usually unknown.
Part 3: Why are diseases becoming common?1. Global warming?
• Many people blame global warming.
• But likely much more complex.
2. Nutrient enrichment - Bruno et al. 2003
• Experiments done with YBD and Aspergillosis.
• Controls were disease only, experimental with added nitrogen and phosphorus.
Results - Aspergillosis
• Nutrients increased severity of disease in sea fans.
Results - YBD
• Presence of nutrients increased rate at which YBD developed in two species of coral.
3. Dust? -
Garrison et al. 2003
• Airborne dust from Africa and Asia carries many contaminants to reefs.
• Global warming and desertification increasing dust, therefore increasing contaminants.
Part 4: How do diseases affect conservation?Effects are widespread
Many studies have documented widespread coral decline in almost ALL coral species.
Porter et al. 2001 showed many declines 1996-1998 NOT due to coral bleaching but disease.
• Porter et al. 2001 cont
• Green & Bruckner 2000
• Green & Bruckner 2000
Many examples of diseases spreading, many examples of reef degradation (show many photos).
Overview of disease
• All diseases have negative effects.
• Only WBD has changed communities drastically.
• Pacific 15 years behind Atlantic.
• Compounded negative influences more severe for coral reefs.
Part 5: Preliminary results of field surveys of Terpios outbreaks in the Nansei Islands, Japan
Terpios hoshinota Rützler and Muzik 1993
Terpios in the Nansei Islands - history
Outbreak noticed in Mariana Is. 1973. (Bryan 1973 )
Terpios-Nansei project
Assess the current distribution of Terpios in the Nansei Islands.
Establish monitoring sites.
If present, characterize sexual reproduction & ecology.
Methods
Survey all major islands by snorkel/scuba (Reimer).
Monthly/bi-monthly sampling at designated locations – histology (Hirose), genetics (Chen).
Permanent transects at massive outbreak (Reimer), analyses (Reimer, Nozawa).
Preliminary results
Three situations observed: none, small amounts, massive outbreak
Disappearance?
Yonama, Tokunoshima had massive outbreak (87.9% cover) in 1986 (Marine Park Center Foundation 1986).
Discussion
Terpios absent or present in small numbers in most reefs in Nansei Islands (38/39 examined locations).
Coverage does not appear to fluctuate much in most locations.
Discussion & Questions
Massive outbreaks still occur in Nansei Islands.
How long do outbreaks last?
“Recovery” observed at Yonama, but is this true recovery? At least, not a dead-end.
Results suggest outbreaks are linked to reef degradation, but factors not clear.
Future work
Permanent transect results & analyses.
Try to quantify speed at which massive outbreaks can occur.
Combine analyses with genetic, histological results.
Examine Yakomo (current outbreak location) to understand causes of outbreaks. Why this location?
Part 6: Conclusions.Conclusion 1
• Disease more widespread on reefs in Caribbean.
• More research? Partially.
• Monitoring in Pacific very critical.
Conclusion 2
• Only one disease has permanently changed community structure (WBD).
• Other diseases locally important.
Conclusion 3
• Very few studies have investigated in detail mortality rates.
• Monitoring of individual colonies needed.
Conclusion 4
• Diseases increasing.
• Bleaching appears to be more critical, but two problems appear related.
Conclusion 5
• Diseases not well understood.
• Many diseases affect many species; possibly more or less diseases.
• Pathogens need to be investigated.
Conclusion 6
• While bleaching currently more serious, foolish to ignore diseases.
• May be “indicator” of serious problems, similar to amphibians.
What needs to be done
• <3% of reefs in danger have low human impact.
• More research needed on human influences and pathogens.
• Management and conservation then follow.
References:
1. Green & Bruckner. 2000. The significance of coral disease epizootiology for coral reef conservation. Biological Conservation 96: 347-361.
2. Aronson & Precht. 2001. White-band disease and the changing face of Caribbean coral reefs. Hydrobiologia 460: 25-38.
3. Garrison et al. 2003. African and Asian dust: from desert soils to coral reefs. BioScience 53: 469-481.
4. Bruno et al. 2003. Nutrient enrichment can increase the severity of coral diseases. Ecology Letters 6: 1056-1061.
5. Kuta & Richardson. 2002. Ecological aspects of black band disease of corals: relationships between disease incidence and environmental factors. Coral Reefs 21: 393-398.
6. Porter et al. 2001. Patterns of spread of disease in the Florida Keys. Hydrobiologia 460: 1-24.
7. Reimer, Hirose, et al. new Terpios papers.
1. Quick introduction to diseases.
2. Common coral reef diseases.
3. Why are diseases becoming common?
4. How do diseases affect conservation?
5. Terpios: a new threat
6. Conclusions
2. Common coral reef diseases.
3. Why are diseases becoming common?
4. How do diseases affect conservation?
5. Terpios: a new threat
6. Conclusions
Part 1: DiseaseExample 1: Plague in humans
• Plagues have struck humans many times.
• Often kill 10-50% of population.
• Caused by an influenza virus.
• Two most infamous cases are 13th century Black Plague, and 1919-1920 Spanish Influenza.
• No one knows where plagues came from.
• Spread through common routes of trade.
• Spread faster in modern cases.
• Often affects young adults worse due to “cytokine storms”.
Spanish Influenza
• In some countries fatalities were as high as 50%.
• Killed more people than WWI.
How does this happen?
• New mutation in influenza virus that most humans do not have capability to respond to.
• Genetic variation provides resistance.
• SARS is a more recent case.
Example 2:
Introduction of a new disease into an isolated area
Elm trees common in North America and Eurasia.
Preyed upon by two species of bark beetles.
Beginning in the 1910s, some elms began to die.
Die-offs became rapid in 1960s.
Bark beetles somehow involved in the disease.
Survival of elms close to 0%.
• The causative agents of DED are ascomycete microfungi.
• Carried by the elm bark beetles.
• Three species are now recognized: Ophiostoma ulmi, which afflicted Europe in 1910, reaching North America on imported timber in 1928, Ophiostoma himal-ulmi, a species endemic to the western Himalaya, and the extremely virulent species, Ophiostoma novo-ulmi, which was first described in Europe and North America in the 1940s and has devastated elms in both areas since the late 1960s.
• The origin of O. novo-ulmi remains unknown but may have arisen as a hybrid between O. ulmi andO. himal-ulmi.
• Plagues have struck humans many times.
• Often kill 10-50% of population.
• Caused by an influenza virus.
• Two most infamous cases are 13th century Black Plague, and 1919-1920 Spanish Influenza.
• No one knows where plagues came from.
• Spread through common routes of trade.
• Spread faster in modern cases.
• Often affects young adults worse due to “cytokine storms”.
Spanish Influenza
• In some countries fatalities were as high as 50%.
• Killed more people than WWI.
How does this happen?
• New mutation in influenza virus that most humans do not have capability to respond to.
• Genetic variation provides resistance.
• SARS is a more recent case.
Example 2:
Introduction of a new disease into an isolated area
Elm trees common in North America and Eurasia.
Preyed upon by two species of bark beetles.
Beginning in the 1910s, some elms began to die.
Die-offs became rapid in 1960s.
Bark beetles somehow involved in the disease.
Survival of elms close to 0%.
• The causative agents of DED are ascomycete microfungi.
• Carried by the elm bark beetles.
• Three species are now recognized: Ophiostoma ulmi, which afflicted Europe in 1910, reaching North America on imported timber in 1928, Ophiostoma himal-ulmi, a species endemic to the western Himalaya, and the extremely virulent species, Ophiostoma novo-ulmi, which was first described in Europe and North America in the 1940s and has devastated elms in both areas since the late 1960s.
• The origin of O. novo-ulmi remains unknown but may have arisen as a hybrid between O. ulmi andO. himal-ulmi.
Part 2: Common coral reef diseasesIntroduction to
coral reef diseases
• Bacteria observed in corals in early 1900s.
• Diseases noticed in 1970s, seemingly increasing over last 30 years.
• 34 mass events, affecting sponges, seagrasses, cetaceans, urchins, fish, molluscs, corals.
• Have changed composition of reefs.
Diseases affecting Scleractinia
• Many diseases named, but very little known.
• Most pathogens still unknown.
• Most common in Atlantic (Green & Bruckner).
• Not to be confused with coral bleaching.
Green & Bruckner 2000
Black Band Disease (BBD) Caused by numerous cyanobacteria (500 spp.) as a microbial mat.
Mat makes the colored band.
First observed in 1973.
Moves 3mm to 1cm/day.
Found in 42 spp. of coral.
Kuta & Richardson 2002
• BBD correlates strongly with depth, temperature, nitrites.
• Also correlates with diversity and orthophosphate.
White band disease: Pathogen unknown, may be bacteria. Noticed in 1981.
Tissue loss from base to tip.
Affects two species, Acropora cervicornis and A. palmata.
Moves 3mm to 1cm/day.
• WBD has drastically altered Caribbean reefs.
• Shifts in coral species.
• Loss of overall coral cover; algae increasing.
• Both species now “threatened”.
• Losses of over 98% of A. cervicornis. Locally extinct.
White plague: Affects many species, but no acroporoids.
Caused by Aurantimonas bacteria.
First observed in 1977.
Aspergillosis: Caused by terrestrial fungi.
Affect mainly Atlantic gorgonians.
Also affects waterfowl.
Noted in 1997.
Tumors: Similar to cancer.
Affects mainly A. palmata.
Irregular growth, no zooxanthellae.
Noted in 1960s and 1970s.
Other diseases: Many other diseases.
Mostly known from Atlantic.
Yellow band disease, yellow spot disease, white pox disease, brown band disease.
Most noted for first time in last 20 years.
Pathogens usually unknown.
Part 3: Why are diseases becoming common?1. Global warming?
• Many people blame global warming.
• But likely much more complex.
2. Nutrient enrichment - Bruno et al. 2003
• Experiments done with YBD and Aspergillosis.
• Controls were disease only, experimental with added nitrogen and phosphorus.
Results - Aspergillosis
• Nutrients increased severity of disease in sea fans.
Results - YBD
• Presence of nutrients increased rate at which YBD developed in two species of coral.
3. Dust? -
Garrison et al. 2003
• Airborne dust from Africa and Asia carries many contaminants to reefs.
• Global warming and desertification increasing dust, therefore increasing contaminants.
Part 4: How do diseases affect conservation?Effects are widespread
Many studies have documented widespread coral decline in almost ALL coral species.
Porter et al. 2001 showed many declines 1996-1998 NOT due to coral bleaching but disease.
• Porter et al. 2001 cont
• Green & Bruckner 2000
• Green & Bruckner 2000
Many examples of diseases spreading, many examples of reef degradation (show many photos).
Overview of disease
• All diseases have negative effects.
• Only WBD has changed communities drastically.
• Pacific 15 years behind Atlantic.
• Compounded negative influences more severe for coral reefs.
Part 5: Preliminary results of field surveys of Terpios outbreaks in the Nansei Islands, Japan
Terpios hoshinota Rützler and Muzik 1993
Terpios in the Nansei Islands - history
Outbreak noticed in Mariana Is. 1973. (Bryan 1973 )
Terpios-Nansei project
Assess the current distribution of Terpios in the Nansei Islands.
Establish monitoring sites.
If present, characterize sexual reproduction & ecology.
Methods
Survey all major islands by snorkel/scuba (Reimer).
Monthly/bi-monthly sampling at designated locations – histology (Hirose), genetics (Chen).
Permanent transects at massive outbreak (Reimer), analyses (Reimer, Nozawa).
Preliminary results
Three situations observed: none, small amounts, massive outbreak
Disappearance?
Yonama, Tokunoshima had massive outbreak (87.9% cover) in 1986 (Marine Park Center Foundation 1986).
Discussion
Terpios absent or present in small numbers in most reefs in Nansei Islands (38/39 examined locations).
Coverage does not appear to fluctuate much in most locations.
Discussion & Questions
Massive outbreaks still occur in Nansei Islands.
How long do outbreaks last?
“Recovery” observed at Yonama, but is this true recovery? At least, not a dead-end.
Results suggest outbreaks are linked to reef degradation, but factors not clear.
Future work
Permanent transect results & analyses.
Try to quantify speed at which massive outbreaks can occur.
Combine analyses with genetic, histological results.
Examine Yakomo (current outbreak location) to understand causes of outbreaks. Why this location?
Part 6: Conclusions.Conclusion 1
• Disease more widespread on reefs in Caribbean.
• More research? Partially.
• Monitoring in Pacific very critical.
Conclusion 2
• Only one disease has permanently changed community structure (WBD).
• Other diseases locally important.
Conclusion 3
• Very few studies have investigated in detail mortality rates.
• Monitoring of individual colonies needed.
Conclusion 4
• Diseases increasing.
• Bleaching appears to be more critical, but two problems appear related.
Conclusion 5
• Diseases not well understood.
• Many diseases affect many species; possibly more or less diseases.
• Pathogens need to be investigated.
Conclusion 6
• While bleaching currently more serious, foolish to ignore diseases.
• May be “indicator” of serious problems, similar to amphibians.
What needs to be done
• <3% of reefs in danger have low human impact.
• More research needed on human influences and pathogens.
• Management and conservation then follow.
References:
1. Green & Bruckner. 2000. The significance of coral disease epizootiology for coral reef conservation. Biological Conservation 96: 347-361.
2. Aronson & Precht. 2001. White-band disease and the changing face of Caribbean coral reefs. Hydrobiologia 460: 25-38.
3. Garrison et al. 2003. African and Asian dust: from desert soils to coral reefs. BioScience 53: 469-481.
4. Bruno et al. 2003. Nutrient enrichment can increase the severity of coral diseases. Ecology Letters 6: 1056-1061.
5. Kuta & Richardson. 2002. Ecological aspects of black band disease of corals: relationships between disease incidence and environmental factors. Coral Reefs 21: 393-398.
6. Porter et al. 2001. Patterns of spread of disease in the Florida Keys. Hydrobiologia 460: 1-24.
7. Reimer, Hirose, et al. new Terpios papers.
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