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