November 21, 2012
Reverse taxonomy examples
Outline
1. Trouble-shooting: dangers of reverse taxonomy.
2. Examples of reverse taxonomy from mammals (terrestrial, marine).
3. Atlantic and Pacific corals.
4. Four species of COTS.
5. Deep-sea zoanthids.
Part 1 - dangers of reverse taxonomy
What is morphological convergence?
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)
In other words, distinct lineages look similar morphologically.
Not to be confused with the “ghost” of molecular convergence.
Much more common than thought!
Many recent phylogenetic studies have shown morphological convergence is widespread.
Butterflies, birds, lizards, algae, trees, even zoanthids!
Famous recent examples include Atlantic and Pacific corals.
Extinct-extant convergence: Similar “shapes” or body plans have appeared many times throughout the fossil record, and may even remind us of extant species.
Cryptospecies
Many “undiscovered” large vertebrate species may yet await description (e.g. Amato et al. 1998; Dung et al. 1993).
These are from the deep sea, remote regions, or are cryptic in other ways.
One famous example is theorized to exist in mountain regions of the world.
Rarely seen, but many clues (sightings, footprints, etc).
Giant unknown hominids?
Many legends exist of “giant apes” or “hairy men”.
Common in the Himalayas (yeti) and in western North America (sasquatch).
Despite large size, very little physical evidence they exist.
Evolutionary history of Gigantopithids
These cryptospecies may have evolved from extinct Gigantopithelus (Matthiesson 1979).
Fossils of Gigantopithelus known from Asia, until 3K ybp.
Possible sister lineage to humans.
Materials and Methods
Trips made to remote regions of Nepal 1992-1995, within the Himalaya mountain range (Matthiessen & Laird 1992; 1995).
Region home to the “ye-the” or “mehti”; yeti in English (described in Herge 1960; Matthiessen 1979).
Extensive trekking, traps, and local guides utilized.
Very little concrete evidence found, although highly likely to exist in the mysterious Lo Monthang valley.
Hair samples
Hair found by local guides in Lo Monthang valley, conclusively identified by them as “mehti” hair.
Hair deposited in local temple.
In 2003, request made to Nepalese government to examine hair granted.
DNA analyses
DNA well-preserved in hair.
Used mt 12S rDNA, excellent mammal marker, with modified universal primers L1091 and H1478 (Kocher et al. 1989).
Acquired sequences aligned with 15 known mammalian groups, including homonids, chimpanzees, gorillas, whales, bovine, armadillo, and Perissodactyla (horses, rhinoceros, and zebra) sequences (all GenBank).
Resulting SOAP alignment (Loytynoja & Milinkovitch 2001) subjected to MP, NJ, and Bayes analyses (Felsenstein 1985) using PAUP v 4.0b4a (Swofford 1997).
ML consensus tree, with KH tests (Kishino & Hasegawa 1989).
Results
Yeti formed highly supported monophyly with ungulates (horses, zebra, donkey, well within Perissodactyla.
Identical mt 12S rDNA to X9547 and U02581.
Well removed from primates, and outgroups.
Conclusions:
Despite “primate” appearance, the yeti is ungulate (=related to horses).
Yeti have undergone extensive morphological convergence with primates despite being genetically distant.
This idea was first proposed in Herge 1960!
Questions
Do you believe the results? Why or why not?
What else could cause these results?
What can we learn from this?
How can we prevent such things from happening?
Part 2 - New species (marine & terrestrial)
2a. A 3rd species of elephant
Background
African elephant traditionally one species with 2 major subspecies: Loxodonta africana africana and L. africana cyclotis.
Recent research suggests may be separate species, or even 4 species.
Different DNA markers, different results.
In this study, used genomic results to analyze number of species.
Samples from Mastodon, Mammoth, Asian Elephant, two populations of African Elephant.
Results
Africa-Asia split 4.2-9.0 mya.
Based on DNA, Forest & Savanna split 2.6-5.6 mya.
Asian & Mammoth split 2.5-5.4 mya.
Conclusions:
2 species of African elephant.
Asian closely related to Mammoth!
Assumptions need re-examination.
2b. Dalebout et al. 2002. A new species of beaked whale Mesoplodon perrini sp. n. (Cetacea: Ziphiidae) discovered through mitochondrial DNA sequences. Marine Mammal Science 18: 577-608.
Introduction
• Beaked whales are rare, with cryptic lifestyles. Most never observed alive.
• 12 species described in last 100 years!
• Mesoplodon hectori common in southeast Pacific.
Materials & Methods
• 5 specimens of beaked whale stranded in California, 1977-1995.
• Thought to be M. hectori based on morphology.
• Researchers then examined 2 mt DNA markers…
Results
• Results surprisingly show five specimens not M. hectori.
• New species!
• Re-examination shows morphological differences as well.
Discussion
• Authors suggest genetic voucher material for all taxa.
• Also state there are likely 40 marine mammal species still unknown!
• Cookiecutter sharks feed on M. perrini.
• Who knows what species await description?
Recent news:
"This is good reminder," said Constantine, "of how large the oceans are, and of how little we know about them. "
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
Part 3 Atlantic & Pacific corals
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
• Coral phylogeny has been in flux for 10+ years.
• Perhaps corallimorphs within hard corals.
• Here examine 127 species, 75 genera, 17 families.
• Four markers; 2 nuclear, 2 mitochondrial.
• Corals monophyletic.
• 11/16 families not monophyletic.
• Corresponding morphological characters found.
• Corallimorphs not part of stony corals.
• Many Atlantic corals are very unique, and should be conserved.
• Some clades vulnerable to extinction (II, V, VI, XV, XVIII+XX).
• Ability to conserve depends on knowing what to conserve.
• Re-organize based on DNA, re-examine morphology.
• Atlantic corals must be protected more strongly.
• Basic ideas need to be re-examined (e.g. favids).
Part 4 - Crown-of-thorns
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
• Acanthaster planci outbreaks threaten coral reefs.
• Causes of outbreaks not clear.
• Species has long-lived larvae, but apparent population structure.
• Here used COI sequences from 237 samples.
• Four clades found, 8.8-10.6% divergent.
• Diverged 1.95-3.65 mya.
• Species show geographical partitioning. Due to sea level changes.
• All populations expanding.
• Four species, SIO, NIO, Red Sea, and Pacific.
• Outbreaks mainly seen in Pacific - could this be a species difference?
• Clearly more research needed, critical for coral reef management.
Part 5. Deep-sea zoanthids
Background:
Until 2007, all described deep-sea zoanthids are placed in Epizoanthidae despite morphological and ecological differences.
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。
No deep-sea zoanthids formally described from the Pacific.
太平洋の深海スナギンチャクは全く分類されていない。
None described from limited environments.
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。
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.
おそらく、珍しくはない。
Potential new zoanthid?
During Shinkai 6500 dive #884 (June 2005), several unidentified zoanthid-like samples “accidentally” collected off Muroto, Nankai Trough, depth=approx. 3300 m.
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。
Back checks of images show that the sample organism is apparently quite common at the dive site.
画像をチェックすると、この生き物が非常に多い。
Lives on mudstone but not loose sediment.
固い泥岩の上に存在、泥上には存在しない。
No high-resolution in situ images exist.
綺麗な画像が無い。
Only 12 polyps collected.
ポリプは12個しか採取されなかった。
External morphology
Samples appeared to be zoanthid-like based on: sand encrustation and polyp shape. No tentacle data available.
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。
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.
単体性、極限環境の初めてのスナギンチャク。
Internal morphology
As expected, cross section using normal (wax-embedded) methods gave poor results.
パラフィン切片での結果はあまりよくない。
Attempted to set sample in epoxy resin, cut a section, and polish to necessary thickness but failed.
レジンでの切片も無理。
Another possibility is digestion of outer surface of polyp.
フ酸での切片は可能だが、非常に危ない。
Could obtain mesentery count number from rough cross-sections (19-22).
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。
We examined nematocysts. These can differ between species but do not tell anything about relationship.
Phylogenetic results:
Obtained mt COI, mt16S rDNA, and 5.8S rDNA sequences confirm samples are zoanthid, but divergent from all known zoanthid families.
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。
Particularly, divergent from all known groups of deep-sea zoanthids described.
特に、今までの深海のスナギンチャクと違う。
Bootstrap support for monophyly 100% (all methods, all markers).
遺伝子解析の結果の確率が非常に高い。
Based on external morphology and genetic results, these samples are a new family of zoanthid: Abyssoanthidae.
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。
However, several questions remain regarding ecology and reproduction of this new family.
今後、日本周辺の深海で調査を行う予定。
More species?
Images suggest more specimens present in Japan Trench at 5600 m.
In autumn 2007, we went to investigate and collect specimens.
17 day cruise, 3 dives, on RV Yokosuka and the Shinkai 6500.
Presence of zoanthids confirmed, many specimens collected.
Also, collected an octocoral, also an undescribed species.
Found on other benthos, found in limited environments.
Below 1000m very few samples, these specimens are invaluable to science.
Specimens were examined using morphology and DNA.
Specimens collected were very similar in morphology to A. nankaiensis.
DNA was slightly (1-2 base pairs/marker) different.
DNA, environment (5600 vs 3300 m) different enough to describe a new species; A. convallis.
Overall conclusions:
1. Genetics already impacting our understanding of diversity.
2. Expect more surprises in the future.
3. Massive revision of all coral reef organisms!
References:
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
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
3. Dalebout et al. 2002. A new species of beaked whale Mesoplodon perrini sp. n. (Cetacea: Ziphiidae) discovered through phylogenetic analyses of mitochondrial DNA sequences. Marine Mammal Science 18: 577-608.
4.Thompson et al. 2012. The world’s rarest whale. Current Biology 22(21) pp. R905 - R906.
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.
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
7. Reimer et al. 2004-2010. Various papers on zoanthid phylogeny.
No comments:
Post a Comment