Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation

Genome Biology and Evolution
D J ParkerM G Ritchie

Abstract

The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to ecological specialism from other sources of selection and more random changes is a challenge. Here, we describe the genome of Drosophila montana, which is the most extremely cold-adapted Drosophila species known. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm-adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. We also look for evidence of accelerated divergence between D. montana and D. virilis, a previously sequenced relative, but do not find strong evidence for divergent selection on coding sequence variation. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. Finally, we also resequenced three populations of D. montana from across its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophi...Continue Reading

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Citations

Jul 18, 2019·Evolution; International Journal of Organic Evolution·Stéphanie SherpaLaurence Després
Feb 8, 2020·Molecular Ecology·Jason M JacksonJeffrey D Lozier
Jan 22, 2020·Molecular Biology and Evolution·Jullien M FlynnAndrew G Clark
Mar 18, 2020·Molecular Biology and Evolution·Francesco CicconardiBirgit C Schlick-Steiner
Oct 20, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Martin D GarlovskyRhonda R Snook
Nov 29, 2021·Molecular Ecology Resources·Fang LiGuojie Zhang

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

RAPiD Genomics
Maker2
BUSCO
SSPACE
PRANK
trimmomatic
SNAP
PAML
samtools
codeml

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