November 12 class notes
Genetics part I
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!
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