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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