Data from: Population genomic tests of models of adaptive radiation in Lake Victoria region cichlid fish.

Adaptive radiation is usually thought to be associated with speciation, but the evolution of intraspecific polymorphisms without speciation is also possible. The radiation of cichlid fish in Lake Victoria is perhaps the most impressive example of a recent rapid adaptive radiation, with 600+ very young species. Key questions about its origin remain poorly characterized, such as the importance of speciation versus polymorphism, whether species persist on evolutionary time scales, and if speciation happens more commonly in small isolated or in large connected populations. We used 320 individuals from 105 putative species from Lakes Victoria, Edward, Kivu, Albert, Nabugabo and Saka, in a radiation-wide AFLP genome scan to address some of these questions. We demonstrate pervasive signatures of speciation supporting the classical model of adaptive radiation associated with speciation. A positive relationship between the age of lakes and the average genomic differentiation of their species, and a significant fraction of molecular variance explained by above-species level taxonomy suggest the persistence of species on evolutionary time scales, with radiation through sequential speciation rather than a single starburst. Finally the large gene diversity retained from colonization to individual species in every radiation suggests large effective population sizes and makes speciation in small geographical isolates unlikely.

适应辐射（Adaptive radiation）通常被认为与物种形成紧密相关，但无需物种形成的种内多态性演化同样具备可行性。维多利亚湖慈鲷的适应辐射或许是近期快速适应辐射最具代表性的例证，其衍生出600余个极为年轻的物种。目前关于该辐射演化起源的核心问题仍未得到充分阐释，例如物种形成与种内多态性的相对重要性、物种能否在演化时间尺度上持续存续，以及物种形成更易发生在小型地理隔离种群还是大型连通种群中。
我们采集了来自维多利亚湖、爱德华湖、基伍湖、艾伯特湖、纳布加博湖与萨卡湖的105个推定物种的320个个体，通过全辐射范围的AFLP（扩增片段长度多态性，Amplified Fragment Length Polymorphism）基因组扫描来解答上述部分问题。研究结果揭示了普遍存在的物种形成信号，佐证了与物种形成相关的经典适应辐射模型。我们发现湖泊年龄与其物种种群的平均基因组分化程度呈正相关，且物种以上分类阶元可解释相当比例的分子变异方差，这表明物种可在演化时间尺度上持续存续，该辐射演化是通过连续的物种形成过程实现的，而非单次爆发式起源。最后，各辐射类群从定殖事件到单个物种均保留了较高的基因多样性，这暗示了较大的有效种群大小，也说明在小型地理隔离种群中发生物种形成的可能性极低。