The transition from ‘well-marked varieties’ of a single species into ‘well-defined species’—especially in the absence of geographic barriers to gene flow (sympatric speciation)—has puzzled evolutionary biologists ever since Darwin 1 , 2 . Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process 3 . Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs 4 , but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories 5 . Here, within a young species complex of neotropical cichlid fishes ( Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry. Population genomic analyses of Midas cichlid fishes in young Nicaraguan crater lakes suggest that sympatric speciation is promoted by polygenic architectures.

中文翻译：

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同域物种形成过程中基因组分歧的对比特征


自达尔文以来，从单一物种的“明确标记的变种”到“明确定义的物种”的转变——尤其是在基因流动不存在地理障碍（同域物种形成）的情况下——一直困扰着进化生物学家 1 , 2 。基因流抵消了全基因组分化的积累，这是物种形成的标志，并增加了完成物种形成过程的不可逆生殖障碍（不相容性）进化的可能性 3 。理论预测，不同选择的性状的遗传结构可以影响同域物种形成是否发生 4 ，但该理论的实证检验很少，因为由于物种独特的生物学和进化历史，很难收集和合成跨物种的综合数据 5 。在这里，在新热带慈鲷鱼（Amphilophus spp.）的年轻物种复合体中，我们分析了种群和物种之间的基因组差异。通过生成新的基因组组装并对 453 个基因组进行重新测序，我们发现了被认为对分化很重要的性状的遗传结构。影响生态性能和/或配偶选择的单基因或寡基因性状不同的物种表现出显着的局部基因组分化。相比之下，在多基因性状上存在差异的物种之间的分化在基因组上广泛存在，并且总体上要高得多，这与有效且稳定的全基因组基因流障碍的进化相一致。因此，我们得出的结论是，简单的性状结构并不总是像之前建议的那样有利于基因流的物种形成，而多基因结构可以促进同域中快速稳定的物种形成。 对尼加拉瓜火山口湖中的弥达斯慈鲷进行的群体基因组分析表明，多基因结构促进了同域物种形成。