Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where species numbers and phenotypic divergence in two closely related lineages are notably different. We investigated one such natural experiment using two de novo assembled and 40 resequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; nonradiating), have resulted in such disparate evolutionary outcomes. Although both lineages inhabit many of the same Nicaraguan lakes, whole‐genome inferred demography suggests that priority effects are not likely to be the cause of the dissimilarities. Also, genome‐wide levels of selection, transposable element dynamics, gene family expansion, major chromosomal rearrangements and the number of genes under positive selection were not markedly different between the two lineages. To more finely investigate particular subsets of the genome that have undergone adaptive divergence in Midas cichlids, we also examined if there was evidence for ‘molecular pre‐adaptation’ in regions identified by QTL mapping of repeatedly diverging adaptive traits. Although most of our analyses failed to pinpoint substantial genomic differences, we did identify functional categories containing many genes under positive selection that provide candidates for future studies on the propensity of Midas cichlids to radiate. Our results point to a disproportionate role of local, rather than genome‐wide factors underlying the propensity for these cichlid fishes to adaptively radiate.

中文翻译：

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火山口湖慈鲷鱼适应性辐射的比较基因组景观

从生态机会到基因组组成的各种因素可以解释为什么只有一些谱系形成适应性辐射。虽然罕见，但特定系统可以在相同的生态环境中提供自然实验，其中两个密切相关的谱系的物种数量和表型差异显着不同。我们使用两个从头组装和 40 个重新测序的基因组研究了一个这样的自然实验，并询问为什么两个密切相关的新热带慈鲷鱼谱系，Amphilophus citrinellus物种复合体（Midas cichlids；radiating）和Archocentrus centrarchus(Flyer cichlid; nonradiating)，导致了如此不同的进化结果。尽管两个谱系都居住在许多相同的尼加拉瓜湖泊中，但全基因组推断的人口统计学表明，优先效应不太可能是造成差异的原因。此外，两个谱系之间的全基因组选择水平、转座因子动态、基因家族扩展、主要染色体重排和正选择下的基因数量没有显着差异。为了更精细地研究在 Midas 慈鲷发生适应性分化的特定基因组子集，我们还检查了在通过重复分化适应性特征的 QTL 定位确定的区域中是否存在“分子预适应”的证据。尽管我们的大多数分析未能确定实质性的基因组差异，我们确实确定了包含许多正选择基因的功能类别，这些基因为未来对 Midas 慈鲷辐射倾向的研究提供了候选者。我们的结果表明，这些丽鱼科鱼类适应性辐射的倾向背后，是局部因素而非全基因组因素的不成比例作用。