Data from: Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

Models of speciation-with-gene-flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here we present an analysis of whole genome data from a pair of cactophilic fruit flies, Drosophila mojavensis and D. arizonae, which are reproductively isolated in the wild and differ by several large inversions on three chromosomes. We found an increase in divergence at rearranged compared to colinear chromosomes. Using the density of divergent sites in short sequence blocks we fit a series of explicit models of species divergence in which gene flow is restricted to an initial period after divergence and may differ between colinear and rearranged parts of the genome. These analyses show that D. mojavensis and D. arizonae have experienced post-divergence gene flow which ceased around 270 KY ago and was significantly reduced in chromosomes with fixed inversions. Moreover, we show that these inversions most likely originated around the time of of species divergence which is compatible with theoretical models of speciation with gene flow.

存在基因流的物种形成（speciation-with-gene-flow）模型已证实，在基因流存在的背景下，不同染色体结构间的重组率降低可促进局部适应性基因的固定，并推动物种形成进程。然而，通过实证验证以下结论始终极具挑战：染色体倒位（inversion）确实降低了基因流，且其起源于物种分化启动之时或分化后不久，而非源自祖先多态性。本研究对一对嗜仙人掌果蝇（cactophilic fruit fly）——莫哈维果蝇（Drosophila mojavensis）与亚利桑那果蝇（Drosophila arizonae）——的全基因组数据展开分析。这两个物种在野外存在生殖隔离，且在三条染色体上存在多处大型倒位差异。研究发现，相较于共线性染色体（colinear chromosome），染色体重排区域的分化水平更高。本研究基于短序列片段内分歧位点的密度，拟合了一系列明确的物种分化模型：这些模型假定基因流仅局限于分化后的初始阶段，且基因组中共线性区域与重排区域的基因流水平可能存在差异。分析结果显示，莫哈维果蝇与亚利桑那果蝇曾经历过分化后的基因流，该基因流于约27万年前（270 KY）终止，且在携带固定倒位的染色体中，基因流水平显著降低。此外，本研究证实这些倒位极有可能起源于物种分化发生的同期，这一结果与存在基因流的物种形成理论模型相符。