Detecting 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 tested for signatures of cold adaptation in population genomic divergence. We first derived the climatic variables associated with the geographic distribution of 24 populations across two continents to trace the scale of environmental variation experienced by the species, and measured 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, while controlling for effects of demography and population structure. The top candidate SNPs were enriched on the X and fourth chromosomes, and they also lay 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 fourth chromosomes, which also showed highest interpopulation F_ST. This study demonstrates that ecological selection can drive genomic divergence at different scales, from candidate genes to chromosome-wide effects.

中文翻译：

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冷适应驱动生态专家 Drosophila montana 的种群基因组分化

在比较基因组学中检测生态适应的特征具有挑战性，但分析具有特征地理分布（例如临床变异）的种群样本可以帮助识别与重要生态变异有共变的基因。在这里，我们分析了冷适应物种Drosophila montana的地理变异模式跨表型、基因型和环境条件，并测试了群体基因组差异中的冷适应特征。我们首先推导出与横跨两大洲的 24 个种群的地理分布相关的气候变量，以追踪该物种所经历的环境变化的规模，并测量了来自不同地理环境的 6 个种群的苍蝇耐寒性的变化。然后，我们对这六个种群进行了全基因组测序，并使用贝叶斯方法来识别遗传分化与气候变量和种群表型测量相关的 SNP，同时控制人口统计学和种群结构的影响。最佳候选 SNP 富集在 X 和第四染色体上，并且它们也位于与该物种及其近亲的其他耐寒性和种群差异研究有关的基因附近。我们得出结论，生态适应导致了d。montana种群在整个基因组中，特别是在 X 和第四染色体上，也显示出最高的种群间F _ST。这项研究表明，生态选择可以在不同尺度上推动基因组分化，从候选基因到全染色体效应。