Transcript The Population Genomics of a Fast Evolver: High Levels of Diversity

Genetics Presentation:
Sea Squirts
Catherine Dong
9/6/12
Bio303 H
Dr. Ely
The Population Genomics of a
Fast Evolver: High Levels of
Diversity, Functional Constraint,
and Molecular Adaptation in the
Tunicate Ciona intestinalis
Georgia Tsagkogeorga1,2,*, Vincent Cahais1, and Nicolas Galtier1
1Universite ́ 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 phyla
Amino 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 mutation
High rate due to strong adaptive processes
Or, protein evolution could be accelerated
due to less efficient natural selection
Expected more in small pop. Size
Method
Gathered 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 singlenucleotide 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 calling
Determines 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