Museum genomics reveals the hybrid origin of an extinct crater lake endemic

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.

火山口湖鱼类是常见的进化研究模式系统，近期研究表明基因流在推动快速适应与物种形成中发挥关键作用。然而，针对这类年轻火山口湖的研究常因人为介导的灭绝而变得复杂。因此，整合近期灭绝物种遗传数据的博物馆基因组学方法，对于解析这些脆弱生态系统的复杂演化历史至关重要。
本研究聚焦于一种已灭绝的南半球火山口湖特有虹银汉鱼——埃查姆虹银汉鱼（Melanotaenia eachamensis）的演化历史。我们对澳大利亚阿瑟顿台地现存的虹银汉鱼种群开展了全面采样，并结合历史博物馆馆藏标本，以解析该灭绝火山口湖种群的演化起源，以及该生态区域内的基因流动态。
该灭绝火山口湖物种与所有邻近种群均存在遗传分化，其成因是两个近缘河流支系间的历史基因渐渗——这与其他典型火山口湖物种形成系统类似，但此次历史基因流并未足以形成物种集群。
我们的研究结果表明，博物馆基因组学方法可与现存种群采样相结合，成功解析涉及近期灭绝物种的复杂物种形成动态。