Wednesday, November 16, 2011

November 16th class

NOTICE: Please attend November 30; 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.
5. Diversity in Symbiodinium

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.
• 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 surprisingly show five specimens not M. hectori.
• New species!
• Re-examination shows morphological differences as well.
• 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?
• 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.

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

Part 5: 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.

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.

Tuesday, November 15, 2011

November 9th class

1. DNA phylogeny introduction, methods.
DNA marker
Bootstrap value
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.
The origin of novel traits in a lineage.
Changes cause some traits to persist while others perish.
DNA and phylogenetics
All cells contain DNA - the code or blueprint of life.
This code has only four different ÅglettersÅh: A, G, C, T.
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.
Many studies use one or a few markers to investigate relations.
By collecting the same marker from different samples and then analyzing them, we can make a tree.
It is thought/hoped a tree is similar to how evolution occurred.
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.
b. nuclear DNA
evolves faster in Cnidaria, opposite to most animals.
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
• 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

What about deep-sea zoanthids?
• 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
• 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
• Samples appeared to be zoanthid-like based on: sand encrustation and polyp shape. No tentacle data available.
• スナギンチャクと同様に、砂を取り込んでいる。ポリプが閉じている。
• However, samples have several unique features: free-living and inhabited a deep sea methane cold seep. Morphology and ecology do not fit with any known zoanthid families.
• 単体性、極限環境の初めてのスナギンチャク。

Internal morphology?
• As expected, cross section using normal (wax-embedded) methods gave poor results.
• パラフィン切片での結果はあまりよくない。
• Attempted to set sample in epoxy resin, cut a section, and polish to necessary thickness but failed.
• レジンでの切片も無理。
• Another possibility is digestion of outer surface of polyp.
• フ酸での切片は可能だが、非常に危ない。
• Could obtain mesentery count number from rough cross-sections (19-22).
• 状態が悪い切片で、約19〜22隔膜を確認できたが、形など観察できなかった。
Genetic results
• Obtained mt COI, mt16S rDNA, and 5.8S rDNA sequences confirm samples are zoanthid, but divergent from all known zoanthid families.
• 今回のサンプルはスナギンチャク目に入っているが、今まで知られているスナギンチャクと離れている。
• Particularly, divergent from all known groups of deep-sea zoanthids described.
• 特に、今までの深海のスナギンチャクと違う。
• Bootstrap support for monophyly 100% (all methods, all markers).
• 遺伝子解析の結果の確率が非常に高い。
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。

Finally - a discussion about why DNA cannot solve everything (Milinkovitch et al. 2004).
You MUST know what specimens you are working with!

1. Chapter 4 of Molecular Markers, Natural History, and Evolution 2nd edition – JC Avise. 2004. Sinauer. Sunderland, Massachusetts.
2. Reimer et al. 2004-2008. Various papers on zoanthid phylogeny.
3. Milinkovitch et al. 2004. Molecular phylogenetic analyses indicate extensive molecular convergence between “yeti” and primates. Mol Phylogenet Evol 31: 1-3.
4. CReefs homepage:

November 2nd class

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.
99.5% of species go extinct before we even describe them.
Without knowledge of species, how can we protect them?
Therefore, taxonomy and diversity VERY important.
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.
The origin of novel traits in a lineage.
Changes cause some traits to persist while others perish.
DNA and phylogenetics
All cells contain DNA - the code or blueprint of life.
This code has only four different "letters": A, G, C, T.
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.
Many studies use one or a few markers to investigate relations.
By collecting the same marker from different samples and then analyzing them, we can make a tree.
It is thought/hoped a tree is similar to how evolution occurred.
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.
b. mitochondrial DNA - slow in Cnidaria, fast in other animals. Again generalization.
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.

Part 4 - 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 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.
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.

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
4. 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.
5. Snyder & Burgess. 2007. The Indo-Pacific red lionfish, Pterois volitans (Pisces: Scorpaenidae), new to Bahamian ichthyofauna. Coral Reefs 26: 175.
6. Hamner et al. 2007. Mitochondrial cytochrome b analysis reveals two invasive lionfish species with strong founder effects in the western Atlantic. J Fish Biol 71: 214-222.

Thursday, October 27, 2011

October 26th, 2011 class

Coral Reef Diversity and Conservation
October 27, 2010
Class 2: Introduction to the Coral Reef Ecosystems and Biodiversity

Introduction to Coral Reefs:
1. Coral reefs (large scale)
2. Coral (the animal)
3. Biodiversity
4. Example study of human influences on coral reef (Sandin et al. 2008)

1. Coral reefs (large scale)
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 in another class), where they compete with macroalgae (more later).

Reefs can be geological structures, and living ecosystems.
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!

2. Coral (the animal)

a. 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.; abbreviated here as ZX=zooxanthellae).
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.

b. 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!

c. Dangers facing coral reefs: Bleaching, acidification (will discuss this more in another class taught by Kurihara-sensei). Perhaps 90% of reefs dead by 2050, NOAA says 60% by 2030.

d. Species diversity for many organisms unknown. 99.5% of species go extinct before we identify them. Without knowledge of species how do we protect them? Taxonomy and diversity study important. but... training takes time, pay is poor, and many organisms VERY hard to identify in traditional methods.

3. Biodiversity;
a. Less than 0.2% of the earth, 25% or more of the ocean’s species! 10% of fish caught. Protect land as breakwaters, and valuable for tourism. All of this despite low nutrients and compounds in the surrounding water.
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!

b. Diversity? How to measure it?
Biodiversity=number of species or genera, OTUs (operational taxonomic units)
Coral reefs <0.2% of the earth's surface, 25-50% of marine species.
Reefs increase surface area, 15X for large animals, more for smaller. More niches = more specialized animals.
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!
"New" techniques: SCUBA, submersibles, molecular techniques, have allowed a re-examination of biodiversity.
Often, "reverse" taxonomy, using DNA to identify specimens of interest, then going back to look at morphology.

4. Wrap-up using Sandin et al. (2008): Just how much biomass was on reefs before humans? What is a healthy reef? Line Islands study.
Recent papers, including the one from which handout came from (Sandin et al. 2008), show that the biomass of coral reefs may be inverted. Healthy reefs have 85% of fish biomass in sharks!! Go over paper quickly.
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 images from Bonotsu 2011 and destroyed coral reef.

Emphasize the link between conservation and biodiversity.

VI. Recommended reading (bold in particular):
1. SA Sandin 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.

Tuesday, October 11, 2011


Instructor and Class Information

Time & Place: Science 528, Weds 8:30-10:00
Instructor: James Reimer
Office: Science 353
Office hours: Anytime except Wedsnesdays

Class Schedule:
12 Oct 1. 登録調整と説明
19 Oct No class (Happy Monday)
26 Oct 2. サンゴ礁生態系の紹介
2 Nov 3. 遺伝学の紹介
9 Nov 4. 系統樹の説明
16 Nov 5. サンゴ礁生態系についての研究紹介I
23 Nov No class (holiday)
30 Nov 6. サンゴ礁生態系についての研究紹介II & Project発表の説明
7 Dec 7. サンゴ礁生態系についての研究紹介III
14 Dec 8. 未記載種の発見!
21 Dec 9. 網状進化の研究紹介
28 Dec 10. Coral Reef Species (英語video)
11 Jan 11. Guest lecturer - 木村先生: Human DNA
18 Jan 12. 保全学についての研究紹介 (GBR)
25 Jan 13. Project発表
1 Feb 14. DNA Barcoding and CoMLの紹介
8 Feb 15. Final Test