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.

歧化选择（divergent selection）是同域生态成种（sympatric ecological speciation）的主要驱动力，同时也可对异域种群（allopatric populations）间的分化产生显著作用。解析歧化选择在全基因组层面的影响，往往是阐明适应与生态成种遗传基础的首要环节。
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优质模型系统。来自尼加拉瓜古老大湖的迈达斯慈鲷种群独立定殖孤立的年轻火山口湖，由此通过湖内同域成种作用反复演化出适应性辐射（adaptive radiation）。
本研究针对两批独立演化的火山口湖物种及其大湖源种群开展全基因组扫描（genome scan），共检测到1030个多态性AFLP标记，每个物种的样本量约为30个个体。我们识别出了可能参与同域多样化过程的歧化选择靶区域：希洛阿火山口湖物种群中此类区域占比0.3%，阿波约古老火山口湖辐射类群中占比1.7%。
研究未发现不同火山口湖类群共享同一基因组区域的证据。不过，本研究数据证实存在一定程度的遗传平行性：51个火山口湖与大湖的异常位点（outlier loci）中有7个被两类火山口湖类群共享（占比13.7%），该平行性与两类火山口湖类群的异域分化过程相关。
此外，研究结果显示，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的单系性，并证实两类辐射类群存在平行的分支顺序，且均以沿浮游-底栖轴（limnetic-benthic axis）的初级分化为核心特征。