Class 4 - Genetics in Conservation & DNA Phylogeny
Outline:
1. Introduction to genetics, diversity and conservation.
2. How genetics can be used in conservation.
3. DNA phylogeny introduction, methods.
4. Examples from zoanthid research.
1. Introduction to genetics, diversity and conservation.
Link between diversity and conservation:
Species diversity (# of species) for many groups of animals and plants unknown - lack of taxonomy.
分類学の研究が足りないせいで、色々な生物の集団の種類多様性（種の数）がほとんど知れていない状態。
99.5% of species go extinct before we even describe them.
99.5%の種類は、分類する前に絶滅になってしまう。
Without knowledge of species, how can we protect them?
種類の分類が無いと、保全ができない。
Therefore, taxonomy and diversity VERY important.
分類学や多様性の理解が重要な研究。
BUT…
Not enough taxonomy specialists, training takes time, not good pay!
Many animals and plants are VERY hard to identify using traditional methods!
Remember that...
Biodiversity = Number of taxa (species, genera), or ecosystem types, etc.
Biodiversity = bioresources.
Bioresources = long-term economic well-being.
Conserving biodiversity is important; we need to understand baseline biodiversity.
Many “neglected taxa” remain.
History of measuring marine benthic biodiversity
Marine biodiversity less understood than terrestrial.
Many marine ecosystems have high biodiversity; particularly coral reefs.
Early biodiversity work focused on hard corals, sponges, easy to preserve taxa.
Collectors did not enter the ecosystem or observe living specimens.
Type specimens in Europe or N. America; ICZN problematic.
Currently almost all marine benthos taxa have gaps.
DNA can be used to differentiate cryptic species - example adult Astraptes spp.
There are many new methods that have helped us understand diversity:
a. SCUBA - brings scientists into marine environment
b. deep-sea subs and ROVS - same as SCUBA but deeper
c. DNA - allows us to confirm without (hopefully) bias what relations exist between organisms.
2. How genetics can be used in conservation.
A. Minimizing inbreeding and loss of genetic diversity e.g. Florida panther with outside popn individuals introduced into gene pool, results seen to alleviate inbreeding.
B. Identifying populations of concern.
Example: Asiatic lions in Gir Forest, India, shown to be genetically distinct from other lions, with low genetic diversity.
Steps then taken to protect this population. Also, rare "pine" tree from Aus, with seemingly identical population.
C. Resolving population structure.
Example: If a species has many isolated populations, can examine if translocation is needed.
For example wolves in the Alps.
D. Resolving taxonomic uncertainty.
Particularly true for marine species, invertebrates, plants.
Many examples, including: sea stars, whales, zoanthids, tuatara.
Talked about tuatara and Antarctic minke whale.
E. Defining management units within species.
Often different populations within species have different lifestyles, habits, or ranges that should be managed separately.
E.g. salmon and different populations with different lifestyles that need different management styles.
F. Detecting hybridization.
Can be done with mt DNA.
Some species in danger of disappearing due to this; examples include the Ethiopian wolf.
G. Non-intrusive sampling.
Very useful for reclusive or endangered animals.
Can be done with feces, hair, or even food.
H. Choosing sites for re-introduction of species.
Recent fossils or museum specimens can indicate where species used to be.
Example is the northern hairy-nosed wombat.
I. Choosing the best population to use in re-introductions.
Often island populations considered valuable resource; but in case of Barrow Island wallabies, low genetic variability. This population should not be used for re-introduction plans.
J. Forensics.
Identifying what came from where.
Example 1: Research has shown 2-20% of whale meat sold in Japan is not the whale it is advertised to be, but protected species.
Example 2: Over 50% of fish in several restaurants were not as advertised!
K. Understanding species biology.
Again, use of mt DNA very useful in understanding reproduction due to maternal inheritance.
Also, comparing and contrasting with nuclear DNA data can indicate potential reticulate evolution.
Can determine sexes of hard to identify species.
Parenthood also determinable. e.g. monitor lizard "virgin" births.
3. DNA phylogeny introduction, methods.
Vocabulary:
Primer
Alignment
DNA marker
Tree
Bootstrap value
Clade
Monophyletic
Polyphyletic
In order to understand phylogeny we must understand evolution:
The Ågmodern synthesisÅh of evolution is the combination of Darwin's and Mendel's theories.
The theory underlying the modern synthesis has three major aspects:
The common descent of all organisms from a single ancestor.
全ての生き物は共通の祖先から進化した。
The origin of novel traits in a lineage.
それぞれのグループはそれぞれの特徴を持つ。
Changes cause some traits to persist while others perish.
様々な変化によって、あるグループは生き残り、あるグループは絶滅する。
DNA and phylogenetics
All cells contain DNA - the code or blueprint of life.
全ての細胞には遺伝子が入っている。遺伝子は生き物の設計図。
This code has only four different ÅglettersÅh: A, G, C, T.
遺伝子は４つのコードしかない。
Usual length 105 to 1010 base pairs.
生き物のひとつの細胞にある遺伝子の長さは105 to 1010 。
Genome projects read everything in one organism, but takes time and expensive.
全ての遺伝子を読むことは時間とお金の無駄。
Many studies use one or a few markers to investigate relations.
遺伝子の短い部分だけでも系統関係が解析できる。
By collecting the same marker from different samples and then analyzing them, we can make a tree.
いくつかのサンプルから同じマーカーを読んで、並べてから、解析し系統樹を作る。
It is thought/hoped a tree is similar to how evolution occurred.
系統樹から進化が見えると思われる。
DNA may be a way to have non-specialists identify species quickly!
So, DNA tree = evolutionary tree (or so we hope)
In a cell, two major types of DNA we will study:
. mitochondrial DNA (mt DNA)
evolves very slow in Cnidaria (Anthozoa), opposite to most animals.
他の動物と違い、刺胞動物で進化が遅い。
b. nuclear DNA
evolves faster in Cnidaria, opposite to most animals.
他の動物と違い、刺胞動物で進化が早い。
Example DNA markers:
COI, cytochrome oxidase subunit 1 - mt DNA, used for many studies, much data available.
16S rDNA - mt DNA, useful in zoanthids! some indels, especially V5 region.
Understanding phylogenetic trees:
Calculation methods:
1. MP - maximum parsimony. Least changes. Character-based.
2. ML - maximum likelihood. Must specify evolution model. Character-based.
3. NJ - neighbour-joining. Simplest method, variable evolutionary rates, distance-based.
4. Bayes - like ML on sets of trees!
Calculation done by software.
Bootstrap values:
Values show possibility that this clade/shape is true.
Values under 50% not used.
Values >70% desirable, above 90% confident.
Bayes >95%!
Trees reflect evolution.
Can make conservation decisions from these, or taxonomic decisions.
“Reverse taxonomy”.
Other notes:
More markers better than few.
Analyses also better with many methods.
Be careful of contamination or misidentification.
Back up with other data.
In the future:
Whole genomes will become cheaper due to 454 and new technology.
Cloning? Examination of extinct species. e.g. Wooly mammoth
Thursday, November 20, 2008
Thursday, November 6, 2008
Class 2008.11.5
About 30 people today, so hopefully the rest will be using the notes here...
1. Quick slide show of JDR's trip to Australia last week. A couple of notes about Australia and marine science:
a. Australia is well ahead of Japan in terms of management and education - hope Japan can catch up!
b. Critical thinking in particular needs to be worked on - let's try that in this class.
On to the serious part of the class.
Part 1 - Corals and their symbionts
Corals are part of
Cnidaria - animals that have one hole that serves as both mouth and anus. This is surrounded by tentacles. All Cnidaria and only cnidarians have nematocysts, defense and feeding. Two main shapes, polyp and medusa. Life cycle alternates between these two shapes; main for corals is polyps, main for jellyfish is medusae.
Anthozoa = includes octocorals and hexacorals.
Hexacorallia = includes corals, anemones, zoanthids, corallimorphs, antipatharians and cerianthids. Have mesenteries in multiples of 6.
Corals - may be colonial or solitary, zooxanthellate or azooxanthellate. Zooxanthellate colonial species responsible for making coral reefs. Polyps (living tissue) surrounded by calcium carbonate skeleton. Classification traditionally uses skeletal characteristics; color and size also used. Polyps include a mouth and oral disk surrounded by tentacles, as well as zooxanthellae (Symbiodinium spp.; ZX).
Skeletons have much microstructure, important for many other animals as homes, especially when coral dead. Refuge from predators etc. Many types of corals - show pictures of these.
Also, zoanthids - related order to corals. Colonial like corals, soft like anemones. Many species have ZX. Very variable morphology even within species.
When understanding coral or other cnidarians on the reef, please remember that the holobiont is important.
Holobiont = host (animal) + ZX + bacteria, viruses, etc. Host may be same species, but if ZX are different, this has implications for biology and ecology of holobiont.
ZX are dinoflagellates with chlorophyll. Live inside host, give energy from sunlight to host.
ZX look similar, thought to be one species, but DNA etc. have revealed diversity, now 8 clades (A to H). Most ZX sensitive to high ocean temperatures. Usually 30C is considered a threshold. Different clades or subclades may have different physiology. ZX thylakoids degrade at hot temperatures, causing coral bleaching. Also can happen at low (<15C).
Research example: Zoanthus sansibaricus at different locations in Japan has different ZX clades!
Dangers facing coral reefs: Bleaching, acidification (will discuss this more in another class). Perhaps 90% of reefs dead by 2050.
Species diversity for many organisms unknown. 99.5% of species go extinct before we identify them. Without knowledge of species how do we protect them? Taxonomy and diversity study important. but... training takes time, pay is poor, and many organisms VERY hard to identify in traditional methods.
REFRESH TIME, followed by activity - terms:
locus 遺伝子座 ex. DNA marker
genotype 遺伝子型 ex. individuals
genome 全遺伝子情報 ex. human genome project
alleles 対立遺伝子 ex. flies with different antennae
polymorphic 多型 ex. sexually produced fish
monomorphic 単一型 ex. asexual coral clones
genetic distance 遺伝子距離 ex. taxonomy (sometimes)
Part 2 - Genetic diversity - variety of alleles or genotypes in a group being investigated.
Overview: quick explanation of evolution. Species gradually diverge; develop unique traits. Some groups disappear, others continue to evolve. Adaptations always needed.
Genetic diversity is required to adapt to changing environments (ex: Hawaiian honeycreeprs). Environments are ALWAYS changing, never static. Many methods to measure genetic diversity. Large populations usually have high diversity; small populations are a concern.
Diveristy needed, give examples we have seen - industrial melanism. Also failures to adapt - chestnut trees and Okinawan pines.
Low genetic diversity also leads to less reproductive success, more inbreeding. Ex: European royal families! Maintaining different populations important.
How do we measure genetic diversity?
1. quantative measurement - morphology. size, shape, height, weight, etc. But not due only to genes, also environment and expression. Difficult to assess. Can be done in absence of other methods, cheap.
2. deleterious alleles - results from inbreeding, i.e. flies. But not good for conservation!
3. proteins - started in 1960s, slight changes in sizes form species or individuals. Uses electrophoresis. Need blood or organs, invasive.
4. DNA - many methods, always new developments. We will discuss
a. nuclear DNA - fast evolving in Cnidaria, slower in other animals - very general rule. More later.
b. mitochondrial DNA - slow in Cnidaria, fast in other animals. Again generalization.
c. Microsatellites - used for population studies; repeats of DNA. Development time is considerable.
More on these next week!
Can use DNA to identify species new and old.
5. Chromosomes - often clear differences between species. But no genetic distance or often no idea of relationships between species.
Endangered species have low genetic diversity, due to bottlenecks and reduced populations. Shown for many species (ex. nene).
Variation over space and time - higher dispersal means less variation within species, lower dispersal means more variation. Give example of humans. Large populations more stable than small populations which lose genetic diversity quickly.
References:
1. Corals of the World. JEN Veron. 2000. AIMS, Melbourne. Volume 1.
2. Introduction to Conservation Genetics. R Frankham et al. 2002. Cambridge. Ch. 3
1. Quick slide show of JDR's trip to Australia last week. A couple of notes about Australia and marine science:
a. Australia is well ahead of Japan in terms of management and education - hope Japan can catch up!
b. Critical thinking in particular needs to be worked on - let's try that in this class.
On to the serious part of the class.
Part 1 - Corals and their symbionts
Corals are part of
Cnidaria - animals that have one hole that serves as both mouth and anus. This is surrounded by tentacles. All Cnidaria and only cnidarians have nematocysts, defense and feeding. Two main shapes, polyp and medusa. Life cycle alternates between these two shapes; main for corals is polyps, main for jellyfish is medusae.
Anthozoa = includes octocorals and hexacorals.
Hexacorallia = includes corals, anemones, zoanthids, corallimorphs, antipatharians and cerianthids. Have mesenteries in multiples of 6.
Corals - may be colonial or solitary, zooxanthellate or azooxanthellate. Zooxanthellate colonial species responsible for making coral reefs. Polyps (living tissue) surrounded by calcium carbonate skeleton. Classification traditionally uses skeletal characteristics; color and size also used. Polyps include a mouth and oral disk surrounded by tentacles, as well as zooxanthellae (Symbiodinium spp.; ZX).
Skeletons have much microstructure, important for many other animals as homes, especially when coral dead. Refuge from predators etc. Many types of corals - show pictures of these.
Also, zoanthids - related order to corals. Colonial like corals, soft like anemones. Many species have ZX. Very variable morphology even within species.
When understanding coral or other cnidarians on the reef, please remember that the holobiont is important.
Holobiont = host (animal) + ZX + bacteria, viruses, etc. Host may be same species, but if ZX are different, this has implications for biology and ecology of holobiont.
ZX are dinoflagellates with chlorophyll. Live inside host, give energy from sunlight to host.
ZX look similar, thought to be one species, but DNA etc. have revealed diversity, now 8 clades (A to H). Most ZX sensitive to high ocean temperatures. Usually 30C is considered a threshold. Different clades or subclades may have different physiology. ZX thylakoids degrade at hot temperatures, causing coral bleaching. Also can happen at low (<15C).
Research example: Zoanthus sansibaricus at different locations in Japan has different ZX clades!
Dangers facing coral reefs: Bleaching, acidification (will discuss this more in another class). Perhaps 90% of reefs dead by 2050.
Species diversity for many organisms unknown. 99.5% of species go extinct before we identify them. Without knowledge of species how do we protect them? Taxonomy and diversity study important. but... training takes time, pay is poor, and many organisms VERY hard to identify in traditional methods.
REFRESH TIME, followed by activity - terms:
locus 遺伝子座 ex. DNA marker
genotype 遺伝子型 ex. individuals
genome 全遺伝子情報 ex. human genome project
alleles 対立遺伝子 ex. flies with different antennae
polymorphic 多型 ex. sexually produced fish
monomorphic 単一型 ex. asexual coral clones
genetic distance 遺伝子距離 ex. taxonomy (sometimes)
Part 2 - Genetic diversity - variety of alleles or genotypes in a group being investigated.
Overview: quick explanation of evolution. Species gradually diverge; develop unique traits. Some groups disappear, others continue to evolve. Adaptations always needed.
Genetic diversity is required to adapt to changing environments (ex: Hawaiian honeycreeprs). Environments are ALWAYS changing, never static. Many methods to measure genetic diversity. Large populations usually have high diversity; small populations are a concern.
Diveristy needed, give examples we have seen - industrial melanism. Also failures to adapt - chestnut trees and Okinawan pines.
Low genetic diversity also leads to less reproductive success, more inbreeding. Ex: European royal families! Maintaining different populations important.
How do we measure genetic diversity?
1. quantative measurement - morphology. size, shape, height, weight, etc. But not due only to genes, also environment and expression. Difficult to assess. Can be done in absence of other methods, cheap.
2. deleterious alleles - results from inbreeding, i.e. flies. But not good for conservation!
3. proteins - started in 1960s, slight changes in sizes form species or individuals. Uses electrophoresis. Need blood or organs, invasive.
4. DNA - many methods, always new developments. We will discuss
a. nuclear DNA - fast evolving in Cnidaria, slower in other animals - very general rule. More later.
b. mitochondrial DNA - slow in Cnidaria, fast in other animals. Again generalization.
c. Microsatellites - used for population studies; repeats of DNA. Development time is considerable.
More on these next week!
Can use DNA to identify species new and old.
5. Chromosomes - often clear differences between species. But no genetic distance or often no idea of relationships between species.
Endangered species have low genetic diversity, due to bottlenecks and reduced populations. Shown for many species (ex. nene).
Variation over space and time - higher dispersal means less variation within species, lower dispersal means more variation. Give example of humans. Large populations more stable than small populations which lose genetic diversity quickly.
References:
1. Corals of the World. JEN Veron. 2000. AIMS, Melbourne. Volume 1.
2. Introduction to Conservation Genetics. R Frankham et al. 2002. Cambridge. Ch. 3
Wednesday, October 22, 2008
Class 2008.10.22
Coral Reef Diversity and Conservation
October 22, 2008
Class 1: Introduction to the Coral Reef Ecosystems
Pre-class announcements: Please attend the class on December 3rd, this is the day I assign reports, and make report teams. If you know of someone who has never attended, please tell them.
Anything I say in class may appear on the final test. Take notes. Lots of ideas, some new and some old, but please ask questions anytime.
1. Warm-up: Divide into groups of 2-3. Have students look at picture, assess the diversity of different pictures, and tell me which is “most healthy” etc.
Go through answers row-by-row. Get ideas, see what they know and don’t know.
Make sure students understand that healthy is all relevant, and can be different from different organisms points of view. For reefs; healthy can mean no humans! Large animals in abundance, healthy coral in abundance, low amounts of algae and slime, etc. If so, there are very few healthy coral reefs. 24% in danger of total collapse, 26% in danger of high degradation (Precht & Robbart 2006) within 50 years. Others say 80% (Veron 2001). Species numbers add here too. 5-10% already dead. One of the most endangered ecosystems on earth.
2. Always remember conservation; we will come back there.
3. Introduction to Coral Reefs:
a. What are coral reefs? How do they form?
Biggest structures made by living organisms. GBR is 1000s of km long.
Thus we may think they are tough and permanent, but they are not, and only top thin layer is generally alive.
Existed before hard corals existed, different groups have taken turns making reefs.
Modern reefs due to symbiosis between coral and zooxanthellae, can get nutrients from water, but limited to warm clear shallow water (more on this later), where they compete with macroalgae (more later).
Reefs can be geological structures, and living ecosystems. Unusual.
For geology, reefs affected by oceans going up and down, changes in temp and current. Shorter scales, typhoons, tsunamis, crown-of-thorns, etc.
Even shorter; bleaching, fishing, dynamite, coral reef trade, shellfish, etc.
Recently sea level has not changed so much, resulting in reefs today, but past there were many changes. Underwater cave example even.
Many reefs are like forests, tear them down and build them up.
Anyone been diving? Different levels of shelves are often indicators of past sea levels.
b. Different types of coral reefs
Starting with Darwin, many people have attempted to classify reefs into types. Humans like to classify.
Can be classified broadly into 3 types, as Darwin did. Rainwater, pounding of waves, and coralline algae make limestone from dead corals. Often reef edges have no corals, but much coralline algae. Also rubble, which may become reef in the future. Usually brought here by waves.
1: Fringing reefs: close to coastlines, may include rocks and other things besides dead coral. Briefly describe picture. Lagoons often muddy, corals on seaward edge, much variation in communities. Often lagoons may have low species diversity, while reef slopes often have highest diversity. Explain parts of the reef. Lagoon, edge,slope, channel.
2: Barrier reefs: Basically fringing reefs but further from shore, due to changes in sea level and time etc. Made almost entirely of carbonate. Often have channels for massive currents to flow through. May be a barrier reef followed by a fringing reef.
3:Atoll: walls of a reef around a lagoon, from a sunken island. Darwin first thought of this.
Many grades between these three types. Also, platform reefs that do not fit any of the classes above. Mention deep sea reefs too.
c. Geological history of coral reefs, currents etc.
Now: Reefs found in Pacific, Atlantic, and Indian. Reefs need to be in areas over 18C, this is a good temperature for ZX, for coralline algae. Reefs are not found in areas with poor visibility, with little wave action, although corals may be found there. Need also to out-compete algae.
There is little correlation between coral species numbers and reefs, as many reefs are built by just a few species. But there is a link between reefs and overall biological diversity (more on this later).
History: known from 2 billion years ago. Explain these using timelines.
First reefs built by stromatolites (blue green algae mounds that can take up sediment), then archaeocyaths (like sponges), then corals (not modern ones) along with sponges, bryozoans.
Probably in this period the first endosymbiotic symbioses evolved.
Two types of corals: Rugose and Tabulate, but died when dinosaurs did. After this no reefs for a long time.
Modern corals appeared in Triassic, have dominated reef building since then. Show maps? Show some old extinct reefs.
In mid-cretaceous, rudist bivalves dominated, probably symbiotic, and then corals came back.
At end of dinosaurs 1/3 of families, 70% of genera became extinct. All species changed!
More recent: Diversity levels have recovered. More diversity with zooxanthellate genera. Results of land shifting and old distributions show that Atlantic genera are much older than Pacific. This does not mean evolution was faster, based on previous patterns and the Tethys Sea.
Closure of Panama very important. No species of corals and few genera shared between Indo-Pacific and Atlantic. Even if many animals look the same, very few shared!
d. Diversity; less than 0.2% of the earth, 25% or more of the ocean’s species! 10% of fish caught. Protect land as breakwaters, and valuable for tourism. All of this despite low nutrients and compounds in the surrounding water.
Corals make very complex structures thanks to their skeletons. Greatly increase amount of habitable areas, or niches, for many different species. Explain about specialized animals, use zoanthids and shogun ebi as examples.
Much problem trying to calculate actual surface area. For macroorganisms, factors of at least 15 (Dahl 1973). Much greater for microorganisms. And this is on the surface alone!
d. Diversity? How to measure it?
Discuss before scuba and ideas at that time
First corals where collected in 1700s when scientific interest began, and first cataloguing. Increased greatly in 1800 and early 1900s. Museums and names.
Corals were particularly easy, as they could be preserved. So, along with fish and sea mammals and macroalage, very extensively documented.
Problems: no observation of living things in situ, no idea of variance, differ from place to place, so many incorrect names.
But, according to ICZN, these names MUST be correct, so we have continued on with bad ideas.
Other animals were largely ignored until 1800s or 1900s, such as anemones, zoanthids, corallimorphs, etc.
Many understudied groups are finally getting reexamined today, along with corals!
e. Discuss problems encountered since with diving, and new methods, briefly
With diving, we realized we had serious problems! Diving started on large scale in the 1960s.
Even then, our ideas of species are outdated, and little has been done on even corals outside a few species.
Thus, the number of species awaiting description is huge, and perhaps impossible. But still we try, for bioresources and chemicals etc. It is well known diversity has economic benefits now and in the future.
Finally now a big push for this. TOL, CoML etc (later).
4. Wrap-up: Just how much biomass was on reefs before humans?
Recent papers, including the one from which handout came from, show that the biomass of coral reefs may be inverted. Healthy reefs have 85% of fish biomass in sharks!!
This has sent researchers back to old papers and accounts.
Discuss old papers where so many sea turtles
Early Atlantic explorers running aground on sea turtles.
Numerous shark stories of huge numbers of sharks.
Even in Okinawa, giant clams over 100 kg. The sea is richer than we can imagine in untouched places, but we have never seen or almost never will see. We are missing so-called “baseline” data, and now a race to get some!
SHOW MOVIE OF SHARKS. Ask first maybe if anyone has ever seen a shark, and how many.
5. Activity Answers: Go over my ideas. Show word file. Explain not biomass, and perhaps how things would be different.
6. Recommended reading:
1. SA Sandlin et al. 2008. Baselines and Degradation of Coral Reefs in the Northern Line Islands. PloS One 3 (2) e1548:1-11.
2. EA Dinsdale et al. 2008. Microbial Ecology of Four Coral Atolls in the Northern Line Islands. PloS One 3 (2) e1584: 1-17.
3. N Knowlton, JBC Jackson. 2008. Shifting Baselines, Local Impacts, and Global Change on Coral Reefs. PloS Biology 6 (2) e54:215-220.
4. Corals of the World – JEN Veron. 2000. Australian Institute of Marine Science. Melbourne.
October 22, 2008
Class 1: Introduction to the Coral Reef Ecosystems
Pre-class announcements: Please attend the class on December 3rd, this is the day I assign reports, and make report teams. If you know of someone who has never attended, please tell them.
Anything I say in class may appear on the final test. Take notes. Lots of ideas, some new and some old, but please ask questions anytime.
1. Warm-up: Divide into groups of 2-3. Have students look at picture, assess the diversity of different pictures, and tell me which is “most healthy” etc.
Go through answers row-by-row. Get ideas, see what they know and don’t know.
Make sure students understand that healthy is all relevant, and can be different from different organisms points of view. For reefs; healthy can mean no humans! Large animals in abundance, healthy coral in abundance, low amounts of algae and slime, etc. If so, there are very few healthy coral reefs. 24% in danger of total collapse, 26% in danger of high degradation (Precht & Robbart 2006) within 50 years. Others say 80% (Veron 2001). Species numbers add here too. 5-10% already dead. One of the most endangered ecosystems on earth.
2. Always remember conservation; we will come back there.
3. Introduction to Coral Reefs:
a. What are coral reefs? How do they form?
Biggest structures made by living organisms. GBR is 1000s of km long.
Thus we may think they are tough and permanent, but they are not, and only top thin layer is generally alive.
Existed before hard corals existed, different groups have taken turns making reefs.
Modern reefs due to symbiosis between coral and zooxanthellae, can get nutrients from water, but limited to warm clear shallow water (more on this later), where they compete with macroalgae (more later).
Reefs can be geological structures, and living ecosystems. Unusual.
For geology, reefs affected by oceans going up and down, changes in temp and current. Shorter scales, typhoons, tsunamis, crown-of-thorns, etc.
Even shorter; bleaching, fishing, dynamite, coral reef trade, shellfish, etc.
Recently sea level has not changed so much, resulting in reefs today, but past there were many changes. Underwater cave example even.
Many reefs are like forests, tear them down and build them up.
Anyone been diving? Different levels of shelves are often indicators of past sea levels.
b. Different types of coral reefs
Starting with Darwin, many people have attempted to classify reefs into types. Humans like to classify.
Can be classified broadly into 3 types, as Darwin did. Rainwater, pounding of waves, and coralline algae make limestone from dead corals. Often reef edges have no corals, but much coralline algae. Also rubble, which may become reef in the future. Usually brought here by waves.
1: Fringing reefs: close to coastlines, may include rocks and other things besides dead coral. Briefly describe picture. Lagoons often muddy, corals on seaward edge, much variation in communities. Often lagoons may have low species diversity, while reef slopes often have highest diversity. Explain parts of the reef. Lagoon, edge,slope, channel.
2: Barrier reefs: Basically fringing reefs but further from shore, due to changes in sea level and time etc. Made almost entirely of carbonate. Often have channels for massive currents to flow through. May be a barrier reef followed by a fringing reef.
3:Atoll: walls of a reef around a lagoon, from a sunken island. Darwin first thought of this.
Many grades between these three types. Also, platform reefs that do not fit any of the classes above. Mention deep sea reefs too.
c. Geological history of coral reefs, currents etc.
Now: Reefs found in Pacific, Atlantic, and Indian. Reefs need to be in areas over 18C, this is a good temperature for ZX, for coralline algae. Reefs are not found in areas with poor visibility, with little wave action, although corals may be found there. Need also to out-compete algae.
There is little correlation between coral species numbers and reefs, as many reefs are built by just a few species. But there is a link between reefs and overall biological diversity (more on this later).
History: known from 2 billion years ago. Explain these using timelines.
First reefs built by stromatolites (blue green algae mounds that can take up sediment), then archaeocyaths (like sponges), then corals (not modern ones) along with sponges, bryozoans.
Probably in this period the first endosymbiotic symbioses evolved.
Two types of corals: Rugose and Tabulate, but died when dinosaurs did. After this no reefs for a long time.
Modern corals appeared in Triassic, have dominated reef building since then. Show maps? Show some old extinct reefs.
In mid-cretaceous, rudist bivalves dominated, probably symbiotic, and then corals came back.
At end of dinosaurs 1/3 of families, 70% of genera became extinct. All species changed!
More recent: Diversity levels have recovered. More diversity with zooxanthellate genera. Results of land shifting and old distributions show that Atlantic genera are much older than Pacific. This does not mean evolution was faster, based on previous patterns and the Tethys Sea.
Closure of Panama very important. No species of corals and few genera shared between Indo-Pacific and Atlantic. Even if many animals look the same, very few shared!
d. Diversity; less than 0.2% of the earth, 25% or more of the ocean’s species! 10% of fish caught. Protect land as breakwaters, and valuable for tourism. All of this despite low nutrients and compounds in the surrounding water.
Corals make very complex structures thanks to their skeletons. Greatly increase amount of habitable areas, or niches, for many different species. Explain about specialized animals, use zoanthids and shogun ebi as examples.
Much problem trying to calculate actual surface area. For macroorganisms, factors of at least 15 (Dahl 1973). Much greater for microorganisms. And this is on the surface alone!
d. Diversity? How to measure it?
Discuss before scuba and ideas at that time
First corals where collected in 1700s when scientific interest began, and first cataloguing. Increased greatly in 1800 and early 1900s. Museums and names.
Corals were particularly easy, as they could be preserved. So, along with fish and sea mammals and macroalage, very extensively documented.
Problems: no observation of living things in situ, no idea of variance, differ from place to place, so many incorrect names.
But, according to ICZN, these names MUST be correct, so we have continued on with bad ideas.
Other animals were largely ignored until 1800s or 1900s, such as anemones, zoanthids, corallimorphs, etc.
Many understudied groups are finally getting reexamined today, along with corals!
e. Discuss problems encountered since with diving, and new methods, briefly
With diving, we realized we had serious problems! Diving started on large scale in the 1960s.
Even then, our ideas of species are outdated, and little has been done on even corals outside a few species.
Thus, the number of species awaiting description is huge, and perhaps impossible. But still we try, for bioresources and chemicals etc. It is well known diversity has economic benefits now and in the future.
Finally now a big push for this. TOL, CoML etc (later).
4. Wrap-up: Just how much biomass was on reefs before humans?
Recent papers, including the one from which handout came from, show that the biomass of coral reefs may be inverted. Healthy reefs have 85% of fish biomass in sharks!!
This has sent researchers back to old papers and accounts.
Discuss old papers where so many sea turtles
Early Atlantic explorers running aground on sea turtles.
Numerous shark stories of huge numbers of sharks.
Even in Okinawa, giant clams over 100 kg. The sea is richer than we can imagine in untouched places, but we have never seen or almost never will see. We are missing so-called “baseline” data, and now a race to get some!
SHOW MOVIE OF SHARKS. Ask first maybe if anyone has ever seen a shark, and how many.
5. Activity Answers: Go over my ideas. Show word file. Explain not biomass, and perhaps how things would be different.
6. Recommended reading:
1. SA Sandlin et al. 2008. Baselines and Degradation of Coral Reefs in the Northern Line Islands. PloS One 3 (2) e1548:1-11.
2. EA Dinsdale et al. 2008. Microbial Ecology of Four Coral Atolls in the Northern Line Islands. PloS One 3 (2) e1584: 1-17.
3. N Knowlton, JBC Jackson. 2008. Shifting Baselines, Local Impacts, and Global Change on Coral Reefs. PloS Biology 6 (2) e54:215-220.
4. Corals of the World – JEN Veron. 2000. Australian Institute of Marine Science. Melbourne.
Tuesday, October 14, 2008
Class 2008.10.15
Today I introduced the class guidelines and rules. Here are the details (this repeats some of the information from the first posting):
サンゴ礁多様性保全学（後期）
時限・教室
後期 水曜日 1時限 理327
URL：http://ryukyucoral2008.blogspot.com/
単位数：2
担当者：REIMER James Davis（理学部353号室；jreimer@sci.u-ryukyu.ac.jp）
オフィスアワー：午後以降
備考（メッセージ）
毎週の授業内容紹介をブログにuploadする（授業後）。授業は日本語で行うが、スライドとブログは主に英語になる。毎週参考文献を紹介する。
授業内容と方法
主にサンゴ礁生態系における無脊椎動物の最新の研究を紹介して、どのように生物の多様性を理解し、保全を行うことができるかを考察する。簡単に遺伝学的な情報の利用法も紹介する。
達成目標
サンゴ礁生態系の著しい多様性を理解する。
サンゴ礁生態系の生物の最新研究を知る。
遺伝学的な情報の利用の仕方を理解する。
評価基準と評価方法
1. 中期のレポート: 70%
2. 期末テスト: 30%
授業計画
15.Oct 1. 登録調整と説明
22.Oct 2. サンゴ礁生態系の紹介
5.Nov 3. 遺伝学の紹介
12.Nov 4. 系統樹の説明
19.Nov 5. サンゴ礁生態系についての研究紹介I
26.Nov 6. サンゴ礁生態系についての研究紹介II
3.Dec 7. 中期レポートの説明
10.Dec 8. サンゴ礁生態系についての研究紹介III
17.Dec 9. 網状進化の研究紹介
24.Dec 10. 保全学についての研究紹介I
7.Jan 11. 保全学についての研究紹介II
14.Jan 12. DNA Barcoding and the Tree of Lifeの紹介
21.Jan 13. 期末テスト
教科書
1: 特に指定しない
参考書
1: Coral Reef Restoration Handbook – W. Precht (ed.). 2006. CRC Taylor & Francis, New York.
2: Introduction to Conservation Genetics – R. Frankham, J.D. Ballou, D.A. Briscoe. 2002. Cambridge University Press, Cambridge.
3. Molecular Markers, Natural History, and Evolution (2nd edtion) – J.C. Avise. 2004. Sinauer, Sunderland, MA.
4. Corals of the World – JEN Veron. 2000. Australian Institute of Marine Science. Melbourne.
As well, we played a "bingo" introduction game. See you next week!
サンゴ礁多様性保全学（後期）
時限・教室
後期 水曜日 1時限 理327
URL：http://ryukyucoral2008.blogspot.com/
単位数：2
担当者：REIMER James Davis（理学部353号室；jreimer@sci.u-ryukyu.ac.jp）
オフィスアワー：午後以降
備考（メッセージ）
毎週の授業内容紹介をブログにuploadする（授業後）。授業は日本語で行うが、スライドとブログは主に英語になる。毎週参考文献を紹介する。
授業内容と方法
主にサンゴ礁生態系における無脊椎動物の最新の研究を紹介して、どのように生物の多様性を理解し、保全を行うことができるかを考察する。簡単に遺伝学的な情報の利用法も紹介する。
達成目標
サンゴ礁生態系の著しい多様性を理解する。
サンゴ礁生態系の生物の最新研究を知る。
遺伝学的な情報の利用の仕方を理解する。
評価基準と評価方法
1. 中期のレポート: 70%
2. 期末テスト: 30%
授業計画
15.Oct 1. 登録調整と説明
22.Oct 2. サンゴ礁生態系の紹介
5.Nov 3. 遺伝学の紹介
12.Nov 4. 系統樹の説明
19.Nov 5. サンゴ礁生態系についての研究紹介I
26.Nov 6. サンゴ礁生態系についての研究紹介II
3.Dec 7. 中期レポートの説明
10.Dec 8. サンゴ礁生態系についての研究紹介III
17.Dec 9. 網状進化の研究紹介
24.Dec 10. 保全学についての研究紹介I
7.Jan 11. 保全学についての研究紹介II
14.Jan 12. DNA Barcoding and the Tree of Lifeの紹介
21.Jan 13. 期末テスト
教科書
1: 特に指定しない
参考書
1: Coral Reef Restoration Handbook – W. Precht (ed.). 2006. CRC Taylor & Francis, New York.
2: Introduction to Conservation Genetics – R. Frankham, J.D. Ballou, D.A. Briscoe. 2002. Cambridge University Press, Cambridge.
3. Molecular Markers, Natural History, and Evolution (2nd edtion) – J.C. Avise. 2004. Sinauer, Sunderland, MA.
4. Corals of the World – JEN Veron. 2000. Australian Institute of Marine Science. Melbourne.
As well, we played a "bingo" introduction game. See you next week!
Wednesday, October 8, 2008
Student Numbers and 1st class
There are over 50 students registered for this class! Obviously I am going to be busy preparing.
The first class will be next Wednesday, October 15th, in Science Room 327, starting at 8:30. See you then.
The first class will be next Wednesday, October 15th, in Science Room 327, starting at 8:30. See you then.
Sunday, October 5, 2008
Welcome to Coral Reef Diversity and Conservation
This is a class at the University of the Ryukyus, taught by JD Reimer in the fall semester.
Here is the schedule for 2008 (in Japanese):
15.Oct 1. 登録調整と説明
22.Oct 2.サンゴ礁生態系の紹介
5.Nov 3. 遺伝学の紹介
12.Nov 4. 系統樹の説明
19.Nov 5. サンゴ礁生態系についての研究紹介I
26.Nov 6. サンゴ礁生態系についての研究紹介II
3.Dec 7. 中期レポートの説明
10.Dec 8. サンゴ礁生態系についての研究紹介III
17.Dec 9. 網状進化の研究紹介
24.Dec 10. 保全学についての研究紹介I
7.Jan 11. 保全学についての研究紹介II
14.Jan 12. DNA Barcoding and the Tree of Lifeの紹介
21.Jan 13. 期末テスト
Please watch this site for more information and weekly updates on the class.
Here is the schedule for 2008 (in Japanese):
15.Oct 1. 登録調整と説明
22.Oct 2.サンゴ礁生態系の紹介
5.Nov 3. 遺伝学の紹介
12.Nov 4. 系統樹の説明
19.Nov 5. サンゴ礁生態系についての研究紹介I
26.Nov 6. サンゴ礁生態系についての研究紹介II
3.Dec 7. 中期レポートの説明
10.Dec 8. サンゴ礁生態系についての研究紹介III
17.Dec 9. 網状進化の研究紹介
24.Dec 10. 保全学についての研究紹介I
7.Jan 11. 保全学についての研究紹介II
14.Jan 12. DNA Barcoding and the Tree of Lifeの紹介
21.Jan 13. 期末テスト
Please watch this site for more information and weekly updates on the class.
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