Department of Biological Sciences, 206 Boyden Hall, Rutgers University-Newark, 195 University Ave, Newark, NJ 07102, USA.
Science and Education, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
Mol Phylogenet Evol. 2021 Jul;160:107109. doi: 10.1016/j.ympev.2021.107109. Epub 2021 Feb 18.
Mud snakes (Serpentes: Homalopsidae) are a family of 55 described, mainly aquatic, species primarily distributed throughout mainland Southeast Asia and the Indo-Australian Archipelago. Although they have been the focus of prior research, the basic relationships amongst genera and species remain poorly known. We used a combined mitochondrial and nuclear gene dataset to infer their phylogenetic relationships, using the highest levels of taxon and geographic sampling for any homalopsid phylogeny to date (62% generic and 62% species coverage; 140 individuals). Our results recover two reciprocally monophyletic groups: the fangless Brachyorrhos and its sister clade comprised of all rear-fanged homalopsids. Most genera and interspecific relationships were monophyletic and strongly supported, but intergeneric relationships and intraspecific population structure lack support. We find evidence of both undescribed diversity as well as cases of taxonomic inflation within several species. Tree-based species delimitation approaches (mPTP) support potential new candidate species as distinct from their conspecifics and also suggest that many named taxa may not be distinct species. Divergence date estimation and lineage-through-time analyses indicate lower levels of speciation in the Eocene, with a subsequent burst in diversification in the Miocene. Homalopsids may have diversified most rapidly during the Pliocene and Pleistocene, possibly in relation to tectonic shifts and sea-level fluctuations that took place in Sundaland and the Sahul Shelf. Our analyses provide new insights on homalopsid taxonomy, a baseline phylogeny for the family, and further biogeographic implications demonstrating how dynamic tectonics and Quaternary sea level changes may have shaped a widespread, diverse family of snakes.
泥蛇（Serpentes：Homalopsidae）是一个由 55 种描述的蛇类家族，主要分布在东南亚大陆和印度-澳大利亚群岛。尽管它们一直是先前研究的焦点，但属种之间的基本关系仍然知之甚少。我们使用线粒体和核基因的组合数据集来推断它们的系统发育关系，这是迄今为止任何泥蛇系统发育学中使用的最高分类和地理采样水平（62%的属和 62%的种覆盖率；140 个个体）。我们的结果恢复了两个互为单系的群：无牙的 Brachyorrhos 和由所有后齿蛇组成的姐妹群。大多数属和种间关系是单系的，并且得到了强有力的支持，但属间关系和种内种群结构缺乏支持。我们发现了未描述的多样性的证据，以及在几个物种中存在分类膨胀的情况。基于树的物种界定方法（mPTP）支持潜在的新候选种与同一种群的其他种明显不同，并且还表明许多命名的分类群可能不是独特的种。分歧时间估计和谱系时间分析表明，始新世的物种形成水平较低，随后在中新世出现了多样化的爆发。泥蛇可能在更新世和更新世期间最快地多样化，这可能与发生在巽他大陆和萨赫尔大陆架的构造变化和海平面波动有关。我们的分析为泥蛇的分类学、该家族的基础系统发育以及进一步的生物地理学意义提供了新的见解，展示了动态构造和第四纪海平面变化如何塑造了一个广泛多样的蛇类家族。
