Class 2008.11.12

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