McCluskey Braedan M, Batzel Peter, Postlethwait John H
Minnesota Supercomputing Institute, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA.
Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
G3 (Bethesda). 2025 Feb 5;15(2). doi: 10.1093/g3journal/jkae299.
Since the description of zebrafish (Danio rerio) in 1822, the identity of its closest living relative has been unclear. To address this problem, we sequenced the exomes of 10 species in genus Danio, using the closely related Devario aequipinnatus as outgroup, to infer relationships across the 25 chromosomes of the zebrafish genome. The majority of relationships within Danio were remarkably consistent across all chromosomes. Relationships of chromosome segments, however, depended systematically upon their genomic location within zebrafish chromosomes. Regions near chromosome centers identified Danio kyathit and/or Danio aesculapii as the closest relative of zebrafish, while segments near chromosome ends supported only D. aesculapii as the zebrafish sister species. Genome-wide comparisons of derived character states revealed that danio relationships are inconsistent with a simple bifurcating species history but support an ancient hybrid origin of the D. rerio lineage by homoploid hybrid speciation. We also found evidence of more recent gene flow limited to the high recombination ends of chromosomes and several megabases of chromosome 20 with a history distinct from the rest of the genome. Additional insights gained from incorporating genome structure into a phylogenomic study demonstrate the utility of such an approach for future studies in other taxa. The multiple genomic histories of species in the genus Danio have important implications for comparative studies in these morphologically varied and beautiful species and for our understanding of the hybrid evolutionary history of zebrafish.
自1822年斑马鱼（Danio rerio）被描述以来，其现存最近亲缘物种的身份一直不明。为解决这一问题，我们对斑马鱼属的10个物种的外显子组进行了测序，并以亲缘关系较近的似等鳍波鱼（Devario aequipinnatus）作为外类群，以推断斑马鱼基因组25条染色体间的关系。斑马鱼属内的大多数关系在所有染色体上都非常一致。然而，染色体片段的关系系统地取决于它们在斑马鱼染色体中的基因组位置。靠近染色体中心的区域确定加氏波鱼（Danio kyathit）和/或埃氏波鱼（Danio aesculapii）是斑马鱼的最亲近亲缘物种，而靠近染色体末端的片段仅支持埃氏波鱼作为斑马鱼的姐妹物种。对衍生性状状态的全基因组比较表明，波鱼属的关系与简单的二叉分支物种历史不一致，但支持通过同倍体杂交物种形成的斑马鱼谱系的古老杂交起源。我们还发现了更近期基因流的证据，其仅限于染色体的高重组末端以及20号染色体上几个兆碱基的区域，其历史与基因组的其他部分不同。将基因组结构纳入系统发育基因组学研究中获得的其他见解证明了这种方法对未来其他分类群研究的实用性。斑马鱼属物种的多种基因组历史对这些形态多样且美丽的物种的比较研究以及我们对斑马鱼杂交进化历史的理解具有重要意义。
