Gresham Sophie, Rusuwa Bosco, Ngochera Maxon, Turner George F, Genner Martin J, Malinsky Milan, Svardal Hannes
Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.
Department of Biological Sciences, Chancellor College, University of Malawi, Zomba, Malawi.
Mol Ecol. 2025 Jul;34(13):e17786. doi: 10.1111/mec.17786. Epub 2025 Jun 10.
Comparative studies of whole genomes have increasingly shown that genetic introgression between closely related species is surprisingly common across the tree of life, making the description of biodiversity and understanding the process of speciation complex and challenging. The adaptive radiation of cichlid fishes in Lake Malawi, that is characterised by hybrid origins and cases of recent introgression, provides a valuable model system to study the evolutionary implications of introgression. However, many potential sources of introgression into the radiation have not yet been investigated. Here we use whole genome data from 239 species from Lake Malawi and 76 species from surrounding African river and lake systems to identify previously unknown introgression events involving the Malawi radiation. Computing genome-wide excess allele sharing (ABBA-BABA statistics) and window-based statistics, we find that three independent riverine cichlid lineages show significantly higher allele sharing with the Malawi radiation than expected, suggesting historical genetic exchange. Introgressed haplotypes are distributed relatively uniformly across the Malawi radiation, indicating that most hybrid-derived polymorphism was acquired and sorted before the formation of the contemporary Malawi radiation. Our results point towards several previously unknown contributors to the Malawi cichlid hybrid swarm and show that the history of one of the largest vertebrate radiations is more complex than previously thought.
全基因组的比较研究越来越多地表明，亲缘关系密切的物种之间的基因渐渗在整个生命之树中出奇地普遍，这使得生物多样性的描述以及对物种形成过程的理解变得复杂且具有挑战性。马拉维湖丽鱼科鱼类的适应性辐射，其特点是具有杂交起源和近期基因渐渗的情况，为研究基因渐渗的进化影响提供了一个有价值的模型系统。然而，许多可能渗入该辐射群体的潜在来源尚未得到研究。在这里，我们使用来自马拉维湖239个物种以及非洲周边河流和湖泊系统76个物种的全基因组数据，来识别涉及马拉维辐射群体的先前未知的基因渐渗事件。通过计算全基因组过量等位基因共享（ABBA - BABA统计量）和基于窗口的统计量，我们发现三个独立的河流丽鱼科谱系与马拉维辐射群体的等位基因共享显著高于预期，这表明存在历史上的基因交换。渐渗单倍型在马拉维辐射群体中相对均匀地分布，这表明大多数杂交衍生的多态性是在当代马拉维辐射群体形成之前获得并分类的。我们的结果指向了几个先前未知的对马拉维丽鱼科杂交群体有贡献的因素，并表明最大的脊椎动物辐射群体之一的历史比之前认为的更为复杂。
