撒哈拉以南黑腹果蝇的种群基因组学：非洲多样性和非非洲混合
Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture
摘要：
我们报道了139株野生型D. melanogaster，代表了来自该物种撒哈拉以南祖先范围的22个种群样本，以及一个欧洲种群。大多数基因组测序超过25倍深度从单倍体胚胎。结果表明，在许多非洲人口的非非洲混合物的普遍影响，激励开发和应用一种新的混合物检测方法。混合比例各不相同的人口，更大的混合物在城市地区。混合物水平在基因组中也不同，局部峰和谷表明非中性渐渗过程。来自同一地点的基因组在血统上存在明显差异，这表明非洲人群中可能存在隔离机制。在去除pupelium混合基因组片段后，在南部非洲（例如赞比亚）观察到最大的遗传多样性〈动〉<动>，而其他种群的多样性在很大程度上与从这一潜在祖先区域的地理扩张相一致。欧洲人口显示不同程度的多样性减少每个染色体臂，和一些非洲人口显示染色体臂特异性多样性减少。欧洲样本中的倒位与染色体臂多样性的强烈升高有关。进行基因组扫描以鉴定可能代表阳性选择靶的基因座。在基因调控中具有不同作用的基因附近有不成比例数量的候选选择性扫描区。欧洲-非洲FST的离群值被发现富集在局部升高的世界性混合物的基因组区域中，这可能反映了其中一些基因座在驱动非非洲等位基因渗入非洲人群中的作用。
英文摘要：
(ABRIDGED) We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa FST were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations.
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