Data from: Diabolical survival in Death Valley: recent pupfish colonization, gene flow, and genetic assimilation in the smallest species range on earth

One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis, survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 U.S. Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of over 13,000 loci to infer the demographic history of pupfishes in Death Valley. Instead of relicts isolated 2-3 Mya throughout repeated flooding of the entire region by inland seas as currently believed, we present evidence for frequent gene flow among Death Valley pupfish species and divergence after the most recent flooding 13 kya. We estimate that Devils Hole was colonized by pupfish between 105 – 830 years ago, followed by genetic assimilation of pelvic fin loss and recent gene flow into neighboring spring systems. Our results provide a new perspective on an iconic endangered species using the latest population genomic methods and support an emerging consensus that timescales for speciation are overestimated in many groups of rapidly evolving species.

作为全球最濒危的脊椎动物之一，魔洞鳉（Cyprinodon diabolis）存活于近乎绝境的环境中：位于地球最热沙漠——死亡谷内的一处狭窄地下裂隙。
该物种因1976年具有里程碑意义的美国最高法院案件（确认联邦政府对其独特栖息地的地下水使用权），成为了保护领域的标志性物种。然而，关于该物种仍有一个悬而未决的核心问题：魔洞鳉在这如同地狱般的极端环境中已存续了多久？
本研究利用针对超过13000个基因座（locus，复数形式为loci）的下一代测序（next-generation sequencing）技术，推断死亡谷内鳉鱼的种群历史。现有观点认为，整个区域曾多次被内陆海泛滥，该区域的鳉鱼类群于200万至300万年前（Mya，million years ago）成为孤立的孑遗种群；但本研究的证据表明，死亡谷内的鳉鱼物种间存在频繁的基因交流，且其分化发生在最近一次内陆海泛滥后的13000年前（kya，thousand years ago）。
我们估算得出，魔洞于105至830年前被鳉鱼定植，随后发生了骨盆鳍缺失的遗传同化过程，且近期仍有基因流入周边的泉水生态系统。
本研究借助最新的种群基因组学方法，为这一标志性濒危物种提供了全新的研究视角，同时也佐证了一个渐成共识的观点：在众多快速演化的物种类群中，物种形成的时间尺度被高估了。