Data from: Population genetic evidence for cold adaptation in European Drosophila melanogaster populations

We studied Drosophila melanogaster populations from Europe (the
Netherlands and France) and Africa (Rwanda and Zambia) to uncover genetic
evidence of adaptation to cold. We present here four lines of evidence for
genes involved in cold adaptation from four perspectives: (1) the
frequency of SNPs at genes previously known to be associated with
chill-coma recovery time (CCRT), startle reflex (SR), and resistance to
starvation stress (RSS) vary along environmental gradients and therefore
among populations; (2) SNPs of genes that correlate significantly with
latitude and altitude in African and European populations overlap with
SNPs that correlate with a latitudinal cline from North America; (3) at
the genome-wide level, the top candidate genes are enriched in gene
ontology (GO) terms that are related to cold tolerance; (4) GO enriched
terms from North American clinal genes overlap significantly with those
from Africa and Europe. Each SNP was tested in 10 independent runs of
Bayenv2, using the median Bayes factors to ascertain candidate genes. None
of the candidate genes were found close to the breakpoints of cosmopolitan
inversions, and only four candidate genes were linked to QTLs related to
CCRT. To overcome the limitation that we used only four populations to
test correlations with environmental gradients, we performed simulations
to estimate the power of our approach for detecting selection. Based on
our results we propose a novel network of genes that is involved in cold
adaptation.