Cold adaptation drives population genomic divergence in the ecological specialist , Drosophila montana

Cold adaptation drives population genomic divergence in the ecological specialist, Drosophila montana

10.1101/2020.04.20.050450 ◽

2020 ◽

Author(s):

R. A. W. Wiberg ◽

V. Tyukmaeva ◽

A. Hoikkala ◽

M. G. Ritchie ◽

M. Kankare

Keyword(s):

Cold Tolerance ◽

Cold Adaptation ◽

Ecological Adaptation ◽

Climatic Variables ◽

Population Divergence ◽

Candidate Snps ◽

Clinal Variation ◽

Ecological Selection ◽

Genomic Divergence ◽

Drosophila Montana

ABSTRACTDetecting signatures of ecological adaptation in comparative genomics is challenging, but analysing population samples with characterised geographic distributions, such as clinal variation, can help identify genes showing covariation with important ecological variation. Here we analysed patterns of geographic variation in the cold-adapted species Drosophila montana across phenotypes, genotypes and environmental conditions and searched for signatures of cold adaptation in populations’ genomic divergence. We first derived the climatic variables associated with the geographic distribution of 24 populations across two continents to trace the whole scale of environmental variation experienced by the species, and measure variation in the cold tolerance of the flies of six populations from different geographic contexts. We then performed pooled whole genome sequencing of these six populations, and used Bayesian methods to identify SNPs where genetic differentiation is associated with both climatic variables and the population phenotypic measurements. The top candidate SNPs were enriched on the X and 4th chromosomes, and they also lie near genes implicated in other studies of cold tolerance and population divergence in this species and its close relatives. We conclude that ecological adaptation has contributed to the divergence of D. montana populations throughout the genome and in particular on the X and 4th chromosomes, which also showed highest interpopulation Fst. This study demonstrates that ecological selection can drive genomic divergence at different scales, from candidate genes to chromosome-wide effects.

Download Full-text

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

Genome Biology and Evolution ◽

10.1093/gbe/evy147 ◽

2018 ◽

Vol 10 (8) ◽

pp. 2086-2101 ◽

Cited By ~ 14

Author(s):

Darren J Parker ◽

R Axel W Wiberg ◽

Urmi Trivedi ◽

Venera I Tyukmaeva ◽

Karim Gharbi ◽

...

Keyword(s):

Cold Adaptation ◽

Genomic Divergence ◽

Drosophila Montana

Download Full-text

Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation

10.1101/282582 ◽

2018 ◽

Cited By ~ 1

Author(s):

D. J. Parker ◽

R. A. W. Wiberg ◽

U. Trivedi ◽

V. I. Tyukmaeva ◽

K. Gharbi ◽

...

Keyword(s):

Cold Adaptation ◽

Sequence Variation ◽

Synonymous Substitution ◽

Drosophila Species ◽

Cold Adapted ◽

Outlier Loci ◽

Genomic Divergence ◽

Genomic Adaptation ◽

Drosophila Montana ◽

Selective Process

AbstractThe genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to their ecological specialism from other sources of selection and more random changes is a challenge. Here we describe the genome of Drosophila montana, the most extremely cold-adapted Drosophila species. We describe the genome, which is similar in size and gene content to most Drosophila species. We look for evidence of accelerated divergence from a previously sequenced relative, and do not find strong evidence for divergent selection on coding sequence variation. 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. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. We also re-sequenced three populations of D. montana representing 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 Drosophila species, implying some continuity of selective process at these different evolutionary scales.

Download Full-text