Genetics Presentation: Sea

SquirtsCatherine Dong

9/6/12Bio303 H

Dr. Ely

The Population Genomics of a Fast Evolver: High Levels of

Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate

Ciona intestinalisGeorgia Tsagkogeorga1,2,*, Vincent Cahais1, and Nicolas

Galtier11Universite 2 Montpellier 2, CNRS UMR 5554, Institut des

Sciences de l’Evolution de Montpellier, Montpellier, France 2School of Biological and Chemical Sciences, Queen Mary

University of London, London, United Kingdom Accepted: June 20, 2012

Tunicate Ciona intestinalis

Goal: What are the causes of high amino acid substitution rates in tunicates?

A urochordata (sea squirt)Closet invertebrate relative to humans

Phylogenomics is the intersection

of the fields of evolution and genomics

Fast evolving animal phylaAmino acid substitution rate, across

proteins are higher than other lineages.

amino acid substitution

Where the similarity between sequences depends on their divergence time (time at which two lineages separated from each other) and the substitution rates are recorded

Tunicates (and nematodes and platyhelminthes) evolve much faster than cnidarians and vertebrates in regards to protein sequences

Problem: why do some proteins evolve faster in some groups and slow in others?

Many evolutionary forces affect aa sub rate

Answer: Obvious one is mutationHigh rate due to strong adaptive processesOr, protein evolution could be accelerated due to less efficient natural selection

Expected more in small pop. Size

MethodGathered polymorphism sequence data sets

occurs when two or more clearly different phenotypes exist in the same population of a species

Validate max-likelihood framework for single-nucleotide polymorphism and genotype calling

Used high-throughput short-read typing

complementary DNA (cDNA) is made from mRNA catalyzed by enzymes.

Made cDNA library from 5 micrograms of RNA extracted from each sample>1,500 cDNA sequences and >30,000 SNPs

Next Generation Sequencing (NGS)

Next-generation sequencing of whole transcriptomes gives the opportunity for such a comparative approach across animals, at a reasonable cost.

Sequenced 8 tunicates in the wild

Single-nucleotide polymorphism(SNP)

DNA sequence variation in a single nucleotide pair

Genotype callingDetermines the genotype for each individual at each site.

Conclusion

Proteome has high within-species diversity, efficient purifying selection, substantial percentage of adaptive amino acid sub

Increased rate of aa seq. evolution in tunicates (compared to vertebrates) is consequence of 2-6 times higher per-year mutation rate and adaptive evolution, not due to relaxing of natural selection.

Significance

Tunicates offer promising comparative perspectives with respect to their slow-evolving sister group, vertebrates

Questions?

http://gbe.oxfordjournals.org/content/4/8/740.full.pdf