The Genomics of Speciation in <em>Drosophila</em>: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

In nature, closely related species may hybridize while still retaining their distinctive identities. Chromosomal regions that experience reduced recombination in hybrids, such as within inversions, have been hypothesized to contribute to the maintenance of species integrity. Here, we examine genomic sequences from closely related fruit fly taxa of the Drosophila pseudoobscura subgroup to reconstruct their evolutionary histories and past patterns of genic exchange. Partial genomic assemblies were generated from two subspecies of Drosophila pseudoobscura (D. ps.) and an outgroup species, D. miranda. These new assemblies were compared to available assemblies of D. ps. pseudoobscura and D. persimilis, two species with overlapping ranges in western North America. Within inverted regions, nucleotide divergence among each pair of the three species is comparable, whereas divergence between D. ps. pseudoobscura and D. persimilis in non-inverted regions is much lower and closer to levels of intraspecific variation. Using molecular markers flanking each of the major chromosomal inversions, we identify strong crossover suppression in F1 hybrids extending over 2 megabase pairs (Mbp) beyond the inversion breakpoints. These regions of crossover suppression also exhibit the high nucleotide divergence associated with inverted regions. Finally, by comparison to a geographically isolated subspecies, D. ps. bogotana, our results suggest that autosomal gene exchange between the North American species, D. ps. pseudoobscura and D. persimilis, occurred since the split of the subspecies, likely within the last 200,000 years. We conclude that chromosomal rearrangements have been vital to the ongoing persistence of these species despite recent hybridization. Our study serves as a proof-of-principle on how whole genome sequencing can be applied to formulate and test hypotheses about species formation in lesser-known non-model systems.在自然界中，亲缘关系较近的物种可发生杂交，同时仍能维持各自独特的物种身份。有假说指出，杂种中重组率降低的染色体区域（例如倒位（inversion）区域），可助力维持物种的完整性。本研究对拟暗果蝇类群（Drosophila pseudoobscura subgroup）内亲缘关系相近的果蝇类群的基因组序列展开分析，以重构其演化历史以及过往的基因交流模式。我们对拟暗果蝇（Drosophila pseudoobscura）的两个亚种以及外类群（outgroup）物种miranda果蝇（Drosophila miranda）进行了部分基因组组装。将这些新获得的组装结果与已公开的拟暗果蝇指名亚种（D. ps. pseudoobscura）和仿拟暗果蝇（Drosophila persimilis）的基因组组装进行比对，这两个物种在北美西部有着重叠的分布范围。在倒位区域内，三个物种每两者之间的核苷酸分歧（nucleotide divergence）水平相当；而在非倒位区域，拟暗果蝇指名亚种与仿拟暗果蝇之间的核苷酸分歧水平要低得多，且更接近种内变异（intraspecific variation）的水平。我们利用每个主要染色体倒位侧翼的分子标记，发现F1杂种中存在显著的交叉抑制（crossover suppression）现象，其抑制范围可延伸至倒位断点之外超过2兆碱基对（Mbp）。这些交叉抑制区域同样表现出与倒位区域相关的高核苷酸分歧水平。最后，通过与地理隔离的亚种——拟暗果蝇波哥大亚种（D. ps. bogotana）进行比对，我们的研究结果表明，北美地区的拟暗果蝇指名亚种与仿拟暗果蝇之间曾发生常染色体基因交流（autosomal gene exchange），这一事件发生在亚种分化之后，时间大概率距今不超过20万年。我们得出结论：尽管近期发生了杂交，染色体重排对于这些物种的持续存续至关重要。本研究为如何将全基因组测序（whole genome sequencing）应用于构建并验证鲜为人知的非模式系统中的物种形成假说提供了原理验证（proof-of-principle）范例。