Data from: Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next-generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non-cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.

自然界中最著名的同域物种形成（sympatric speciation）范例之一，是喀麦隆火山口湖特有分布的丽鱼科鱼类（cichlid fishes）单系辐射（monophyletic radiations）类群。然而，针对单系性（monophyly）的系统发育推断（phylogenetic inference），可能无法检测到包含部分异域隔离（allopatric isolation）的复杂定殖历史——例如被全基因组基因流（genome-wide gene flow）掩盖的双次入侵事件。在此类场景下，种群基因组学方法更适合验证同域物种形成的相关假说。本研究对喀麦隆境内所有4个同域分布的火山口湖丽鱼科鱼类辐射类群，以及全非洲的外类群（outgroups）进行了全面采样，并结合下一代测序（next-generation sequencing）技术对数万个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）进行基因分型。我们发现大量证据表明，在初始定殖后，这4个辐射类群均与邻近的河川种群之间存在基因流。在部分案例中，部分同域分布物种与外类群的亲缘关系较其他物种更近，这与二次基因流促进其物种形成的结论相符。本研究结果并未否定喀麦隆丽鱼科鱼类存在同域物种形成的可能，反而揭示了伴随基因流的复杂物种形成历史——其中包含异域与同域两个阶段，最终同时形成了生殖隔离的物种与处于初期分化的物种复合体。目前尚存的最佳非丽鱼科同域物种形成范例，均涉及微生境内部的选型交配（assortative mating）。我们推测，该特征或许是自然界中完成同域物种形成过程的必要条件。