Data from: Model-based comparisons of phylogeographic scenarios resolve the intraspecific divergence of cactophilic Drosophila mojavensis

The cactophilic fly Drosophila mojavensis exhibits considerable intraspecific genetic structure across allopatric geographic regions and shows associations with different host cactus species across its range. The divergence between these populations has been studied for more than 60 years, yet their exact historical relationships have not been resolved. We analysed sequence data from 15 intronic X-linked loci across populations from Baja California, mainland Sonora-Arizona and Mojave Desert regions under an isolation-with-migration model to assess multiple scenarios of divergence. We also compared the results with a pre-existing sequence dataset of 8 autosomal loci. We derived a population tree with Baja California placed at its base and link their isolation to Pleistocene climatic oscillations. Our estimates suggest the Baja California population diverged from an ancestral Mojave Desert/mainland Sonora-Arizona group around 230-270 Kya, while the split between the Mojave Desert and mainland Sonora-Arizona populations occurred one glacial cycle later, 117-135 Kya years ago. Although we found these three populations to be effectively allopatric, model ranking could not rule out the possibility of a low-level of gene flow between two of them. Finally, the Mojave Desert population showed a small effective population size, consistent with a historical population bottleneck. We show that model-based inference from multiple loci can provide accurate information on the historical relationships of closely related groups allowing us to set into historical context a classic system of incipient ecological speciation.嗜仙人掌莫哈韦果蝇（Drosophila mojavensis）在异域地理区域中展现出显著的种内遗传结构，且在其分布范围内与不同宿主仙人掌物种形成稳定关联。该类群的种群分化研究已逾60年，但其确切的历史亲缘关系仍未得到明确解析。我们基于隔离与迁移模型（isolation-with-migration model），对下加利福尼亚、索诺拉-亚利桑那大陆以及莫哈韦沙漠种群的15个X连锁内含子基因座的序列数据开展分析，以评估多种分化情景。同时，我们将本次分析结果与已有的8个常染色体基因座序列数据集进行对比。本研究构建了种群系统发育树，显示下加利福尼亚种群位于该树的基部，并将该种群的隔离事件与更新世气候振荡相关联。估算结果表明，下加利福尼亚种群与祖先莫哈韦沙漠/索诺拉-亚利桑那大陆种群的分化时间约为230–270千年前（Kya）；而莫哈韦沙漠种群与索诺拉-亚利桑那大陆种群的分化则晚了一个冰期周期，发生在117–135千年前（Kya）。尽管我们发现这三个种群实质上处于异域分布状态，但模型排序分析无法排除其中两个种群间存在低水平基因交流的可能性。最后，莫哈韦沙漠种群的有效种群规模较小，这与历史上发生过的种群瓶颈效应相符。本研究证实，基于多基因座的模型推断能够为近缘类群的历史亲缘关系提供精准信息，从而帮助我们将这一典型的初期生态物种形成研究系统置于具体的历史背景之中。