November 2nd class

Class 3 - Genetics (linked to biodiversity and conservation)

Part 1 Review

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.

ANSWERS to words:
locus　遺伝子座 ex. DNA marker
genotype　遺伝子型 ex. individuals
genome　全遺伝子情報 ex. human genome project
alleles　対立遺伝子 ex. flies with different antennae
polymorphic　多型 ex. sexually produced fish
monomorphic　単一型 ex. asexual coral clones
genetic distance　遺伝子距離 ex. taxonomy (sometimes)

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)

Genetic diversity is required to adapt to changing environments (ex: Hawaiian honeycreeprs). Environments are ALWAYS changing, never static. Many methods to measure genetic diversity. Large populations usually have high diversity; small populations are a concern.
Diveristy needed, give examples we have seen - industrial melanism. Also failures to adapt - chestnut trees and Okinawan pines.
Low genetic diversity also leads to less reproductive success, more inbreeding. Ex: European royal families! Maintaining different populations important.
How do we measure genetic diversity?
1. quantative measurement - morphology. size, shape, height, weight, etc. But not due only to genes, also environment and expression. Difficult to assess. Can be done in absence of other methods, cheap.
2. deleterious alleles - results from inbreeding, i.e. flies. But not good for conservation!
3. proteins - started in 1960s, slight changes in sizes form species or individuals. Uses electrophoresis. Need blood or organs, invasive.
4. DNA - many methods, always new developments. We will discuss

c. Microsatellites - used for population studies; repeats of DNA. Development time is considerable.
In a cell, two major types of DNA we will study:
a. nuclear DNA - fast evolving in Cnidaria, slower in other animals - very general rule. More later.
他の動物と違い、刺胞動物で進化が早い
b. mitochondrial DNA - slow in Cnidaria, fast in other animals. Again generalization.
他の動物と違い、刺胞動物で進化が遅い。
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.
More on these next week!
Can use DNA to identify species new and old.
5. Chromosomes - often clear differences between species. But no genetic distance or often no idea of relationships between species.

Endangered species have low genetic diversity, due to bottlenecks and reduced populations. Shown for many species (ex. nene).
Variation over space and time - higher dispersal means less variation within species, lower dispersal means more variation. Give example of humans. Large populations more stable than small populations which lose genetic diversity quickly.

Part 3- 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.

Part 4 - Lionfish invading the Atlantic

Lionfish known from the Indo-Pacific.
Mainly eat reef fish, and often larvae or juveniles.
Popular in the aquarium trade despite poison.
Marine fish introductions less common.
Most introductions due to purposeful introduction for fisheries, or released aquarium fish.
Success often investigated.
Whitfield et al. (2002) document several sightings (n=19) of Pterois volitans along E. Atlantic.
Four specimens collected, numerous juveniles sighted, two collected.
First introduction of Pacific fish to Atlantic.
Likely limited by cold waters, but surviving.
Can spread to Bermuda and Caribbean.
Similar fish in this region overfished, niche is available perhaps!
Introduction?
Introduction method; 2 possibilities.
Ballast water possible, but no reports thus far.
Aquaria very likely. Specimens known to have been released occasionally.
Morphology appears to be typical of aquaria types.
Effects?
No fish in region used to lionfish.
No predators.
Need genetic and temperature studies.
Modeling needed.
Spreading populations
Since sightings in 2000, lionfish have spread.
Now known (Snyder&Burgess 2006) from Bahamas.
Apparently spreading throughout Caribbean.
Easy to document spread.
Genetic studies
Since Whitfield et al (2002), more studies.
Hamner et al. (2007) used mt DNA to examine specimens.
Two markers (cyt B, 16S rDNA) previously used on lionfish in native ranges.
Found two species of lionfish; P. volitans (93%) and P. miles (7%).
Very reduced genetic diversity!
Minimum-spanning network analyses - P. volitans
Atlantic specimens likely from Indonesia.
P. miles source unknown.
Reduced genetic diversity clear.
Founder effect! Minimum of 3 P. volitans and 1 P. miles established populations.
Invasions may be rapid and irreversible.
Education needed.


References:
1. Corals of the World. JEN Veron. 2000. AIMS, Melbourne. Volume 1.
2. Introduction to Conservation Genetics. R Frankham et al. 2002. Cambridge. Ch. 3
3. Molecular markers, selection and natural history. 2nd edition. J Avise. 2004. Ch.4
4. Whitfield et al. 2002. Biological invasion of the Indo-Pacific lionfish Pterois volitans along the Atlantic coast of North America. Mar Ecol Prog Ser 235: 289-297.
5. Snyder & Burgess. 2007. The Indo-Pacific red lionfish, Pterois volitans (Pisces: Scorpaenidae), new to Bahamian ichthyofauna. Coral Reefs 26: 175.
6. Hamner et al. 2007. Mitochondrial cytochrome b analysis reveals two invasive lionfish species with strong founder effects in the western Atlantic. J Fish Biol 71: 214-222.