Supporting data for "Genomes reveal pervasive distant hybridization in nature among cyprinid fishes"

Genomic data has unveiled a fascinating aspect of the evolutionary past, showing that the mingling of different species through hybridization has left its mark on the histories of numerous life forms. However, the relationship between hybridization events and the origins of cyprinid fishes remains unclear. <br>In this study, we generated <i>de novo</i> assembled genomes of eight cyprinid fishes and conducted phylogenetic analyses on 24 species. Widespread allele sharing across species boundaries was observed within seven subfamilies of cyprinid fishes. Interestingly, we noted conservative divergence in the testis and incomplete reproductive isolation between the herbivorous <i>Megalobrama amblycephala</i> and the carnivorous <i>Culter alburnus</i>. Significant differences in the expression of four genes (<i>dpp2, ctrl, psb7, </i> and <i>ppce</i>) in the liver and intestine, accompanied by variations in enzyme activities, indicated swift divergence in digestive enzyme secretion. Moreover, we identified introgressed genes linked to organ development in sympatric fishes with analogous feeding habits within the <i>Cultrinae</i> and <i>Leuciscinae</i> subfamilies. <br>Our findings highlight the significant role played by incomplete reproductive isolation and frequent gene flow events, particularly those associated with the development of digestive organs, in driving speciation among cyprinid fishes in diverse freshwater ecosystems.

基因组数据揭示了演化历史中一个引人入胜的层面，表明不同物种间通过杂交发生的遗传交融，已在众多生命的演化历史中留下了印记。然而，杂交事件与鲤科（Cyprinidae）鱼类的起源之间的关联仍不明晰。
本研究中，我们对8种鲤科鱼类进行了从头（de novo）组装基因组构建，并对24个物种开展了系统发育分析。我们在7个鲤科鱼类亚科中，观测到了跨物种界限的广泛等位基因共享现象。有趣的是，我们发现草食性的团头鲂（Megalobrama amblycephala）与肉食性的翘嘴鲌（Culter alburnus）之间存在保守的性腺分化以及不完全的生殖隔离。肝脏与肠道中4个基因（dpp2、ctrl、psb7及ppce）的表达量存在显著差异，同时伴随酶活性变化，这表明消化酶分泌系统发生了快速分化。此外，我们在鲌亚科（Cultrinae）和雅罗鱼亚科（Leuciscinae）中，鉴定出了与同域分布且摄食习性相似的鱼类的器官发育相关的渐渗基因。
本研究结果表明，不完全生殖隔离与频繁的基因流事件，尤其是与消化器官发育相关的基因流事件，在多样淡水生态系统中的鲤科鱼类物种形成过程中发挥了重要作用。