As the crow, flies : identifying genomic loci contributing to adaptation in Drosophila and the corvid radiation
Abstract
Identifying loci that contribute to adaptive traits is an important goal of
evolutionary biology. I take a comparative genomic approach to identify loci that have
responded to divergent selection. First I consider the challenges of identifying consistent
genomic responses to selection during experimental evolution. I use population genetic
simulations to show that commonly applied statistical tests perform poorly and identify
superior methods. These will also be useful in comparing allele frequencies in other
contexts. Next I analyse whole genome data from an experimental evolution study of
Drosophila pseudoobscura evolving under altered mating systems. I find that around
300 SNPs show consistent allele frequency differences between experimental
treatments. These are clustered in genomic regions which also show signatures of
selective sweeps or background selection. These regions contain genes with mutant
phenotypes related to changes already documented in this system. In another chapter I
use a novel approach to identify markers potentially influencing female re-mating rate
among lines of D. pseudoobscura. I use simulations to show that there are more fixed
differences between extreme pairs of isofemale lines from different populations than
expected by chance. Many of the genes are implicated in female mating behaviour in
other studies. I then focus on local adaptation in wild Drosophila montana populations.
I use Bayesian methods to relate genetic and environmental differentiation among
populations. Finally, I take a broader comparative approach using multiple genomes
from 14 species of crow to identify potential signatures of selection in the New
Caledonian (NC) (Corvus moneduloides) and Hawai’ian crow (Corvus hawaiiensis)
lineages. The NC and, more recently, Hawai’ian crows are of great interest for their
unusual tool-using foraging behaviour. I find only modest evidence for greater rates of
molecular evolution at coding regions within these lineages. This thesis applies novel
techniques to genomic data to identify candidate loci for evolutionary divergence in
these different systems and highlight analytical methods that will be generally useful in
other systems.
Type
Thesis, PhD Doctor of Philosophy
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