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.
Thursday, January 14, 2010
Thursday, January 7, 2010
January 6th class notes
Happy New Year!
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.
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.
Saturday, December 19, 2009
December 16th class notes & report outline
Class notes:
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.
Coral Reef Diversity and Conservation
J.D. Reimer
Assignment Information:
You and your team (2~3 people) must apply for research funding for the following research grant:
The MISE Coral Reef Conservation Fund
This fund provides grants for projects that build private-public partnerships through research that aims to reduce and prevent the degradation of coral refs and associated reef habitats (seagrass beds, mangroves, etc). Projects will be for two years from April 2010.
Part 1 - Application: please submit the following to Science room 353 by 17:00 on Monday, January 25th.
1. Cover page (1 page): Include group name, and project title.
2. Research background and goals (2 pages maximum): provide a background that anyone with science training can understand, clearly state the project goal(s), and explain the necessity of the project.
3. Methods (2 pages maximum): Include detailed explanation of methods used, and a concrete timeline to be followed. If research facilities and equipment are to be used at an institution, include details.
4. Expected results (1 page maximum): Describe concretely what results can be expected, how these results will benefit coral reefs, and how these results will benefit future coral reef conservation research.
5. Team outline (2 pages maximum): Include team member information on skills, relevant work history and experience, and scientific publications (if any). Designate roles for each person. Do NOT include personal private information.
6. Budget (1 page maximum): Divide budget into the following items; 1) travel expenses, 2) equipment (over 100,000 JPY), 3) expendables & items less than 100,000 JPY, 4) other expenses (guides, part-time jobs, rentals, post, etc). Include a budget for 2 years. Budgets may not exceed 30,000,000 JPY in total for 2 years, and cannot be more than 20,000,000 JPY in one year.
Part 2 – Visual presentation: Wednesday, January 27th
All teams will give a 5-minute PowerPoint presentation on their projects on during class. Other students and JDR will vote on their project; this will be 20% of your project mark. There are no rules on this presentation other than the time limit and the use of PowerPoint.
Hints:
a. Your project must be realistic, and must include as many details as possible to make it easy to understand. It can be as simple or large-scale as possible, but ideas must be logical. The project can build on other plans, but these plans must be referenced.
b. Using scientific references increases the amount of knowledge you have access to. On the other hand, using information without references will decrease your score. Use Google Scholar or other sources of information to access scientific literature quickly. Space is limited, so choose references well.
c. Figures and graphs greatly help make ideas easy to understand.
d. For budgets, catalogues may be useful. Please visit JDR’s lab to borrow any catalogue you need.
Marking:
This project is very open-ended. Grades will be assigned based on:
1. originality (new ideas, etc.): 20 points
2. necessity: 20 points
3. realistic possibility: 20 points
4. style & background research: 20 points
5. visual presentation and votes: 20 points
Remember:
Reports are to be done in groups of 2-3 people.
Please write which person did what part of the report.
Due date is January 25th by 17:00.
If you have any questions or problems please contact JDR as soon as you can, either at his office or by e-mail.
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.
Coral Reef Diversity and Conservation
J.D. Reimer
Assignment Information:
You and your team (2~3 people) must apply for research funding for the following research grant:
The MISE Coral Reef Conservation Fund
This fund provides grants for projects that build private-public partnerships through research that aims to reduce and prevent the degradation of coral refs and associated reef habitats (seagrass beds, mangroves, etc). Projects will be for two years from April 2010.
Part 1 - Application: please submit the following to Science room 353 by 17:00 on Monday, January 25th.
1. Cover page (1 page): Include group name, and project title.
2. Research background and goals (2 pages maximum): provide a background that anyone with science training can understand, clearly state the project goal(s), and explain the necessity of the project.
3. Methods (2 pages maximum): Include detailed explanation of methods used, and a concrete timeline to be followed. If research facilities and equipment are to be used at an institution, include details.
4. Expected results (1 page maximum): Describe concretely what results can be expected, how these results will benefit coral reefs, and how these results will benefit future coral reef conservation research.
5. Team outline (2 pages maximum): Include team member information on skills, relevant work history and experience, and scientific publications (if any). Designate roles for each person. Do NOT include personal private information.
6. Budget (1 page maximum): Divide budget into the following items; 1) travel expenses, 2) equipment (over 100,000 JPY), 3) expendables & items less than 100,000 JPY, 4) other expenses (guides, part-time jobs, rentals, post, etc). Include a budget for 2 years. Budgets may not exceed 30,000,000 JPY in total for 2 years, and cannot be more than 20,000,000 JPY in one year.
Part 2 – Visual presentation: Wednesday, January 27th
All teams will give a 5-minute PowerPoint presentation on their projects on during class. Other students and JDR will vote on their project; this will be 20% of your project mark. There are no rules on this presentation other than the time limit and the use of PowerPoint.
Hints:
a. Your project must be realistic, and must include as many details as possible to make it easy to understand. It can be as simple or large-scale as possible, but ideas must be logical. The project can build on other plans, but these plans must be referenced.
b. Using scientific references increases the amount of knowledge you have access to. On the other hand, using information without references will decrease your score. Use Google Scholar or other sources of information to access scientific literature quickly. Space is limited, so choose references well.
c. Figures and graphs greatly help make ideas easy to understand.
d. For budgets, catalogues may be useful. Please visit JDR’s lab to borrow any catalogue you need.
Marking:
This project is very open-ended. Grades will be assigned based on:
1. originality (new ideas, etc.): 20 points
2. necessity: 20 points
3. realistic possibility: 20 points
4. style & background research: 20 points
5. visual presentation and votes: 20 points
Remember:
Reports are to be done in groups of 2-3 people.
Please write which person did what part of the report.
Due date is January 25th by 17:00.
If you have any questions or problems please contact JDR as soon as you can, either at his office or by e-mail.
Sunday, December 13, 2009
December 9th class
NOTICE: Please attend next week; we assign the reports on this day!
Today`s class: Outline
• 1. A new species of whale!
• 2. Atlantic and Pacific corals.
• 3. Four species of COTS.
• 4. Review of Symbiodinium and coral bleaching.
Part 1 - 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 2 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 3 - 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!
Part 4 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.
References:
1. 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.
2. 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.
3. 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
Today`s class: Outline
• 1. A new species of whale!
• 2. Atlantic and Pacific corals.
• 3. Four species of COTS.
• 4. Review of Symbiodinium and coral bleaching.
Part 1 - 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 2 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 3 - 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!
Part 4 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.
References:
1. 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.
2. 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.
3. 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
Tuesday, December 8, 2009
December 2nd class
1. 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
Part 2 – examples from zoanthids
“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 3- CReefs trip
•November 8th – December 1st
•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)!
Details:
On Heron Island, on southern Great Barrier Reef (GBR). Heron Is. has a resort and a research station. Very beautiful setting.
Heron Island home to seabirds, rails, and important nesting ground for sea turtles.
Research station very new – well set up, running sea water, wet and dry labs.
CReefs, biodiversity of coral reef animals, team consisted of: 1) scientists from all over the world, 2) boat guides/divers, 3) a photographer, 4) a blogger, and 5) a chef. A great team and well-supported.
Many locations of the southern GBR investigated, based on preferences, weather, and distance, etc. Very flexible plan. Boats went out almost every day! Sampling methods varied based on taxa being investigated. Diving rules strictly followed for safety reasons. All permits and paperwork were done to follow all rules local, national, and international. Much sharing of specimens to prevent waste.
I found 270 specimens, at 33 sites, many new species!
http://www.creefs.org/index_h.html
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
Part 2 – examples from zoanthids
“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 3- CReefs trip
•November 8th – December 1st
•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)!
Details:
On Heron Island, on southern Great Barrier Reef (GBR). Heron Is. has a resort and a research station. Very beautiful setting.
Heron Island home to seabirds, rails, and important nesting ground for sea turtles.
Research station very new – well set up, running sea water, wet and dry labs.
CReefs, biodiversity of coral reef animals, team consisted of: 1) scientists from all over the world, 2) boat guides/divers, 3) a photographer, 4) a blogger, and 5) a chef. A great team and well-supported.
Many locations of the southern GBR investigated, based on preferences, weather, and distance, etc. Very flexible plan. Boats went out almost every day! Sampling methods varied based on taxa being investigated. Diving rules strictly followed for safety reasons. All permits and paperwork were done to follow all rules local, national, and international. Much sharing of specimens to prevent waste.
I found 270 specimens, at 33 sites, many new species!
http://www.creefs.org/index_h.html
Wednesday, November 4, 2009
お知らせ
Notes while JDR is in Australia.
Nov. 11th: No class next week.
Nov. 18th: Kurihara-sensei – Ocean acidification – human impacts, threats to coral reef organisms.
Nov. 25th: Kimura-sensei – Spread of humans across the Pacific – genetic diversity, adaptation.
Blogs updated semi-regularly.
Email: jreimer@sci.u-ryukyu.ac.jp
Skype: evenings best.
Nov. 11th: No class next week.
Nov. 18th: Kurihara-sensei – Ocean acidification – human impacts, threats to coral reef organisms.
Nov. 25th: Kimura-sensei – Spread of humans across the Pacific – genetic diversity, adaptation.
Blogs updated semi-regularly.
Email: jreimer@sci.u-ryukyu.ac.jp
Skype: evenings best.
November 4th class
About 30 people today, so hopefully the rest will be using the notes here...
Class 3 - Genetics (linked to biodiversity and conservation)
Part 1 Review
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.
ANSWERS to words:
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.
In order to understand phylogeny we must understand evolution:
The modern synthesis 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 "letters": A, G, C, T.
遺伝子は４つのコードしかない。
Usual length 1,000,000 to 100,000,000,000 base pairs.
生き物のひとつの細胞にある遺伝子の長さは,000,000 to 100,000,000,000 。
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)
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
c. Microsatellites - used for population studies; repeats of DNA. Development time is considerable.
In a cell, two major types of DNA we will study:
a. nuclear DNA - fast evolving in Cnidaria, slower in other animals - very general rule. More later.
他の動物と違い、刺胞動物で進化が早い
b. mitochondrial DNA - slow in Cnidaria, fast in other animals. Again generalization.
他の動物と違い、刺胞動物で進化が遅い。
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.
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.
Part 3- 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.
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
3. Molecular markers, selection and natural history. 2nd edition. J Avise. 2004. Ch.4
Class 3 - Genetics (linked to biodiversity and conservation)
Part 1 Review
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.
ANSWERS to words:
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.
In order to understand phylogeny we must understand evolution:
The modern synthesis 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 "letters": A, G, C, T.
遺伝子は４つのコードしかない。
Usual length 1,000,000 to 100,000,000,000 base pairs.
生き物のひとつの細胞にある遺伝子の長さは,000,000 to 100,000,000,000 。
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)
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
c. Microsatellites - used for population studies; repeats of DNA. Development time is considerable.
In a cell, two major types of DNA we will study:
a. nuclear DNA - fast evolving in Cnidaria, slower in other animals - very general rule. More later.
他の動物と違い、刺胞動物で進化が早い
b. mitochondrial DNA - slow in Cnidaria, fast in other animals. Again generalization.
他の動物と違い、刺胞動物で進化が遅い。
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.
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.
Part 3- 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.
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
3. Molecular markers, selection and natural history. 2nd edition. J Avise. 2004. Ch.4
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