Phylogenomics of Fresh and Formalin Specimens Resolves the Systematics of Old World Mud Snakes (Serpentes: Homalopsidae) and Expands Biogeographic Inference
Phylogenomics of Fresh and Formalin Specimens Resolves the Systematics of Old World Mud Snakes (Serpentes: Homalopsidae) and Expands Biogeographic Inference
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DOI：
10.18061/bssb.v2i1.9393
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发表时间：
2023-09
期刊：
影响因子：
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通讯作者：
Justin M. Bernstein;Hugo De Souza;John C. Murphy;H. Voris;Rafe M. Brown;Edward Myers;Sean Harrington;K. Shanker;Sara Ruane
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文献类型：
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作者：
Justin M. Bernstein;Hugo De Souza;John C. Murphy;H. Voris;Rafe M. Brown;Edward Myers;Sean Harrington;K. Shanker;Sara Ruane
随着对不同群体及其生物地理学的系统学研究更加集中，我们对亚洲和澳大利亚生物多样性的了解不断扩大。从历史上看，海平面的波动以及现在分离的陆地的循环连接和分离被用来解释通过物种泵机制产生的生物多样性的积累。然而，最近的研究表明，大陆的地质变化和物种扩散事件可能是对这些地区生物多样性的更好解释。我们利用研究较少且分布广泛的泥蛇（蛇类：Homalopsidae）来研究这些过程，使用来自新鲜组织的约 4,800 个核位点的目标捕获方法和来自博物馆标本的福尔马林组织的补充线粒体数据。我们使用这些数据集来重建该群体的第一个解析的系统发育，确定其生物地理起源，并测试有关海平面变化和栖息地选择对其多样化的作用的假设。分歧年代测定和祖先分布范围的估计支持了渐新世的起源以及约2000万年前后齿类群从东南亚大陆和巽他大陆的多样化，随后向东和向西扩散。 GeoHiSSE 模型表明，祖先后牙谱系向水生环境的生态位扩张并没有影响它们的多样化率。我们的研究结果强调，更新世海平面变化和栖息地特异性并不是导致Homalopsidae现存物种丰富的主要原因，而且东南亚大陆的地质变化可能是该类群多样性的主要驱动力。我们还强调使用新鲜和降解的组织以及核 DNA 和线粒体 DNA 的重要性，以填补鲜为人知但高度多样化且概念上重要的群体的知识空白。在这里，Homalopsidae 代表了一种非传统但有效的模型研究系统，用于理解陆地、海洋和淡水环境之间的转变。
Our knowledge of the biodiversity of Asia and Australasia continues to expand with more focused studies on systematics of various groups and their biogeography. Historically, fluctuating sea levels and cyclic connection and separation of now-disjunct landmasses have been invoked to explain the accumulation of biodiversity via species pump mechanisms. However, recent research has shown that geological shifts of the mainland and species dispersal events may be better explanations of the biodiversity in these regions. We investigate these processes using the poorly studied and geographically widespread Mud Snakes (Serpentes: Homalopsidae) using a target capture approach of ~4,800 nuclear loci from fresh tissues and supplemental mitochondrial data from formalin tissues from museum specimens. We use these datasets to reconstruct the first resolved phylogeny of the group, identify their biogeographic origins, and test hypotheses regarding the roles of sea-level change and habitat selection on their diversification. Divergence dating and ancestral range estimation yielded support for an Oligocene origin and diversification from mainland Southeast Asia and Sundaland in the rear-fanged group ~20 million years ago, followed by eastward and westward dispersal. GeoHiSSE models indicate that niche expansion of ancestral, rear-fanged lineages into aquatic environments did not impact their diversification rates. Our results highlight that Pleistocene sea-level changes and habitat specificity did not primarily lead to the extant species richness of Homalopsidae and that, alternatively, geological shifts in mainland Southeast Asia may have been a major driver of diversity in this group. We also emphasize the importance of using fresh and degraded tissues, and both nuclear and mitochondrial DNA, for filling knowledge gaps in poorly known but highly diverse and conceptually important groups. Here, Homalopsidae represents a non-traditional but effective model study system for understanding transitions between terrestrial, marine, and freshwater environments.