Class 12 - DNA barcoding and the Tree of Life + TEST OUTLINE!

Outline
• 1. Introduction to DNA barcoding.
• 2. Barcoding example 1: Sharks.
• 3. Barcoding example 2: Zoanthids.
• 4. Tree of Life overview.
• 5. Conclusions.
• 6. Test.
Part 1: Introduction to 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
遺伝子バーコードの配列の必要な特徴
A sequence/marker used to barcode should:
• be easy to amplify
• 取りやすい、増えやすい。
• not possess paralogues
• ひとつだけのコピー。
• have conserved regions to design primers efficiently for a broad taxonomic sampling
• プライマーが作りやすい配列。
• be variable enough to distinguish species
• 配列の変化レートは種間の区別ができる。
• but conserved enough within species
• 一方、種内の変化は無いほうがよい。
Barcoding does not aim to solve phylogeny!
遺伝子バーコードの目標は分類だけ。関係などを調べるためではない。
Potential applications
1) Facilitating identification and recognition of named (described) species:
linking life history stages, genders.
雌、雄のリンク。
differentiating cryptic species.
cryptic speciesの区別。
traceability of commercialized species.
食べ物などの産地。
identifying gut contents.
生き物の餌の分類。
2) Surveying and inventorying biodiversity;
Identifying new species.
新種の分類。
Range of species.
種類の分布。

Potential applications
1) Facilitating identification and recognition of named (described) species:
Differentiating cryptic species:
Cryptic speciesの区別:
Astraptes属]
mt COI sequence divergence
among North American birds
北米の鳥類のmt COI遺伝子：種内と属内の変異
Barcode of Life project - information available on the internet.


Strengths:
• Offers an alternative taxonomic identification tool for situations in which morphology is inconclusive.
• Focusing on one or a small number of genes enhances efficiency of effort and application.
• Once a reference database is established it can be applied by non-specialist.
• The cost of DNA sequencing is dropping rapidly due to technical advances.
• Potential capacity for high throughput and processing large numbers of samples.
“barcoding gap” exists for many groups of animals, but not all. One key example are benthic cnidarians.
Other weaknesses include old samples (type specimens) in formalin, no “field DNA barcoder” available yet, and the “barcoding gap” issue.
Part 2 - Using genes to identify shark body parts
Shivji et al. 2002
Background
• Sharks threatened due to shark fin demand.
• Need species by species conservation.
• Difficulties in identification make data questionable.
• Genetic identification needed.
Results
• Investigated ITS-2 with new primer sets.
• Used dried fins from Asia & Mediterranean (n=lots!).
• Identification worked on a global scale to species level.

• This system can be used on many taxa that are hunted or need conservation.
• Coral reef applications: sea turtles, red coral, other CITES species.
Part 3 - barcoding zoanthids
Why barcode Zoantharia? Often specimens are small and poorly preserved - barcoding may help!
Some species have much variation - color etc., while other species look identical!

Barcoding and Zoantharia
• Some observed types have much variation, and their status is unknown.
• 分類ができていない。種内変異が大きい。
• Not usually entered into biodiversity estimates.
• 今まで、多様性の調査では無視されている。
• Among mitochondrial genes, COI and 16S rDNA have been widely used in Zoantharia.
• 今までの遺伝子の論文で、mt DNAがよく使われている。
• An examination of the entire mt genome shows no region with high rates of evolution.
• mt DNAには、早い進化の配列が無い。
• ITS-rDNA can NOT be used.
• ITS-rDNAなどは複数のコピーがあるので、利用できない。
• Other nuclear genes may show potential, but common primers do not work.
• Nuclear DNAが利用可能だが、全てのスナギンチャク類に反応するプライマーは不可能。
Our zoanthid barcoding experiment
スナギンチャク目の遺伝子バーコード実験
• Collected zoanthids from around the world (4 families, 7 genera, 65 samples).
• 世界中からスナギンチャクのサンプルを採取した (4科、7属、65サンプル)。
• Examined their mt COI and mt 16S rDNA sequences.
• mt COI と mt 16S rDNA配列をとって、解析した。
• Asked - how effective are the sequences at identifying genera and species? Can they be used for barcoding?
• これらの配列をバーコードできますか？属レベルまでの有効性は？種レベルまでの有効性は？
Coral life cycle - zoanthids have never been truly observed in many life stages; barcoding could help.
Mitochondrial cytochrome oxidase subunit I - COI配列
• 長さは500~650 bp
• Advantages:
– no alignment problems.
– 綺麗に並べる。
– huge database.
– GenBankで、たくさん情報がある。
– common primers (HCO, LCO).
– プライマーが使いやすい。
• Weaknesses:
– very conserved, occasionally cannot distinguish between congeners.
– 配列の進化が遅い、たまに別種の区別ができない。
mitochondrial 16S rDNA配列
• 長さは530~1000 bp
• Advantages:
– Indels.
– Can make specific primers.
– それぞれの属用のプライマーが作れる。
• Weaknesses:
– Still low variation.
– 配列の進化がCOIと同様に遅い。
– Indels tough to align.
– 並べることが難しい。
– No universal primers.
– 全てのスナギンチャク用のプライマーが無い。
16S-rDNA V5配列
• 130 bp
• Advantage:
– Useable with degraded DNA (old, formalin fixed)
Conclusions:
• Both markers were very similar in their effectiveness (90~95%) in identifying species.
• 両方のマーカーは同様に有効性がある。
• Both markers could discern all genera.
• 両方のマーカーは属レベルまでは完璧。
• mt COI is appropriate for broad investigations, while mt 16S rDNA is better for specialized research.
• COIはスナギンチャク目全体を調べるときによい。16Sはもっと細かいレベルの研究でよい。
• Search for “good” nuclear markers continues.
• もっとよいマーカーをまだ探し中。
• For now, any information is better than none!
• スナギンチャク目の場合、何のデータでもデータが無いよりはよい。
Potentials:Among mitochondrial genes, if COI is the most used gene, the large ribosomal subunit (16S) shows interesting variations.

In 16S, the presence of INDELS specific to different groups of species could be a good signature to barcode the order.

Pure barcoding can be very useful at the most to differentiate groups of closely related species.
Combined with geographical and ecological characters it can be a key feature in the taxonomy of Zoantharia.
Preliminary results showed that the V5 region of 16S could be interesting for other anthozoan orders, such as black corals and sea anemones.


• Investigate spawning timing.
• 産卵タイミングの研究。
• Investigate cross-breeding.
• 交配実験。
• Continue to explore the world for new samples.
• 世界中の新種や多様性調査を行う。
• Examine museum specimens.
• 博物館の標本の形態を調べる。
Part 4 - Tree of Life project
http://www.tolweb.org
• Goal is to have one webpage for every species and group of organisms.
• Organized to reflect evolution.
• Hundreds of contributors.
• Aid in learning.
• Link to other databases.

• Authors enter information (data; images; text).
• Automatically formatted and linked to the TOL.
• Branches & leaves.
DNA tree of life figure - animals are very small portion of diversity of life!
Part 5 - Conclusions
More Conclusions
• Large, international, internet-linked projects will become bigger and bigger.
• “Net 2.0” may help harness “people power” to help conserve coral reefs and other biodiverse ecosystems.
Thanks! References cited:
1. Herbert et al. 2004a. Identification of birds through DNA barcoding. PLoS Biology 2 (10): e312.
2. Herbet et al. 2004b. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. PNAS 101: 14812-14817.
2. Shivji et al. 2001. Genetic identification of pelagic shark body parts for conservation and trade monitoring. Conservation Biol 16: 1036-1047.
3. Sinniger et al. 2008. Potential of DNA sequences to identify zoanthids (Cnidaria: Zoantharia). Zool Sci 25: 1253-1260.
4. Tree of Life Project. http://www.tolweb.org/tree/.
Test overview
• Format: 11 questions; 1 from each class. Answer 7! Questions will be both sentences and multiple choice style.
• Content: Anything from any class; not only slides but also discussion and talk.
• Bonus question from suggested readings and/or video.

Class 11 - Conservation II

Happy New Year!
今年も宜しくお願いします。

Outline
• 1. Centers of endemism.
• 2. How to stop bleaching (?).
• 3. The importance of fish and mangroves to coral reefs.
• 4. Not just coral reefs: how other ecosystems are connected.
• 5. Conclusions.
• 6. Video: Coral reef organisms.
Part 1 - Centers of endemism
Roberts et al. 2002
• Examined 3235 species of fish, corals, snails, lobsters.
• Ranges in 1 X 1 degree squares (cells).
• 7.2 to 53.6% have restricted ranges; vulnerable to extinction.
• Looked for centers of endemism.

• 10 richest centers cover 15.8% of reefs; 0.012% of oceans.
• Contain 44.8 to 54.2% of restricted range species.
• Major biodiversity hotspots.

Hotspots threatened by human activity.
Conservation should focus on these areas.

• Many threats linked to land.
• Many hotspots next to land hotspots.
• Integrating conservation may be effective.
Part 2 -
How to stop bleaching (?)
West & Salm 2003
• What factors help corals against bleaching?
• Reviewed all research up until 2003.

• Many examples of resistance to or recovery from bleaching.

• Many factors contribute to resistance.
• Can be included in management plans.
• Cumulative stresses worse than one stressor.
Many factors contribute to resilience.
Can be included in management plans.
Healthy diverse reefs more stable than reefs under threat.


Mumby et al. 2004
• Reef fish often use mangroves as nurseries.
• But can use other environments, not confined.
• Also, despite deforestation, other pressures (fishing, larval supply) likely larger.
Examined biomass and numbers of grazing fish at reefs with and without connecting mangrove forests.
Consistently shown despite higher fishing pressure reefs with mangroves have more fish!
Reefs that have lost mangrove have extinctions.


• Management should include connected habitats, not islands of each type.
• Future destruction of mangroves will have negative influence on reef.
Mumby et al. 2007
• Caribbean reefs have damage from loss of Diadema antillarum and two species of coral.
• “Sick” reefs characterized by macroalgae.
• Can macroalgae be reversed? Or is it a stable state?

• Used computer modeling and simulation.
• Showed reefs can easily change to other states once D. antillarum died off.
• With only parrotfish as grazers, small negative change in parrotfish numbers results in macroalgae blooms.
• Coral becomes unstable state with low grazing.

• Regular impact of hurricanes worsens with lack of grazers (fish and urchins).
• Modeling useful for conservation targets.
Part 4 - Not just coral reefs: how other ecosystems are connected
Baum et al. 2003
• Examined shark populations in NW Atlantic.
• Sharks caught in large numbers by longline fishing nets.
• No data until this study.


• All species examined showed rapid declines over last 15 years.
• Most species declined over 50%.
• Three species declined over 75%.

• Recommends marine conservation areas AND reduction in fishing.
• This is because sharks have large ranges and slow rates of population growth.
• Sharks worldwide in danger.
James et al. 2005
• Examined leatherback turtle migration and ranges using satellite telemetry (n=38).
• Tagged off E. Canada.
• Leatherback turtle now critically endangered (IUCN) despite worldwide distribution.

• Turtles migrated south to Caribbean and back within 1 year.
• Most turtles avoided areas of protection; and most spent time in areas of longline fishing.

• Turtles vulnerable to 1) northern coastal and 2) shelf water fisheries.
• Action must be taken to prevent; current conservation is not enough.
Part 5 - Conclusions
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. We must do MORE!

Thanks! References cited:
1. Roberts et al. 2002. Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295: 1280-1284.
2. West & Salm. 2003. Resistance and resilience to coral bleaching. Conservation Biol 17: 956-967.
3. Mumby et al. 2004. Mangroves enhance the biomass of coral reef fish communities in the Caribbean. Nature 427: 533-536.
4. Mumby et al. 2007. Thresholds and the resilience of Caribbean coral reefs. Nature 450: 98-101.
5. Baum et al. 2003. Collapse and conservation of shark populations in the northwest Atlantic. Science 299: 389-392.
6. James et al. 2005. Identification of high-use habitat and threats to leatherback sea turtles in northern waters: new directions for conservation. Ecol Letters 8: 195-201.

Class 10 - Conservation I

Outline
• 1. Review of link between diversity and conservation.
• 2. Lionfish invading the Atlantic.
• 3. Red coral in the Mediterranean.
• 4. Coral reef conservation - unique problems.
• 5. Community conservation in the Philippines.
• 6. Conclusions.
Part 1 - Review of biodiversity and conservation
Biodiversity
• Biodiversity = Number of taxa (species, genera), or ecosystem types, etc.
• Biodiversity = bioresources.
• Bioresources = long-term economic well-being.
• Conserving biodiversity is important; we need to understand baseline biodiversity.
• Many “neglected taxa” remain.
保全と多様性のリンク
• Species diversity (# of species) for many groups of animals and plants unknown - lack of taxonomy.
• 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。
• 99.5% of species go extinct before we even describe them.
• 99.5%の種類は、分類する前に絶滅になってしまう。
• Without knowledge of species, how can we protect them?
• 種類の分類が無いと、保全ができない。
• Therefore, taxonomy and diversity VERY important.
• 分類学や多様性の理解が重要な研究。
• BUT…
Dangers facing coral reefs
• Global warming is raising the temperature of the ocean; this kills corals - “coral bleaching”.
• Also, as the oceans become more acidic, it is more difficult for corals to make their skeletons.
• Perhaps 90% of coral reefs will be dead by 2050.


• Crown-of-thorns starfish outbreaks

• Dynamite and cyanide fishing

Part 2 - Lionfish invading the Atlantic

• Lionfish known from the Indo-Pacific.
• Mainly eat reef fish, and often larvae or juveniles.
• Popular in the aquarium trade despite poison.

• Marine fish introductions less common.
• Most introductions due to purposeful introduction for fisheries, or released aquarium fish.
• Success often investigated.

• Whitfield et al. (2002) document several sightings (n=19) of Pterois volitans along E. Atlantic.
• Four specimens collected, numerous juveniles sighted, two collected.
• First introduction of Pacific fish to Atlantic.


• Likely limited by cold waters, but surviving.
• Can spread to Bermuda and Caribbean.
• Similar fish in this region overfished, niche is available perhaps!

Introduction?
• Introduction method; 2 possibilities.
• Ballast water possible, but no reports thus far.
• Aquaria very likely. Specimens known to have been released occasionally.
• Morphology appears to be typical of aquaria types.
Effects?
• No fish in region used to lionfish.
• No predators.
• Need genetic and temperature studies.
• Modeling needed.


Spreading populations
• Since sightings in 2000, lionfish have spread.
• Now known (Snyder&Burgess 2006) from Bahamas.
• Apparently spreading throughout Caribbean.
• Easy to document spread.
Genetic studies
• Since Whitfield et al (2002), more studies.
• Hamner et al. (2007) used mt DNA to examine specimens.
• Two markers (cyt B, 16S rDNA) previously used on lionfish in native ranges.

• Found two species of lionfish; P. volitans (93%) and P. miles (7%).
• Very reduced genetic diversity!
Minimum-spanning network analyses - P. volitans
• Atlantic specimens likely from Indonesia.

• P. miles source unknown.

• Reduced genetic diversity clear.
• Founder effect! Minimum of 3 P. volitans and 1 P. miles established populations.
• Invasions may be rapid and irreversible.
• Education needed.
Part 3 - Red coral in the Mediterranean
Red coral
• Corallium rubrum is a precious coral in the Mediterranean.
• Found 10 -250 m.
• Harvested for long time, over-exploited.
• Harvest reduced 66% in last 15 years.

Population structure
• Two population types, large deep colonies and shallow small colonies.
• Large drop off in shallow water at age 4, due to sponges and collection.

• Genetic distance becomes significant at 100s of kms.
• Thus, preservation of numerous populations needed.
• Management on regional scale needed.
• Must avoid local extinctions.
Conservation recommendations
• Must be managed at national and international scales.
• Only policy that works for such species.
• Set minimum colony sizes, maximum yield per area, harvesting seasons.
Part 4 - Conservation problems unique to coral reefs

• On land, biodiversity hotspots arise from small ranges and endemism.
• Examples include the Galapagos and Ryukyu Islands.

Hughes et al. 2002
• Coral reefs are different.
• Central Indo-Pacific (coral triangle) has very high biodiveristy.
• Arises from many species with large ranges having overlapping ranges in CIP.

• No correlation between numbers of coral endemics and reef fish endemics at locations, even though total numbers related.
• Endemism does not contribute much to high biodiversity of coral reefs.

• Centers of high biodiversity and endemism are separate!
• Two part approach to conservation needed.

Implications for conservation
• 8% of the CIP has 83% of coral species and 58% of fish species.
• CIP protection is cost effective.
• Endemics at peripheral locations (e.g. Red Sea, Madagascar).
• Such locations have lower biodiversity, higher risk for extinction.
Recommendations
• MPAs now too small in size and number, too far apart.
• Focus on fish and mega-fauna, also coral.
• Small and cryptic taxa ignored.
• Need to work more on these taxa.
Part 5 - Community conservation of coral reefs
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 6 - Conclusions

Conclusions 2
• In the future, more conservation plans will be implemented.
• The gap between well protected areas and those not protected will widen.

Conclusion 3
• Very few non-protected reefs will survive.
References cited:
1. Whitfield et al. 2002. Biological invasion of the Indo-Pacific lionfish Pterois volitans along the Atlantic coast of North America. Mar Ecol Prog Ser 235: 289-297.
2. Snyder & Burgess. 2007. The Indo-Pacific red lionfish, Pterois volitans (Pisces: Scorpaenidae), new to Bahamian ichthyofauna. Coral Reefs 26: 175.
3. 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.
4. Santangelo & Abbiati. 2001. Red coral: conservation and management of an over-exploited Mediterranean species. Aquatic Conserv Mar Freshwater Ecosys 11: 253-259.
5. Hughes et al. 2002. Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs. Ecol Let 5: 775-784.
6. White & Vogt. 2000. Philippine coral reefs under threat: lessons learned after 25 years of community-based reef conservation. Mar Poll Bull 40: 537-550.

Class 9 - Reticulate Evolution

Outline
• 1. Review of evolution.
• 2. Introduction to reticulate evolution.
• 3. Examples from plants and fish.
• 4. Examples from corals.
• 5. Examples from zoanthids.
• 6. Conclusions
Part 1 - Evolution

Genetic Diversity
• Required to adapt to change in environment.
• Many methods of measurement.
• Large populations of naturally breeding animals have high genetic diversity.
• Reduced populations are concern.
Cnidaria DNA
刺胞動物の遺伝子
mitochondrial DNA (mt DNA)
• evolves very slow in Cnidaria, opposite to most animals.
• 他の動物と違い、刺胞動物で進化が遅い。
DNA amd phylogenetics: All cells contain DNA - the code or blueprint of life.
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。
This code has only four different “letters”: A, G, C, T.
遺伝子は４つのコードしかない。
Usual length 105 to 1010 base pairs.
生き物のひとつの細胞にある遺伝子の長さは105 to 1010 。
Genome projects read everything in one organism, but takes time and expensive.
全ての遺伝子を読むことは時間とお金の無駄。
Many studies use one or a few “markers” to investigate relations.
遺伝子の短い部分だけでも系統関係が解析できる。

• By collecting the same marker from different samples and then analyzing them, we can make a tree.
• 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。
• It is thought/hoped a tree is similar to how evolution occurred.
• 系統樹から進化が見えると思われる。
Part 2 -
Reticulate Evolution
What is evolution?
進化というのは？
• The descent of all organisms from a common ancestor.
• 全生物は共通の祖先から。
• The development of unique traits in response to environment, etc.
• 環境の変化などのせいで、それぞれのグループがユニークな特徴を持つ。
• Groups gradually “drift” away from each other.
• それぞれのグループが他のグループからだんだん離れる。
• But…
Some problems…
いくつかの問題点がある
• How can “mega”-diversity arise?
• 非常に高い多様性はどうやって進化した？
• Even allowing for rapid evolution, there are cases of “mega”-diversity in very new and small environments, with many species adapted to very specific niches (plants, cichlids etc.).
• 時として、新しい環境で、種の数が想像以上に多い。
• Often hard to accurately explain “species” over large geographic scales.
• large geographic scaleで、種の説明や分類が困難になる場合がある。
• How can hybridization between species be explained?
• 別種のhybridizationも説明がしにくい。
Theory of evolution over time
• Evolution is evolving.
• Darwin - classic model.
• Currently, reticulate evolution is a “rare nuisance”.
• Likely our ideas will develop into an even more complex model.
Reticulate evolution?
網状進化とは？
• The pattern of evolution resulting from recombinational speciation.
• 種類Aと種類Bのハイブリッドによる進化。
• Not generally expected to be a common occurrence, but can explain “mega-diversity” in new environments and unexpected genetic results.
• 普通の進化より珍しいが、新しい環境などでは起こる可能性がある。
• Results in retainment of ancestral patterns in the genome, with “repackaging”.
• 遺伝子の配列は進化（変異）しない。ただ新しい組み合わせができるだけ。
• Believed to occur in many plant groups, and cichlids (fish).
• 植物やアフリカの池の魚類で起こっていると思われている。
Evidence of reticulate evolution
網状進化の証拠
• Without laboratory experiments very hard to infer, but some ways:
• 研究室の実験以外で網状進化をどうやって見つける？
• Shared sequence portions between or within species.
• 種内、また種間の配列を見て、同じ部分があるかどうか？
• Differences between mitochondrial and nuclear DNA.
• ミトコンドリアDNAと核DNAの解析結果が違うかどうか？
Part 3 - Examples of Reticulate Evolution: Plants and Fishes
Example 1: peony flowers
(Sang et al. 1995)
• Sequenced ITS-rDNA of 33 species of Paeonia from Europe and Asia.
• Shrubs and herbs in northern hemisphere.
• Spotty distribution.
Results
• Examined ITS-1 sequences.
• Many species showed additive patterns.
• Subsequent evolution has taken place in some species.

• Many hybrid species Asian.
• Parents of these hybrid species European.
• Suggests hybridization occurred in past.
Conclusions
• Can see historical patterns, useful in species with no fossil history.
• This type of evolution may be common in plants.
• In such cases must be careful with phylogenetics.
Another example:
Cameroonian crater
lake cichlid fish
• Megadiverse group of fish with monophyletic origin.
• Much research shows reticulate evolution may occur when nuclear and mt DNA phylogenies do not match.
• Invasion of new environments could trigger hybridization between species.
Background
• Do hybrid swarms result from large areas with different environments or not?
• Cichlid fish provide great test case!
Barombi Mbo Lake
• 2.5 km in diameter.
• 110 m deep, only oxygen to 40 m.
• Four endemic genera; seven species.
• All on IUCN Red List - critically endangered.
• Evolved over 10000 years.
Materials and methods
• Two mt DNA markers and 2 nuclear markers.
• All types of fish from lake sampled; specimens deposited in museums.
Results
• Differences in mt DNA and nuclear DNA.
• Secondary hybridization after evolution.
• Two ancient lineages formed new species; Pungu madareni.
Conclusions
• Hybrid speciation can make complex species assemblages even without prior hybridization.
Part 4 - Examples of Reticulate Evolution: Corals
Reticulate Evolution in Cnidaria?
刺胞動物門は網状進化する？
• Several studies hint at reticulate evolution in Cnidaria, particularly corals and related groups.
• 特に花虫綱で網状進化の可能性がある。
• Marine environments where coral reefs are found are generally “new”.
• サンゴ礁の環境は比較的新しい。
• Centers of “mega-diversity” with “hyper-evolution” to micro-niches.
• 狭い地域で、多様性が非常に高い。
Acropora spp.
(Odorico & Miller 1997)
• Acropora very diverse, much morphological variation.
• Hybridization known from lab tests.
• ITS-rDNA shown to be a useful tool to detect this.

• Six colonies from five species.
• 18S rDNA and 28S rDNA obtained as well as ITS-rDNA.
Results
• Acropora ITS rDNA very short.
• Unexpected patterns of diversity, even within individuals!
• Such patterns consistent with ongoing reticulate evolution.
Conclusions
• Much more diversity than seen in plant ITS-rDNA.
• Could be due to more hybridization over longer ranges.
• Hybridization may occur over biological (not geological) time scales.
More corals
(Vollmer & Palumbi 2002)
• Examined all three Caribbean Acropora spp.
• Examined 2 nuclear and one mt DNA marker.
Results
• A. cervicornis and A. palmata distinct species.
• A. prolifera are F1 hybrids.
• Shape of A. prolifera depends on which species provided egg.
Conclusions
• F1 hybrids are immortal mules that may occasionally hybridize.
• Hybrids may be common in corals.
Part 5 -
Reticulate evolution in zoanthids
網状進化とスナギンチャク

Zoanthus spp. according to mt COI DNA
mt COIの結果による、マメスナギンチャク属の多様性
• Three species found with varying distribution. All ecologically similar to hard corals.
• ３つの種。生態はイシサンゴと似ている。
• Clear morphological variation between all three species.
• それぞれの種を区別できるようになった。
• This appears to be normal evolution.
• このデータから、普通の進化が推測できる。
核遺伝子(ITS-rDNA)配列結果
• All Z. kuroshio and Z. gigantus sequenced as expected.
• Z. kuroshio と Z. gigantusの結果はそれぞれが単系統。
• Z. sansibaricus had unusual results.
• 一方、 Z. sansibaricusの結果は単系統ではなかった！
• Some (2/3) samples gave expected sequences.
• 2/3のサンプルの配列（sansi）はmt DNAでの系統的位置と同様だったが、
• Some samples had both expected sequences and unknown “B” sequences.
• いくつかのZ. sansibaricus は不思議な “B”配列と普通の配列（sansi） 、両方を持つ。
• Some samples had only “B” sequences.
• 残りのZ. sansibaricus は不思議な “B”配列しか持っていない。
• B is closely related but different than Z. gigantus.
• “B”はZ. gigantus と近縁である。


Zoanthus undergoing reticulate evolution?
マメスナギンチャク属の網状進化？
• Samples with normal sequences and with normal/B, or just B have normal Z. sansibaricus morphology.
• 全てのZ. sansibaricusの形態が同じだった。
• Could B-only be F2 - resulting from backcrossing or F1 x F1 crossing?
• “B”配列しか持っていないサンプルはF2？
• Z. sansibaricus mass spawns, same as coral. No distribution barriers.
• マメスナギンチャク類はサンゴの様に同時に産卵する可能性がある。
• COI and morphology suggests NOT incomplete lineage sorting.
• 形態の結果やmt DNA配列を見ると、 incomplete lineage sortingじゃないと思うことができる。


Possible scenario for Zoanthus evolution
Zoanthus類の進化の説明
• Ancestor of Z.gigantus/B underwent one way hybridization (male B X female sansi), introducing B allele into Z. sansibaricus species.
• Z.gigantus/Bの精子（nuclear DNA）がZ. sansibaricus 種内に入ってきた。
• Modern-day Z. sansibaricus has both B and sansi alleles, ancestral B/giga evolved into modern Z. gigantus.
• 現在のZ. sansibaricusはsansiもBも持っている。
• 現在のZ. gigantusは昔のZ.gigantus/Bから進化した。

More zoanthids
(Reimer et al. 2007b)
• Investigated Palythoa spp. in Japan.
• Thought to be two genera, but mt DNA shows one genus.
• P. tuberculosa and P. mutuki very closely related.

Results
• ITS-rDNA shows two species (P. tuberculosa & P. mutuki) very closely related.
• Some specimens with intermediate morphology also apparently intermediate in phylogeny.
Results (2)
• Alignment of ITS-rDNA shows “reticulate” patterns between intermediates of two species.
• Appears as if some P. tuberculosa DNA has entered into P. mutuki population.

Conclusion 2
• In the future, more reticulate evolution will be found.
• This will impact conservation and our understanding of species.

Conclusion 3
• This will lead to better understanding of other related evolutionary events, such as lateral gene transfer (LGT).
References cited:
1. Sang et al. 1995. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: Implications for biogeography and concerted evolution. PNAS USA 92: 6813-6817.
2. Schliewen & Klee. 2005. Reticulate sympatric speciation in Cameroonian crater lake cichlids. Frontiers Zool 1:5.
3. Odorico & Miller. 1997. Variation in the ribosomal internal transcribed spacers and 5.8S rDNA among five species of Acropora (Cnidaria; Scleractinia): Patterns of variation consistent with reticulate evolution. Mol Biol Evol 14: 465-473.
4. Vollmer & Palumbi. 2002. Hybridization and the evolution of reef coral diversity. Science 296: 2023-2025.
5. Reimer et al. 2007a. Molecular evidence suggesting interspecific hybridization in Zoanthus spp. (Anthozoa: Hexacorallia). Zool Sci 24: 346-359.
6. Reimer et al. 2007b. Diversity and evolution in the zoanthid genus Palythoa (Cnidaria: Hexacorallia) based on nuclear ITS-rDNA. Coral Reefs 26: 399-410.

Class 8 - Disease

Note: Class 7 was an explanation of the report assignment.


Outline
• 1. Quick introduction to diseases.
• 2. Common coral reef diseases.
• 3. Why are diseases becoming common?
• 4. How do diseases affect conservation?
• 5. Conclusions
Part 1: Disease
Example 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 and O. himal-ulmi.
Part 2: Common coral reef diseases
Introduction 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: 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.

Class 6 - Symbiodinium

 Outline
 1. Review of Symbiodinium and coral bleaching.
 2. Investigating diversity of Symbiodinium: past to present.

 Part 1: Review of Symbiodinium and bleaching.
 Dangers facing coral reefs:
 Global warming is raising the temperature of the ocean; this kills corals - “coral bleaching”.
 Also, as the oceans become more acidic, it is more difficult for corals to make their skeletons.
 Perhaps 90% of coral reefs will be dead by 2050.

 Diagram of iving tissue

 Numbers of zooxanthellate genera over time, increase in ZX genera of corals.
 More diverse than ever, showing benefits of symbioses.
 Believed to have started approximately 60 million years ago.
 Symbiodinium spp. in invertebrates
holobiont=host+symbiont(s)
 Corals and symbionts
 Many shallow water corals get their energy from symbiotic zooxanthellae.
 These small animals make it possible for corals to live in the warm oceans.
 But, these symbionts are sensitive to hot ocean temperatures.
 What turns the coral white?
- As a stress response, corals expel the symbiotic zooxanthellae from their tissues
- The coral tissue is clear, so you see the white limestone skeleton underneath
 What can stress a coral?
 High light or UV levels
 Cold temperatures
 Low salinity and high turbidity from coastal runoff events or heavy rain
 Exposure to air during very low tides
 Major: high water temperatures
 Thermal stress
 Corals live close to their thermal maximum limit
 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
 NOAA satellites measure global ocean temperature and thermal stress
 How warm is warm?
 How hot do you think the ocean has to get before corals start to bleach?
 GLOBAL WARMING
 Glaciers and Sea Ice are melting
 World map showing levels of
coral bleaching. Source: ReefBase
 Can corals recover?
 Yes, if the stress doesn’t last too long
 Some corals can eat more zooplankton to help survive the lack of zooxanthellae
 Some species are more resistant to bleaching, and more able to recover
 Can corals recover?
 Corals may eventually regain color by repopulating their zooxanthellae
 Algae may come from the water column
 Or they may come from reproduction of the few cells that remain in the coral
 Can corals recover?
 Corals can begin to recover after a few weeks
 Does bleaching kill corals?
 Yes, if the stress is severe
 Some of the polyps in a colony might die
 If the bleaching is really severe, whole colonies might die
 Bleaching in Puerto Rico killed an 800-year-old star coral colony in 2005
 What else can stress do to corals?
 Question: what is something that happens to people when they are highly stressed?
 What else can stress do to corals?
 Question: what is something that happens to people when they are highly stressed?
 Bleaching and coral disease
 Coral diseases are found around the world

 High temperatures and bleaching can leave corals more vulnerable to disease

 Can quickly kill part or all of the coral colony
 Bleaching and bioerosion
 We have seen that bleaching can kill part or all of a coral colony
 Areas of dead coral are more vulnerable to bioerosion (when animals wear away the coral reef’s limestone structure)
 Storms & coral bleaching
 The same warm water that causes corals to bleach can also lead to strong storms.
 Storms: a mixed blessing
 Storms: a mixed blessing
 Each passing hurricane in 2005 cooled the water in the Florida Keys.


 Part 2: Investigating diversity of Symbiodinium: past to present.
 What are zooxanthellae?
 Algae that live in the coral polyp’s surface layer
 Algae get nutrients and a safe place to grow
 Corals get oxygen and help with waste removal
 Corals also get most of their food from the algae
 Symbiosis overview
 Genus Symbiodinium
 Described in 1962 by H. Freudenthal.
 Within dinoflagellates.
 Was though there was one single species worldwide.

 Morphology & life cycle
 Host species
 Cnidaria (corals, jellyfish, anemone, zoanthids, octocorals).
 Mollusca (clams, snails).
 Platyhelminthes (flatworms).
 Porifera (sponges).
 Protista (forams).
 First genetic studies
 Rowan & Powers 1991.
 Utlized 18S ribosomal DNA.
 Sampled from corals & anemones.
 Found unexpected diversity!
 Recommended further genetic studies.

 Second wave of studies
 Used faster evolving DNA markers.
 Particularly ITS-rDNA.
 Even more diversity!
 Zooxanthellae clade
DNA analyses
Clade: A group composed of all the species descended from a single common ancestor
 Diversity
 Eight major clades known.
 Within each clade many subclades.
 Do not know what taxonomic level clades are equal to.
 Evolution and biogeography
 Many studies have catalogued diversity.
 Can now understand on many scales.
 Can predict evolution.
 Specific types
 Many subclades or types associate with similar hosts.
 Could be co-evolution.
 Symbiodinium in Zoanthus sansibaricus
 We sampled the same species from 4 locations.
 Each host colony was shown to associate with one subclade of Symbiodinium.
 Subclade C1/C3 was common in the north, and subclade A1 was dominant in the south.
 C1/C3 has been shown to be a dominant Indo-Pacific “generalist”, with C15 common in Porites spp., and A1 a shallow-water specialist.
 Modes of transmission & flexibility
 2 major types; a) vertical and b) horizontal.
 Vertical should result in more co-evolution and less flexibility.
 Also, in horizontal, ZX from environment still rare.
 Changes in ZX
over time?
 Changes have been seen over time in content of ZX within coral colonies!
 Particularly after bleaching events.
 ZX shuffling?
 Adaptive Bleaching Hypothesis (ABH).
 Very controversial, large conservation implications.
 Two ways this occurs.
 Diversity within colonies
 Same colony may have different ZX at different locations!
 Differences in types
 Since we know diversity, we can experiment with different conditions.
 Many ZX are easy to culture.
 Control light, temperature, nutrients, etc.

 Can also then experiment in situ.
 Symbiodinium spp. characters
 Believed to alternate between a free-living stage with flagella, and a non-motile stage with chlorophyll.
 Believed to sexually reproduce, although this has not been observed.
 Overall morphological condition can degrade based on non-optimal environmental conditions, in particular low (<15 º C) and high (>30ºC) sustained ocean temperatures.
 “Adaptive bleaching” hypothesis
 Bleaching may enable corals to adopt different classes of zooxanthellae, better suited for a new environment. By:
 ‘symbiont switching’ (a new clade from exogenous sources) or
 ‘symbiont shuffling’ (host contains multiple clades and a shift in dominance occurs).

 Can we protect corals from bleaching?

 Marine invertebrate - Symbiodinium spp. symbioses overview
 Symbiodinium spp. found in many clonal cnidarians (and other invertebrates) in tropical and sub-tropical oceans. Symbiodinium are the main reason coral reefs exist and have large levels of diversity.
 Symbiodinium is now divided into 8 “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.)
 Host species’ association with various clades and subclades of Symbiodinium (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.).
 Also, some host species have been shown to have flexible associations with Symbiodinium 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.
 Need to understand Symbiodinium diversity within zoanthids before any discussion of symbiotic zoanthid ecology can be conducted.
References:
1. Rowan & Powers. 1991. Molecular genetic identification of symbiotic dinoflagellates (zooxanthellae). Marine Ecology Progress Series 71: 65-73.
2. Stat et al. 2006. The evolutionary history of Symbiodinium and scleractinian hosts - Symbiosis, diversity, and the effect of climate change. Plant Ecology, Evolution and Systematics 8: 23-43.
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.
4. Pochon et al. 2004. Biogeographic partitioning and host specialization among foramineferan dinoflagellate symbionts (Symbiodinium; Dinophyta). Marine Biology 139: 17-27.

Class 5 - Reverse taxonomy - DNA and classification

LFrom last week:
Understanding phylogenetic trees
• Branch length:
• 1. Vertical height has no important meaning.
• 2. Horizontal length is very important, tells the genetic distance of each sequence!
Calculation done by software.

Today`s class: Outline
• 1. Examples of reverse taxonomy from zoanthids (my research).
• 2. A new species of whale!
• 3. Atlantic and Pacific corals.
• 4. Four species of COTS.

Part 1
“Reverse taxonomy” = using DNA to find species; then describing morphology:
Zoanthids (Cnidaria: Anthozoa: Hexacorallia)
• Order Zoantharia (=Zoanthidea, Zoanthiniaria)
• Sand-encrusted, colonial
• Found in most marine environments
• Often symbiotic or parasitic
• Morphologically challenging, taxonomically neglected
• Often ignored in biodiversity surveys, non-CITES
Example: specimens in the Pacific:
Specimens 0-50 m, some but not as many as there should be, very few from coral triangle.
Specimens 50-1000 m, much much less.
Specimens >1000 m, only three!


Zoanthus spp. diversity in Japan
日本のマメスナギンチャク属の多様性
• Using genetics, backed up with morphology, currently we can accurately identify three Zoanthus spp. in Japan.
• 遺伝子解析で、綺麗に三つの種類に分かれた。
• Markers used are 16S, COI (both mt DNA) and ITS-rDNA (nuclear).
• Many presumed species not true species.
• 今まで４つの種類と思われていたものは、ひとつの種類だった。
• Oral disk color not a characteristic of species.
• 色は分類ができる特徴ではない。
• Not one morphological characteristic clearly defines each species.
• 一つだけの形態的特徴で分類できない。



Shallow water sampling & research
• Evidence of reticulate evolution, intraspecific variation.
• Many new families, genera and species await description. Unexpected findings.
• Current studies often limited to specimens from Japan.
Large gaps in our knowledge
• Almost complete lack of examination in regions between Japan and Australia. Formalin specimens and lack of modern examination in Australia.
• Lack of trained taxonomists.
• Ignored in almost all biodiversity surveys.
• The deeper we go, less knowledge.
• Biogeography impossible.
Investigating Deep-sea Zoanthids
深海のスナギンチャク類

What about deep-sea zoanthids?
深海のスナギンチャクというのは？
• 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 deep sea zoanthid
謎の深海スナギンチャク？
• 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。


Deep-sea specimens
• Very limited thus far, but specimens divergent.
• Use of ROVs and manned submersibles have resulted in 1 new family, 2 new genera in Japan, several new species (3 missions).
• Found on other benthos, found in limited environments.
• Below 1000m very few samples.
External morphology
外側の形態について
• 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?
内部の形態について？
• 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。
Genetic results
遺伝子解析の結果
• 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。
Abyssoanthus nankaiensis n. fam, n. gen. et n. sp.
Abyssoanthus nankaiensis 新科、新属、新種
• 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。

Part 2 -
A new species of whale!
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?
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.

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. Reimer et al. 2004-2008. Various papers on zoanthid phylogeny.
2. 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.
3. 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.
4. 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

Class 2008.11.12

Class 4 - Genetics in Conservation & DNA Phylogeny

Outline:
1. Introduction to genetics, diversity and conservation.
2. How genetics can be used in conservation.
3. DNA phylogeny introduction, methods.
4. Examples from zoanthid research.

1. Introduction to genetics, diversity and conservation.
Link between diversity and conservation:
Species diversity (# of species) for many groups of animals and plants unknown - lack of taxonomy.
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。
99.5% of species go extinct before we even describe them.
99.5%の種類は、分類する前に絶滅になってしまう。
Without knowledge of species, how can we protect them?
種類の分類が無いと、保全ができない。
Therefore, taxonomy and diversity VERY important.
分類学や多様性の理解が重要な研究。
BUT…
Not enough taxonomy specialists, training takes time, not good pay!
Many animals and plants are VERY hard to identify using traditional methods!

Remember that...
Biodiversity = Number of taxa (species, genera), or ecosystem types, etc.
Biodiversity = bioresources.
Bioresources = long-term economic well-being.
Conserving biodiversity is important; we need to understand baseline biodiversity.
Many “neglected taxa” remain.

History of measuring marine benthic biodiversity
Marine biodiversity less understood than terrestrial.
Many marine ecosystems have high biodiversity; particularly coral reefs.
Early biodiversity work focused on hard corals, sponges, easy to preserve taxa.
Collectors did not enter the ecosystem or observe living specimens.
Type specimens in Europe or N. America; ICZN problematic.
Currently almost all marine benthos taxa have gaps.

DNA can be used to differentiate cryptic species - example adult Astraptes spp.
There are many new methods that have helped us understand diversity:
a. SCUBA - brings scientists into marine environment
b. deep-sea subs and ROVS - same as SCUBA but deeper
c. DNA - allows us to confirm without (hopefully) bias what relations exist between organisms.

2. How genetics can be used in conservation.
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.
B. Identifying populations of concern.
Example: Asiatic lions in Gir Forest, India, shown to be genetically distinct from other lions, with low genetic diversity.
Steps then taken to protect this population. Also, rare "pine" tree from Aus, with seemingly identical population.
C. Resolving population structure.
Example: If a species has many isolated populations, can examine if translocation is needed.
For example wolves in the Alps.
D. Resolving taxonomic uncertainty.
Particularly true for marine species, invertebrates, plants.
Many examples, including: sea stars, whales, zoanthids, tuatara.
Talked about tuatara and Antarctic minke whale.
E. Defining management units within species.
Often different populations within species have different lifestyles, habits, or ranges that should be managed separately.
E.g. salmon and different populations with different lifestyles that need different management styles.
F. Detecting hybridization.
Can be done with mt DNA.
Some species in danger of disappearing due to this; examples include the Ethiopian wolf.
G. Non-intrusive sampling.
Very useful for reclusive or endangered animals.
Can be done with feces, hair, or even food.
H. Choosing sites for re-introduction of species.
Recent fossils or museum specimens can indicate where species used to be.
Example is the northern hairy-nosed wombat.
I. Choosing the best population to use in re-introductions.
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.
J. Forensics.
Identifying what came from where.
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.
Example 2: Over 50% of fish in several restaurants were not as advertised!
K. Understanding species biology.
Again, use of mt DNA very useful in understanding reproduction due to maternal inheritance.
Also, comparing and contrasting with nuclear DNA data can indicate potential reticulate evolution.
Can determine sexes of hard to identify species.
Parenthood also determinable. e.g. monitor lizard "virgin" births.

3. DNA phylogeny introduction, methods.
Vocabulary:
Primer
Alignment
DNA marker
Tree
Bootstrap value
Clade
Monophyletic
Polyphyletic
In order to understand phylogeny we must understand evolution:
The Ågmodern synthesisÅh of evolution is the combination of Darwin's and Mendel's theories.
The theory underlying the modern synthesis has three major aspects:
The common descent of all organisms from a single ancestor.
全ての生き物は共通の祖先から進化した。
The origin of novel traits in a lineage.
それぞれのグループはそれぞれの特徴を持つ。
Changes cause some traits to persist while others perish.
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。
DNA and phylogenetics
All cells contain DNA - the code or blueprint of life.
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。
This code has only four different ÅglettersÅh: A, G, C, T.
遺伝子は４つのコードしかない。
Usual length 105 to 1010 base pairs.
生き物のひとつの細胞にある遺伝子の長さは105 to 1010 。
Genome projects read everything in one organism, but takes time and expensive.
全ての遺伝子を読むことは時間とお金の無駄。
Many studies use one or a few markers to investigate relations.
遺伝子の短い部分だけでも系統関係が解析できる。
By collecting the same marker from different samples and then analyzing them, we can make a tree.
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。
It is thought/hoped a tree is similar to how evolution occurred.
系統樹から進化が見えると思われる。
DNA may be a way to have non-specialists identify species quickly!
So, DNA tree = evolutionary tree (or so we hope)

In a cell, two major types of DNA we will study:
. mitochondrial DNA (mt DNA)
evolves very slow in Cnidaria (Anthozoa), opposite to most animals.
他の動物と違い、刺胞動物で進化が遅い。
b. nuclear DNA
evolves faster in Cnidaria, opposite to most animals.
他の動物と違い、刺胞動物で進化が早い。
Example DNA markers:
COI, cytochrome oxidase subunit 1 - mt DNA, used for many studies, much data available.
16S rDNA - mt DNA, useful in zoanthids! some indels, especially V5 region.

Understanding phylogenetic trees:
Calculation methods:
1. MP - maximum parsimony. Least changes. Character-based.
2. ML - maximum likelihood. Must specify evolution model. Character-based.
3. NJ - neighbour-joining. Simplest method, variable evolutionary rates, distance-based.
4. Bayes - like ML on sets of trees!
Calculation done by software.
Bootstrap values:
Values show possibility that this clade/shape is true.
Values under 50% not used.
Values >70% desirable, above 90% confident.
Bayes >95%!
Trees reflect evolution.
Can make conservation decisions from these, or taxonomic decisions.
“Reverse taxonomy”.
Other notes:
More markers better than few.
Analyses also better with many methods.
Be careful of contamination or misidentification.
Back up with other data.
In the future:
Whole genomes will become cheaper due to 454 and new technology.
Cloning? Examination of extinct species. e.g. Wooly mammoth

Class 2008.11.5

About 30 people today, so hopefully the rest will be using the notes here...

1. Quick slide show of JDR's trip to Australia last week. A couple of notes about Australia and marine science:
a. Australia is well ahead of Japan in terms of management and education - hope Japan can catch up!
b. Critical thinking in particular needs to be worked on - let's try that in this class.

On to the serious part of the class.

Part 1 - Corals and their symbionts

Corals are part of
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.

Anthozoa = includes octocorals and hexacorals.
Hexacorallia = includes corals, anemones, zoanthids, corallimorphs, antipatharians and cerianthids. Have mesenteries in multiples of 6.

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 (Symbiodinium spp.; ZX).
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.

Also, zoanthids - related order to corals. Colonial like corals, soft like anemones. Many species have ZX. Very variable morphology even within species.

When understanding coral or other cnidarians on the reef, please remember that the holobiont is important.
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.

ZX are dinoflagellates with chlorophyll. Live inside host, give energy from sunlight to host.
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).
Research example: Zoanthus sansibaricus at different locations in Japan has different ZX clades!

Dangers facing coral reefs: Bleaching, acidification (will discuss this more in another class). Perhaps 90% of reefs dead by 2050.

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.

REFRESH TIME, followed by activity - terms:
locus　遺伝子座 ex. DNA marker
genotype　遺伝子型 ex. individuals
genome　全遺伝子情報 ex. human genome project
alleles　対立遺伝子 ex. flies with different antennae
polymorphic　多型 ex. sexually produced fish
monomorphic　単一型 ex. asexual coral clones
genetic distance　遺伝子距離 ex. taxonomy (sometimes)

Part 2 - Genetic diversity - variety of alleles or genotypes in a group being investigated.

Overview: quick explanation of evolution. Species gradually diverge; develop unique traits. Some groups disappear, others continue to evolve. Adaptations always needed.

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.
Diveristy needed, give examples we have seen - industrial melanism. Also failures to adapt - chestnut trees and Okinawan pines.
Low genetic diversity also leads to less reproductive success, more inbreeding. Ex: European royal families! Maintaining different populations important.
How do we measure genetic diversity?
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.
2. deleterious alleles - results from inbreeding, i.e. flies. But not good for conservation!
3. proteins - started in 1960s, slight changes in sizes form species or individuals. Uses electrophoresis. Need blood or organs, invasive.
4. DNA - many methods, always new developments. We will discuss
a. nuclear DNA - fast evolving in Cnidaria, slower in other animals - very general rule. More later.
b. mitochondrial DNA - slow in Cnidaria, fast in other animals. Again generalization.
c. Microsatellites - used for population studies; repeats of DNA. Development time is considerable.
More on these next week!
Can use DNA to identify species new and old.
5. Chromosomes - often clear differences between species. But no genetic distance or often no idea of relationships between species.

Endangered species have low genetic diversity, due to bottlenecks and reduced populations. Shown for many species (ex. nene).
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.

References:
1. Corals of the World. JEN Veron. 2000. AIMS, Melbourne. Volume 1.
2. Introduction to Conservation Genetics. R Frankham et al. 2002. Cambridge. Ch. 3

Class 2008.10.22

Coral Reef Diversity and Conservation
October 22, 2008
Class 1: Introduction to the Coral Reef Ecosystems

Pre-class announcements: Please attend the class on December 3rd, this is the day I assign reports, and make report teams. If you know of someone who has never attended, please tell them.
Anything I say in class may appear on the final test. Take notes. Lots of ideas, some new and some old, but please ask questions anytime.

1. Warm-up: Divide into groups of 2-3. Have students look at picture, assess the diversity of different pictures, and tell me which is “most healthy” etc.
Go through answers row-by-row. Get ideas, see what they know and don’t know.
Make sure students understand that healthy is all relevant, and can be different from different organisms points of view. For reefs; healthy can mean no humans! Large animals in abundance, healthy coral in abundance, low amounts of algae and slime, etc. If so, there are very few healthy coral reefs. 24% in danger of total collapse, 26% in danger of high degradation (Precht & Robbart 2006) within 50 years. Others say 80% (Veron 2001). Species numbers add here too. 5-10% already dead. One of the most endangered ecosystems on earth.

2. Always remember conservation; we will come back there.
3. Introduction to Coral Reefs:

a. What are coral reefs? How do they form?
Biggest structures made by living organisms. GBR is 1000s of km long.
Thus we may think they are tough and permanent, but they are not, and only top thin layer is generally alive.
Existed before hard corals existed, different groups have taken turns making reefs.
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), where they compete with macroalgae (more later).

Reefs can be geological structures, and living ecosystems. Unusual.
For geology, reefs affected by oceans going up and down, changes in temp and current. Shorter scales, typhoons, tsunamis, crown-of-thorns, etc.
Even shorter; bleaching, fishing, dynamite, coral reef trade, shellfish, etc.
Recently sea level has not changed so much, resulting in reefs today, but past there were many changes. Underwater cave example even.
Many reefs are like forests, tear them down and build them up.
Anyone been diving? Different levels of shelves are often indicators of past sea levels.

b. Different types of coral reefs
Starting with Darwin, many people have attempted to classify reefs into types. Humans like to classify.
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.
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.
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.
3:Atoll: walls of a reef around a lagoon, from a sunken island. Darwin first thought of this.
Many grades between these three types. Also, platform reefs that do not fit any of the classes above. Mention deep sea reefs too.

c. Geological history of coral reefs, currents etc.
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.
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).

History: known from 2 billion years ago. Explain these using timelines.
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.
Probably in this period the first endosymbiotic symbioses evolved.
Two types of corals: Rugose and Tabulate, but died when dinosaurs did. After this no reefs for a long time.
Modern corals appeared in Triassic, have dominated reef building since then. Show maps? Show some old extinct reefs.
In mid-cretaceous, rudist bivalves dominated, probably symbiotic, and then corals came back.
At end of dinosaurs 1/3 of families, 70% of genera became extinct. All species changed!
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.
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!


d. Diversity; 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.
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.
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!

d. Diversity? How to measure it?
Discuss before scuba and ideas at that time
First corals where collected in 1700s when scientific interest began, and first cataloguing. Increased greatly in 1800 and early 1900s. Museums and names.
Corals were particularly easy, as they could be preserved. So, along with fish and sea mammals and macroalage, very extensively documented.
Problems: no observation of living things in situ, no idea of variance, differ from place to place, so many incorrect names.
But, according to ICZN, these names MUST be correct, so we have continued on with bad ideas.
Other animals were largely ignored until 1800s or 1900s, such as anemones, zoanthids, corallimorphs, etc.
Many understudied groups are finally getting reexamined today, along with corals!
e. Discuss problems encountered since with diving, and new methods, briefly
With diving, we realized we had serious problems! Diving started on large scale in the 1960s.
Even then, our ideas of species are outdated, and little has been done on even corals outside a few species.
Thus, the number of species awaiting description is huge, and perhaps impossible. But still we try, for bioresources and chemicals etc. It is well known diversity has economic benefits now and in the future.
Finally now a big push for this. TOL, CoML etc (later).

4. Wrap-up: Just how much biomass was on reefs before humans?
Recent papers, including the one from which handout came from, show that the biomass of coral reefs may be inverted. Healthy reefs have 85% of fish biomass in sharks!!
This has sent researchers back to old papers and accounts.
Discuss old papers where so many sea turtles
Early Atlantic explorers running aground on sea turtles.
Numerous shark stories of huge numbers of sharks.
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!
SHOW MOVIE OF SHARKS. Ask first maybe if anyone has ever seen a shark, and how many.

5. Activity Answers: Go over my ideas. Show word file. Explain not biomass, and perhaps how things would be different.

6. Recommended reading:
1. SA Sandlin et al. 2008. Baselines and Degradation of Coral Reefs in the Northern Line Islands. PloS One 3 (2) e1548:1-11.
2. EA Dinsdale et al. 2008. Microbial Ecology of Four Coral Atolls in the Northern Line Islands. PloS One 3 (2) e1584: 1-17.
3. N Knowlton, JBC Jackson. 2008. Shifting Baselines, Local Impacts, and Global Change on Coral Reefs. PloS Biology 6 (2) e54:215-220.
4. Corals of the World – JEN Veron. 2000. Australian Institute of Marine Science. Melbourne.

Class 2008.10.15

Today I introduced the class guidelines and rules. Here are the details (this repeats some of the information from the first posting):

サンゴ礁多様性保全学（後期）

時限・教室
後期　水曜日　1時限　理327
URL：http://ryukyucoral2008.blogspot.com/
単位数：2

担当者：REIMER James Davis（理学部353号室；jreimer@sci.u-ryukyu.ac.jp）
オフィスアワー：午後以降

備考（メッセージ）
毎週の授業内容紹介をブログにuploadする（授業後）。授業は日本語で行うが、スライドとブログは主に英語になる。毎週参考文献を紹介する。

授業内容と方法
　主にサンゴ礁生態系における無脊椎動物の最新の研究を紹介して、どのように生物の多様性を理解し、保全を行うことができるかを考察する。簡単に遺伝学的な情報の利用法も紹介する。
達成目標
サンゴ礁生態系の著しい多様性を理解する。
サンゴ礁生態系の生物の最新研究を知る。
遺伝学的な情報の利用の仕方を理解する。

評価基準と評価方法
1. 中期のレポート: 70%
2. 期末テスト: 30%

授業計画
15.Oct 1. 登録調整と説明
22.Oct 2. サンゴ礁生態系の紹介
5.Nov 3. 遺伝学の紹介
12.Nov 4. 系統樹の説明
19.Nov 5. サンゴ礁生態系についての研究紹介I
26.Nov 6. サンゴ礁生態系についての研究紹介II
3.Dec 7. 中期レポートの説明
10.Dec 8. サンゴ礁生態系についての研究紹介III
17.Dec 9. 網状進化の研究紹介
24.Dec 10. 保全学についての研究紹介I
7.Jan 11. 保全学についての研究紹介II
14.Jan 12. DNA Barcoding and the Tree of Lifeの紹介
21.Jan 13. 期末テスト


教科書
1: 特に指定しない

参考書
1: Coral Reef Restoration Handbook – W. Precht (ed.). 2006. CRC Taylor & Francis, New York.
2: Introduction to Conservation Genetics – R. Frankham, J.D. Ballou, D.A. Briscoe. 2002. Cambridge University Press, Cambridge.
3. Molecular Markers, Natural History, and Evolution (2nd edtion) – J.C. Avise. 2004. Sinauer, Sunderland, MA.
4. Corals of the World – JEN Veron. 2000. Australian Institute of Marine Science. Melbourne.

As well, we played a "bingo" introduction game. See you next week!