渗入是一个广泛的进化过程,导致基因组不同部分之间的系统发育不一致,特别是在线粒体和基于核的系统发育重建之间(例如,米托核不一致)。这里,我们使用mtDNA和全基因组核位点提供了第一个基于系统基因组的假设,该假设涉及killifish属Kryptolebias内的进化关系。此外,鉴于多次报道其成员之间进行杂交,我们测试了该属中过去基因渗入的证据。我们的mtDNA系统发育与先前为该属提出的关系基本一致。然而,我们基于核DNA的重建揭示了一个未知的谱系-Kryptolebiassp。\'ESP\'-作为自我受精的红树林灭鱼的姐妹组,K.marmoratus和K.hermaphroditus。对所有个体进行了Kryptolebiassp测序。\'ESP\'具有在雌雄同体中通常观察到的相同的mtDNA单倍型,证明了一个明显的米托核不一致的案例。我们的分析进一步证实了Kryptolebiassp之间渗入的广泛历史。“ESP”和K.雌雄同体。人口基因组学分析表明,两个谱系之间没有当前的基因流动,尽管他们目前的交换和渗入的历史。我们还证实了该属中其他物种对之间的渗入,这些物种对最近被报道形成杂种区。总的来说,我们的研究提供了涵盖大多数Kryptolebias物种的系统基因组重建,揭示了一个隐藏在mito核不一致案例中的新血统,并提供了该属中祖先渗入的多个事件的证据。这些发现强调了在系统发育框架中研究不同基因组信息的重要性,特别是在类群中,在性多样化的红树林中,渗入很常见。
Introgression is a widespread evolutionary process leading to phylogenetic inconsistencies among distinct parts of the genomes, particularly between mitochondrial and nuclear-based phylogenetic reconstructions (e.g., mito-nuclear discordances). Here, we used mtDNA and genome-wide nuclear sites to provide the first phylogenomic-based hypothesis on the evolutionary relationships within the killifish genus Kryptolebias. In addition, we tested for evidence of past introgression in the genus given the multiple
reports of undergoing hybridization between its members. Our mtDNA phylogeny generally agreed with the relationships previously proposed for the genus. However, our reconstruction based on nuclear DNA revealed an unknown lineage - Kryptolebias sp. \'ESP\' - as the sister group of the self-fertilizing mangrove killifishes, K. marmoratus and K. hermaphroditus. All individuals sequenced of Kryptolebias sp. \'ESP\' had the same mtDNA haplotype commonly observed in K. hermaphroditus, demonstrating a clear
case of mito-nuclear discordance. Our analysis further confirmed extensive history of introgression between Kryptolebias sp. \'ESP\' and K. hermaphroditus. Population genomics analyses indicate no current gene flow between the two lineages, despite their current sympatry and history of introgression. We also confirmed introgression between other species pairs in the genus that have been recently reported to form hybrid zones. Overall, our study provides a phylogenomic reconstruction covering most of the Kryptolebias species, reveals a new lineage hidden in a
case of mito-nuclear discordance, and provides evidence of multiple events of ancestral introgression in the genus. These findings underscore the importance of investigating different genomic information in a phylogenetic framework, particularly in taxa where introgression is common as in the sexually diverse mangrove killifishes.