Talavera Adrián, Palmada-Flores Marc, Martínez-Freiría Fernando, Mochales-Riaño Gabriel, Burriel-Carranza Bernat, Estarellas Maria, Fernández-Guiberteau Daniel, Camina Álvaro, Ursenbacher Sylvain, Vörös Judit, Halpern Bálint, Pla Davinia, Calvete Juan José, Mikheyev Alexander S, Marquès-Bonet Tomàs, Carranza Salvador
Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
CREAF, Cerdanyola del Vallès, Catalonia, Spain.
Mol Ecol. 2025 Jul 12:e70019. doi: 10.1111/mec.70019.
Snake genomes attract significant attention from multiple disciplines, including medicine, drug bioprospection, and evolutionary biology. However, genomic research within the Viperidae family has mostly focused on the subfamily Crotalinae, while the true vipers (Viperinae) have largely been overlooked. European vipers (Vipera) have been the subject of extensive research due to their phylogeographic and ecological diversification, as well as their venoms. Nevertheless, phylogeography and systematics in this genus have primarily relied on biased information from mitochondrial genes, which fail to capture the likely effects of introgression and are prone to biases. On the other hand, venom research in this group has been conducted predominantly through proteomics alone. In this study, we generated chromosome-level genome assemblies for three Vipera species and whole-genome sequencing data for 94 samples representing 15 Vipera lineages. This comprehensive dataset allowed us to disentangle the phylogenomic relationships of this genus, affected by mito-nuclear discordance and pervaded by ancestral introgression. Population-level analyses in the Iberian Peninsula, where the three oldest lineages within Vipera meet, revealed signals of recent adaptive introgression between old-diverged and ecologically dissimilar species, whereas chromosomal rearrangements isolate species occupying similar niches. Finally, using transcriptomic and proteomic data, we characterised the Vipera toxin-encoding genes, in which opposing selective forces were unveiled as common drivers of the evolution of venom as an integrated phenotype.
蛇类基因组吸引了包括医学、药物生物勘探和进化生物学在内的多个学科的广泛关注。然而，蝰蛇科的基因组研究主要集中在蝮亚科，而真正的蝰蛇（蝰亚科）在很大程度上被忽视了。欧洲蝰蛇（蝰属）由于其系统地理学和生态多样性以及毒液，一直是广泛研究的对象。然而，该属的系统地理学和系统分类主要依赖于线粒体基因的有偏差信息，这些信息无法捕捉基因渗入的可能影响，并且容易产生偏差。另一方面，该类群的毒液研究主要仅通过蛋白质组学进行。在本研究中，我们为三种蝰蛇物种生成了染色体水平的基因组组装，并为代表15个蝰蛇谱系的94个样本生成了全基因组测序数据。这个全面的数据集使我们能够理清该属的系统发育关系，这种关系受到线粒体-核不一致的影响，并普遍存在祖先基因渗入现象。在伊比利亚半岛进行的种群水平分析中，蝰属中三个最古老的谱系在此交汇，结果揭示了在分化时间久且生态不同的物种之间近期适应性基因渗入的信号，而染色体重排则将占据相似生态位的物种隔离开来。最后，利用转录组学和蛋白质组学数据，我们对蝰蛇毒素编码基因进行了表征，其中发现相反的选择力量是毒液作为一种综合表型进化的常见驱动因素。
