Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are therefore critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between two proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.

中文翻译：

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博物馆基因组学揭示了灭绝的火山口湖特有的混合起源


火山口湖鱼类是常见的进化模型系统，最近的研究表明基因流在促进快速适应和物种形成方面发挥着关键作用。然而，人类造成的灭绝可能会使这些年轻湖泊的研究变得复杂。因此，博物馆基因组学方法整合最近灭绝物种的遗传数据对于理解这些脆弱系统的复杂进化历史至关重要。在这里，我们研究了一种已灭绝的南半球火山口湖特有的彩虹鱼 Melanotaeniaeachamensis 的进化历史。我们对澳大利亚阿瑟顿高原现存的彩虹鱼种群以及历史博物馆材料进行了全面采样，以了解灭绝的火山口湖种群的进化起源以及整个生态区的基因流动动态。由于历史上两个邻近的河流谱系之间的基因渗入，灭绝的火山口湖物种在遗传上与所有其他附近的种群不同，类似于其他著名的火山口湖物种形成系统，但这种历史性的基因流不足以诱导物种聚集。我们的结果表明，博物馆基因组学方法可以成功地与现存采样相结合，以揭示涉及最近灭绝物种的复杂物种形成动态。