Richards Emilie J, Martin Christopher H
Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
PLoS Genet. 2017 Aug 10;13(8):e1006919. doi: 10.1371/journal.pgen.1006919. eCollection 2017 Aug.
Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of variants fixed between specialist species lie in regions with discordant topologies. Top candidate adaptive introgression regions include signatures of selective sweeps and adaptive introgression of genetic variation from a single population in the northwestern Bahamas into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador Island contributed 5 times more to speciation of trophic specialists than adaptive introgression of Caribbean genetic variation; however, four of the 11 introgressed regions came from a single distant island and were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador Island specialist from an island 300 km away approximately 10 kya. The complex emerging picture of the origins of adaptive radiation on San Salvador Island indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive introgression, may be necessary for adaptive radiation in addition to ecological opportunity.
快速多样化通常涉及复杂的基因流历史，这些历史在基因组中留下了关于进化相关性的可变且相互冲突的特征。确定这些进化关系中变异的程度和来源，可以深入了解快速辐射所涉及的进化机制。在这里，我们比较了巴哈马圣萨尔瓦多岛特有的鲤齿鳉属 pupfishes 同域适应性辐射中的42个全基因组以及几个外群 pupfish 物种中与物种表型相关的不一致进化关系，以便了解这些营养特化物种在鲤齿鳉属更大辐射范围内的稀有性。82%的基因组显示圣萨尔瓦多岛物种之间存在密切的进化关系，这反映了它们在地理上的接近性，但特化物种之间固定的绝大多数变异位于拓扑结构不一致的区域。顶级候选适应性渐渗区域包括选择性清除的特征以及来自巴哈马西北部单个种群的遗传变异向每个特化物种的适应性渐渗。圣萨尔瓦多岛遗传变异的硬选择性清除对营养特化物种形成的贡献是加勒比遗传变异适应性渐渗的5倍；然而，11个渐渗区域中的4个来自一个遥远的岛屿，并且与辐射范围内口腔颌骨分化的主轴相关。例如，一个已知对颌骨大小有影响的原癌基因（ski）的现存变异大约在10000年前从300公里外的一个岛屿渐渗到一个圣萨尔瓦多岛特化物种中。圣萨尔瓦多岛适应性辐射起源的复杂新情况表明，多种遗传变异来源促成了该岛上新型营养特化物种的适应性表型。我们的研究结果表明，除了生态机会外，包括罕见的适应性渐渗在内的一系列因素可能是适应性辐射所必需的。
