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.

趋异选择 (divergent selection) 是同域生态物种形成 (sympatric ecological speciation) 的核心驱动因素，同时也可在异域种群 (allopatric populations) 的分化进程中发挥重要作用。解析趋异选择对全基因组范围的影响，通常是阐明适应与生态物种形成背后遗传基础的首要环节。尼加拉瓜地区的迈达斯慈鲷 (Midas cichlid fish, Amphilophus citrinellus) 物种复合群，是研究演化过程的极具价值的模型系统。源自尼加拉瓜大型古老湖泊的迈达斯慈鲷种群，独立定殖于孤立的年轻火山口湖后，通过湖内同域物种形成反复演化出适应性辐射。本研究针对两批独立演化的火山口湖物种群及其大型湖泊源种群开展全基因组扫描 (genome scans)，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。我们在希洛阿 (Xiloá) 火山口湖物种群中发现0.3%的基因组区域处于趋异选择作用下，在更为古老的阿波约 (Apoyo) 火山口湖辐射演化群中这一比例为1.7%；这些区域可能参与了同域物种分化过程。未发现不同火山口湖物种群共享相同受选择基因组区域的证据。不过，研究数据显示两类火山口湖物种群在异域分化过程中存在一定的遗传平行性：51个火山口湖-大型湖泊异常位点 (outlier loci) 中有7个为共享位点，占比13.7%。此外，本研究结果表明，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，明确支持两个火山口湖物种群均为单系群 (monophyly)，并证实两类辐射演化群存在平行的分支顺序，且均沿浮游-底栖生态轴 (limnetic-benthic axis) 发生初次分化。