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Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations

机译:西欧果蝇自然种群中本地适应的全基因组模式。

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摘要

Signatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, several studies based mainly in North American populations showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection might be challenging when analyzing these populations. European populations could help identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden) and Castellana Grotte (Southern Italy). We found low levels of population structure and no evidence of recent African admixture in these two populations. We thus look for patterns of spatially varying selection affecting individual genes and gene sets. Besides single nucleotide polymorphisms, we also investigated the role of transposable elements in local adaptation. We concluded that European populations are a good dataset to identify candidate loci under spatially varying selection. The analysis of the two populations sequenced in this work in the context of all the available D. melanogaster data allowed us to pinpoint genes and biological processes likely to be relevant for local adaptation. Identifying and analyzing populations with low levels of population structure and admixture should help to disentangle selective from non-selective forces underlying patterns of population differentiation in other species as well.
机译:在几种生物中,已在基因组和转录组水平研究了空间变化选择的特征。在果蝇中,大多数研究都对北美和澳大利亚种群进行了分析,从而确定了几个正在选择的基因座和性状。但是,一些主要基于北美人口的研究表明,混合的证据可能有助于观察到的人口分化模式。因此,在分析这些人群时,将人口统计学与选择区分开可能是一个挑战。欧洲人口可以帮助根据空间变化的选择来识别基因座,前提是不会出现非洲人口最近的混杂情况。在这项工作中,我们分别对在相反环境下从种群中收集的42种欧洲菌株的基因组进行测序:斯德哥尔摩(瑞典)和卡斯特拉纳·格罗特(Castellana Grotte)(意大利南部)。我们发现人口结构水平低,没有证据表明这两个人口中最近有非洲混血。因此,我们寻找影响单个基因和基因组的空间变化选择模式。除了单核苷酸多态性,我们还研究了转座因子在局部适应中的作用。我们得出的结论是,欧洲人口是识别在空间变化选择下的候选基因座的良好数据集。在所有可用的D. melanogaster数据的背景下,对这项工作中测序的两个种群的分析使我们能够查明可能与局部适应有关的基因和生物学过程。鉴定和分析种群结构和混合水平较低的种群也应有助于使选择与其他物种的种群分化模式背后的非选择力区分开。

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