State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
College of Life Sciences and Food Engineering, Yibin University, Yibin, China.
Mol Phylogenet Evol. 2020 Jul;148:106807. doi: 10.1016/j.ympev.2020.106807. Epub 2020 Apr 5.
Snakes are one of the most diverse groups of terrestrial vertebrates, with approximately 3500 extant species. A robust phylogeny and taxonomy of snakes is crucial for us to know, study and protect them. For a large group such as snakes, broad-scale phylogenetic reconstructions largely rely on data integration. Increasing the compatibility of the data from different researches is thus important, which can be facilitated by standardization of the loci used in systematic analyses. In this study, we proposed a unified multilocus marker system for snake systematics by conflating 5 mitochondrial markers, 19 vertebrate-universal nuclear protein coding (NPC) markers and 72 snake-specific noncoding intron markers. This marker system is an addition to the large squamate conserved locus set (SqCL) for studies preferring a medium-scale data set. We applied this marker system to over 440 snake samples and constructed the currently most comprehensive systematic framework of the snakes in China. Robust snake phylogenetic relationships were recovered at both deep and shallow evolutionary depths, demonstrating the usefulness of this multilocus marker system. Discordance was revealed by a parallel comparison between the snake tree based on the multilocus marker system and that based on only the mitochondrial loci, highlighting the necessity of using multiple types of markers to better understand the snake evolutionary histories. The divergence times of different snake groups were estimated with the nuclear data set. Our comprehensive snake tree not only confirms many important nodes inferred in previous studies but also contributes new insights into many snake phylogenetic relationships. Suggestions are made for the current Chinese snake taxonomy.
蛇是陆地脊椎动物中最多样化的群体之一，现存约有 3500 种。构建蛇类稳健的系统发育和分类学对于我们了解、研究和保护它们至关重要。对于蛇类这样的大群体，广泛的系统发育重建在很大程度上依赖于数据整合。因此，提高来自不同研究的数据兼容性非常重要，这可以通过标准化系统分析中使用的基因座来实现。在这项研究中，我们通过合并 5 个线粒体标记物、19 个脊椎动物通用核蛋白编码（NPC）标记物和 72 个蛇特异性非编码内含子标记物，提出了一个用于蛇类系统发育的统一多基因座标记系统。这个标记系统是大型有鳞目动物保守基因座集（SqCL）的补充，用于研究中更喜欢中等数据集的情况。我们将这个标记系统应用于 440 多个蛇样本，并构建了目前中国最全面的蛇类系统发育框架。在深度和浅层进化深度都恢复了稳健的蛇类系统发育关系，证明了这个多基因座标记系统的有效性。通过多基因座标记系统构建的蛇类系统发育树与仅基于线粒体基因座构建的蛇类系统发育树之间的平行比较揭示了分歧，强调了使用多种类型的标记物来更好地理解蛇类进化历史的必要性。利用核数据集估计了不同蛇类群体的分歧时间。我们的综合蛇类系统发育树不仅证实了以前研究中推断出的许多重要节点，还为许多蛇类系统发育关系提供了新的见解。为当前中国蛇类分类学提出了建议。
