Data from: Genomic signatures of divergent selection and speciation patterns in a 'natural experiment', the young parallel radiations of Nicaraguan crater lake cichlid fishes

Divergent selection is the main driving force in sympatric ecological speciation and may also play a strong role in divergence between allopatric populations. Characterizing the genome-wide impact of divergent selection constitutes often a first step in the process of unraveling the genetic bases underlying adaptation and ecological speciation. The Midas cichlid fish (Amphilophus citrinellus) species complex in Nicaragua is a powerful system for studying evolutionary processes. Independent colonizations of isolated young crater lakes by Midas cichlid populations from the older and great lakes of Nicaragua resulted in the repeated evolution of adaptive radiations by intralacustrine sympatric speciation. In this study we performed genome scans on two repeated radiations of crater lake species and their great lake source populations (1030 polymorphic AFLPs, n ≈ 30 individuals per species). We detected regions under divergent selection (0.3 % in the crater lake Xiloá flock and 1.7 % in the older crater lake Apoyo radiation) that might be responsible for the sympatric diversification. We find no evidence that the same genomic regions have been involved across crater lake flocks. The data provide evidence, however, for some genetic parallelism (seven out of 51 crater lake to great lake outlier loci are shared; 13.7%) associated with the allopatric divergence of both crater lake flocks. Furthermore, our results suggest that the number of outlier loci involved in sympatric and allopatric divergence increases with time. A phylogeny based on our data clearly supports the monophyly of both crater lake species flocks and provides evidence for a parallel branching order with a primary divergence along the limnetic-benthic axis in both radiations.

分歧选择（Divergent selection）是同域生态物种形成（sympatric ecological speciation）的主要驱动力，同时也可对异域种群（allopatric populations）间的分化发挥重要作用。解析分歧选择的全基因组（genome-wide）影响，通常是阐明适应与生态物种形成背后遗传基础的首要步骤。尼加拉瓜的迈达斯慈鲷（Amphilophus citrinellus）物种复合体是研究进化过程的高效模型体系。来自尼加拉瓜大型古老湖泊的迈达斯慈鲷种群，独立定殖了孤立的年轻火山口湖，由此通过湖内同域物种形成（intralacustrine sympatric speciation）反复演化出适应辐射（adaptive radiations）类群。本研究对两类重复演化的火山口湖物种群及其大型湖泊源种群开展了全基因组扫描（genome scans），共检测到1030个多态性扩增片段长度多态性（Amplified Fragment Length Polymorphism，AFLPs），每个物种的采样个体数约为30。我们在受分歧选择作用的基因组区域中发现了可能参与同域分化的位点：希洛阿火山口湖物种群中此类区域占比0.3%，阿波约较古老火山口湖辐射类群中占比1.7%。未发现不同火山口湖物种群共享相同基因组区域的证据。然而，数据显示两类火山口湖物种群的异域分化存在一定遗传平行性：51个火山口湖-大型湖泊异常位点（outlier loci）中有7个被共享，占比达13.7%。此外，研究结果表明参与同域与异域分化的异常位点数量随时间推移而增加。基于本研究数据构建的系统发育树明确支持两类火山口湖物种群均为单系群（monophyly），并证实两类辐射类群存在平行的分支顺序，二者均沿浮游-底栖轴（limnetic-benthic axis）发生了初始分化。