Phylogenomics reveals novel relationships among Neotropical crocodiles (Crocodylus spp.)

<b>Abstract</b><br/><p>Extant species in the order Crocodylia are remnants of an ancient lineage of large-bodied archosaur reptiles. Despite decades of systematic studies, phylogenetic relationships among members of the genus <i>Crocodylus</i> (true crocodiles) in the Neotropics are poorly understood. Here we estimated phylogenomic relationships among the four extant <i>Crocodylus </i>species in the Americas. Species-tree reconstructions using genotypic data from 17,538 SNPs collected for 33 individuals spanning six <i>Crocodylus </i>species (four ingroup and two outgroup) revealed novel relationships for all Neotropical species. For the first time, <i>C. acutus</i>, the American crocodile, was recovered as monophyletic when individuals from Antillean and continental populations were analyzed together. Our results also contradict previous inferences based on mitochondrial DNA data and a limited number of nuclear markers by robustly grouping Morelet's crocodile (<i>C. moreletii</i>) as the sister species to <i>C. acutus</i>., suggesting a novel phylogeographic hypothesis for the group. The present study punctuates the importance of using nuclear genome-wide information and representative sampling for resolving phylogenetic relationships, especially in broadly distributed species and those with complex evolutionary histories.</p>

**摘要**<br/>鳄目（Crocodylia）现存物种是大型主龙类爬行动物古老支系的孑遗类群。尽管已有数十年的系统学研究，但新热带区鳄属（*Crocodylus*，真鳄）内各物种的系统发育关系仍未被充分阐明。本研究对美洲地区现存的4种鳄属物种开展了系统发育组学关系分析。基于覆盖6种鳄属物种（4个内类群、2个外类群）的33个个体的17538个单核苷酸多态性（Single Nucleotide Polymorphism，SNPs）基因型数据进行物种树重构，结果揭示了新热带区所有鳄属物种的全新系统发育关系。当整合分析安的列斯群岛与大陆种群的个体时，美洲鳄（*Crocodylus acutus*，简称C. acutus）首次被证实为单系群。本研究结果还推翻了此前基于线粒体DNA（mitochondrial DNA）数据与少量核标记得出的推论：通过稳健的聚类分析，将莫雷鳄（*Crocodylus moreletii*，简称C. moreletii）确定为美洲鳄的姐妹物种，这为该类群提出了全新的系统地理学假说。本研究凸显了利用全核基因组信息与代表性采样来阐明系统发育关系的重要性，这对于分布范围广泛、演化历史复杂的物种尤为关键。