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

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 Drosophila species, implying some continuity of selective process at these different evolutionary scales.

SUBMITTER: Parker DJ

PROVIDER: S-EPMC6107330 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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

Parker Darren J DJ Wiberg R Axel W RAW Trivedi Urmi U Tyukmaeva Venera I VI Gharbi Karim K Butlin Roger K RK Hoikkala Anneli A Kankare Maaria M Ritchie Michael G MG

Genome biology and evolution 20180801 8

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 a ...[more]

PMID: 30010752

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Project description:We utilized a candidate gene approach using custom microarray constructed for our study species Drosophila montana and D. virilis to identify genes with modulated expression patterns under low temperature conditions. The flies were exposed to four different treatments (+5°C for 6 days, 0°C for 1 hour, two periods of recovery after cold stress and a control treatment). The aim of the study was to identify potential cold-responsive genes and to investigate differences in gene expression between the species. Microarray analysis revealed altogether 31 out of 219 genes on the array to show expression changes during different stages of cold stress. Among the potential stress tolerance genes detected earlier in D. melanogaster, hsr-omega was upregulated in both species during cold acclimation, expression changes in other genes being treatment- and species specific. Our microarray study clearly showed that different stages of cold response elicit changes at least in genes involved in heat shock response, circadian rhythm and metabolism. Cold- induced gene expression was investigated comparing four different treatments to the control treatment: 1) Cold acclimation: 14 days in control conditions, then 6 days at +5°C 2) Cold hardening: 20 days in control conditions, then1 hour at 0°C 3) 15-min recovery from chill coma: the 20-day-old flies were exposed to -6°C for 16 hours, after which they were let to recover for 15 minutes 4) 1-hour recovery from chill coma: the 20-day-old flies were exposed to -6°C for 16 hours, after which they were let to recover for 1 hour. In control treatment flies were kept for 20 days at 19°C. All the flies were 20-days old at the time of sample collection, and the light:dark cycle was 22 hours of light and 2 hours of dark. Because of the limited space on the array plate, the recovery samples were collected only for D. montana. All the samples were collected 5-6 hours after the lights had been turned on in the chamber and the flies were immediately immersed in liquid nitrogen, after which they were stored at -84ºC. Three pools of ten flies were collected from each treatment group.

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

Publications

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

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