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.适应性辐射（Adaptive radiation）通常被认为与物种形成（speciation）相关，但不伴随物种形成的种内多态性（intraspecific polymorphisms）演化同样可能发生。维多利亚湖慈鲷的适应性辐射或许是近期快速适应性辐射最具代表性的实例，其包含600余个极为年轻的物种。关于该辐射起源的关键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、物种能否在进化时间尺度上持续存在，以及物种形成更易发生在小型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、阿尔伯特湖、纳布加博湖与萨卡湖的105个推定物种的320个个体，通过全辐射类群范围的扩增片段长度多态性（Amplified Fragment Length Polymorphism, AFLP）基因组扫描来解答其中部分问题。研究证实了广泛存在的物种形成相关分子信号，为与物种形成耦合的经典适应性辐射模型提供了支撑。湖泊形成年代与该湖物种的平均基因组分化水平呈正相关，且物种以上分类阶元可解释显著比例的分子变异量，这表明物种能够在进化时间尺度上持续存在，该辐射过程是通过连续物种形成而非单次爆发式事件完成的。最后，各辐射支系从初始定殖到各单一物种均保留了较高的基因多样性，这表明其有效种群规模较大，同时也说明在小型地理隔离种群中发生物种形成的可能性较低。