Class November 20, 2013

Class 2013.11.20 Genetics Part 1(linked to biodiversity and conservation)

Part 1 Review

1. Introduction to genetics, diversity and conservation.

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.

Coral reefs are highly diverse (0.2% of earth's surface, >25% of marine species. Always structure is complex due to varied surfaces=15X more space for large animals, 1000X or more for microbes.

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.

Now, due to new techniques (SCUBA since WWII, research submersibles since WWII, and DNA analyses since 1970s), massive revisions and reconsideration of marine taxa occurring.

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.

Still, currently almost all marine benthos taxa have knowledge gaps.

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!

Part 2 - Genetic diversity - variety of alleles or genotypes in a group being investigated.

Overview: quick explanation of evolution. Species gradually diverge; develop unique traits. Some groups disappear, others continue to evolve. Adaptations always needed.

In order to understand phylogeny we must understand evolution:

The modern synthesis of evolution is the combination of Darwin's and Mendel's theories.

The theory underlying the modern synthesis has three major aspects:

The common descent of all organisms from a single ancestor.

全ての生き物は共通の祖先から進化した。

The origin of novel traits in a lineage.

それぞれのグループはそれぞれの特徴を持つ。

Changes cause some traits to persist while others perish.

様々な変化によって、あるグループは生き残り、あるグループは絶滅する。

DNA and phylogenetics

All cells contain DNA - the code or blueprint of life.

全ての細胞には遺伝子が入っている。遺伝子は生き物の設計図。

This code has only four different "letters": A, G, C, T.

遺伝子は４つのコードしかない。

Usual length 1,000,000 to 100,000,000,000 base pairs.

生き物のひとつの細胞にある遺伝子の長さは,000,000 to 100,000,000,000 。

Genome projects read everything in one organism, but takes time and expensive.

全ての遺伝子を読むことは時間とお金の無駄。

Many studies use one or a few markers to investigate relations.

遺伝子の短い部分だけでも系統関係が解析できる。

By collecting the same marker from different samples and then analyzing them, we can make a tree.

いくつかのサンプルから同じマーカーを読んで、並べてから、解析し系統樹を作る。

It is thought/hoped a tree is similar to how evolution occurred.

系統樹から進化が見えると思われる。

DNA may be a way to have non-specialists identify species quickly!

So, DNA tree = evolutionary tree (or so we hope)

Part 3: How to look at a phylogenetic tree

Branch length:

1. Vertical height has no important meaning.

2. Horizontal length is very important, tells the genetic distance of each sequence!

Calculation done by software (branch length and bootstrap values).

Values show possibility that this clade/shape is true.

Values under 50% not used.

Values >70% desirable, above 90% confident.

Bayes >95%! (Actually, as this is posterior probability, 0.95).

Bootstrap Values and 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 - most complex, searches for "ideal peak" on sets of trees!

Utility of phylogenetic trees:

Trees reflect evolution.

Can make conservation decisions from these, or taxonomic decisions.

“Reverse taxonomy” - when scientists acquire DNA first, then phylogenetic analyses, then look for morphological characters. This has led to a massive reconsideration of species and taxonomy.

Group Activity:

1. Which species are most important to protect? What would you protect if you could only save six species?

References:

1. Chapter 4 of Molecular Markers, Natural History, and Evolution 2nd edition – JC Avise. 2004. Sinauer. Sunderland, Massachusetts.

2. Reimer et al. 2004-2013. 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.

Next week: schedule check and new class schedules!

Class October 30, 2013

October 30, 2013
Introduction to the Coral Reef Ecosystems and Biodiversity

Introduction to Coral Reefs:
Outline:
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, human impacts. 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.

Class October 23, 2013

Class notes 2013.10.23

Outline

1. Classification & taxonomy
2. Taxonomy today
3. Reminder
4. Activity!

1. Classification & taxonomy

What is classification?

Classification is the grouping of things according to characteristics

The science of classifying organisms is known as taxonomy

Early classification systems:

l   Aristotle grouped animals according to the way they moved

l   John Ray (1627-1705) was the first to define the term “species”

Binomial classification:

Started with Linneaus (1707-1778)

•       a two name system for writing scientific names.

•       The genus name is written first (always Capitalized).

•       The species name is written second (never capitalized).

•       Both words are italicized if typed or underlined if hand written.

Example:   Felis concolor or F. concolor

l   "Formal" scientific names should have a third part, the authority.
The authority is not italicized or underlined.

l   The authority is written as an abbreviation of the last name of the person responsible for naming the organism. Since Carolus Linnaeus was the first person to name many plants, the L. for Linnaeus is very common in plant scientific names.

Examples: Quercus alba L.

Abyssoanthus convalis Reimer & Sinniger, 2009

Hierarchical Classification

l   Based on species. Classification goes down, but the basis is “bottom up”.

7 hierarchies in system:

Kingdom                                very broad

Phylum (Division)

Class

Order

Family

Genus

Species                                   very specific

The International Code of Zoological Nomenclature (ICZN) specifically governs the family-genus-species level.

Points to remember:

l   We only know about a fraction of the organisms that exist or have existed on Earth.

l   Taxonomists give a unique scientific name to each species they know about whether it’s alive today or extinct.

l   The scientific name usually comes from one of two “dead”  languages – Latin or ancient Greek.

l   Scientific names are used to avoid problems with common names. Examples: American mountain lion, and “chinu/kurodai”.

2. Taxonomy today

Linnaeus vs. Today

l   Linnaeus grouped plants and animals based on reproductive characteristics

l   Now we group plants and animals based on phylogeny

l   Phylogeny=Evolutionary history, or how the plants and animals are related.

l   We use genetics to figure out how plants and animals are related.

l   In Linnaeus’s day, scientists did not know what evolution was or what DNA and genetics was.

Phylogeny, the evolutionary history of an organism, is the cornerstone of a branch of biology called systematic taxonomy.

Systematics, as systematic taxonomy is commonly called, is the study of the evolution of biological diversity.

•       A phylogenetic tree is a shows a hypothesis about the evolutionary relationships thought to exist among groups of organisms.

•       Trees may or may not show the actual evolutionary history of organisms.

Phylogenetic trees are usually based on a combination of these lines of evidence:

•       Fossil record

•       Morphology

•       Embryological patterns of development

•       Genetic information

Brief discussion on:

1.     Adaptive radiation – and modification of homologous structures.

2.     Convergent evolution – evolving similar adaptations as organisms inhabit similar niches or play similar ecological roles. Analogous structures – traits that morphologically and functionality even though they do not have a common ancestor (organism, or tissue, etc.).

3.     Homology, parallelism, convergence, analogy.

4.     A phylogenetic tree based on a cladistic analysis is called a cladogram.

5.     Dichotomous key: A key is a device for easily and quickly identifying:

a.     an unknown organism.

b.     The dichotomous key is the most widely used type in biological sciences.

c.      The user is presented with a sequence of  choices between two statements, couplets, based on characteristics of the organism. By always making the correct choice, the name of the organism will be revealed.

3. Reminder

In this class we will be discussing a small fraction of total diversity of life. Show a domain of life tree.

Welcome to the 2013 course!

Time & Place: Science 327, Weds 8:30-10:00
許可 code: reim
Instructor: James Reimer.
Office: Science 353

URL: http://ryukyucoral2013.blogspot.com/

Office hours: Anytime except Weds. daytime.

Content:

lUse mainly marine invertebrate examples.lExplore how to understand diversity, using traditional and modern techniques.lExplore conservation and issues with coral reefs.lBasics of climate change and human impact on reefs.

Goals:
•Understand new coral reef research.
•Understand why coral reefs have high importance and diversity.
•Understand basic DNA techniques (and others) and how to use them in conservation.
•Understand the threats coral reefs face from anthropogenic and climate change problems.
•Understand basic conservation techniques.

Evaluation:
lMid-term presentation (in groups of 2-3 people) and very short report: 40%.
lFinal test: 40%
lAttendance: 20% (5 absences = fail)
lYou must pass all three in order to pass the class.

Class outline:

1.  登録調整と説明  (10/23) Introduction to diversity + Red Sea images

2.  (10/30)

3.  サンゴ礁生態系の紹介  (11/20)

4.  遺伝学の紹介  (11/27)

5.  系統樹の説明(12/4)

6.  サンゴ礁生態系についての研究紹介I  (12/11)

7.  サンゴ礁生態系についての研究紹介II  (12/18)

8.  中期レポートの説明  (1/8)

9.  サンゴ礁生態系についての研究紹介III  (1/15)

10.  網状進化の研究紹介  (1/22)  

11.  保全学についての研究紹介I-Great  Barrier  Reef  Park  History  (1/29)

12.  DNA  Barcoding  and  the  Tree  of  Lifeの紹介  (未定)

13.  期末テスト(未定)

14.  group  presentations/test  (未定)

Notes: 10/2、10/9、11/13    授業は休みです（出張のため）

            11/6    授業は休みです（”Happy  Monday”のため）

        『未定』の授業は、学生全員の相談の上、日程を決定する  

Text, reading, references:

Nothing necessary, but you will do better by reading suggested readings.

I may take questions from suggested readings.

Posted on blog and at end of each class.

Basics of taxonomy and other 10/23 class content to be posted soon....