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.

伴基因流的物种形成模型已证实，在基因流存在的情况下，异型染色体构型间的重组抑制可促进局部适应性基因的固定，并推动物种形成。然而，学界长期难以通过实验验证两个关键问题：一是染色体倒位（inversion）确实能够降低基因流，二是这些倒位起源于物种分化起始阶段或分化后不久，而非源自祖先多态性（ancestral polymorphism）。本研究针对一对嗜仙人掌果蝇——莫哈韦果蝇（Drosophila mojavensis）与亚利桑那果蝇（Drosophila arizonae）的全基因组数据展开分析。二者在野外存在生殖隔离，且在三条染色体上存在多处大片段染色体倒位差异。研究团队发现，相较于共线性染色体（colinear chromosome），发生重排的染色体的分化程度更高。基于短序列模块（short sequence block）内的分化位点（divergent site）密度，我们拟合了一系列物种分化的显式模型：该模型设定基因流仅局限于分化后的初始阶段，且基因组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，莫哈韦果蝇与亚利桑那果蝇曾经历分化后基因流，该基因流于约27万年前终止，且在携带固定染色体倒位的染色体中显著减弱。此外，本研究证实这些染色体倒位大概率起源于物种分化时期，这与伴基因流的物种形成理论模型相符。