Species of the order Crocodylia are mostly large, predatory and semi-aquatic reptiles. Crocodylia, the closest living relatives of birds, first appeared in the Late Cretaceous period. In the present study, the complete mitochondrial (mt) genomes of 19 Crocodylia species, including two species (Melanosuchus niger and Caiman yacare) that have not been previously sequenced for mitogenomes, were processed through Illumina sequencing to offer genetic resources and compare with the mitogenomes of Crocodylia species reported previously. In addition, a high-resolution phylogenetic tree of nearly all current recognized species of Crocodylia is constructed based on mitogenomic data. Phylogenetic analyses support monophyly of three families: Alligatoridae (four genera: Alligator, Caiman, Melanosuchus and Paleosuchus), Crocodylidae (three genera: Crocodylus, Mecistops and Osteolaemus) and Gavialidae (two genera: Gavialis and Tomistoma). The tree topology is generally similar to previous studies. Molecular dating suggests that the first split within Crocodylia date back to the Upper Cretaceous (approx. 86.75 Mya). The estimated time to the most recent common ancestor (TMRCA) of Alligatoridae is 53.33 Mya and that of Crocodylidae and Gavialidae is 50.13 Mya, which might be closely linked to climate changes during the Late Palaeocene and Early Eocene. Additionally, this study proves that the diversification rate within Crocodylia began to increase from the Late Eocene (about 36 Mya) and two diversification peak periods of Crocodylia (0–10 Mya and 10–20 Mya) are disclosed, which is roughly consistent with the estimated crocodylian species richness through time. Combining all these clues, we can suggest that climate fluctuation may have played a decisive role in the speciation of Crocodylia.

中文翻译：

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使用基于有丝分裂基因组的数据，现存的鳄科（Reptilia）的近乎完整的系统发育

鳄科的物种主要是大型，掠食性和半水生爬行动物。鸟类中最亲近的亲缘动物鳄属最早出现在白垩纪晚期。在本研究中，通过Illumina测序处理了19种湾鳄属物种的完整线粒体（mt）基因组，其中包括先前尚未为有丝分裂基因组测序的两个物种（Melanosuchus niger和Caiman yacare），以提供遗传资源并与有丝分裂基因组进行比较鳄属物种的数量先前已有报道。此外，基于线粒体基因组数据，构建了几乎所有当前公认的鳄类物种的高分辨率系统树。系统发育分析支持以下三个科的单系：短吻鳄科（四个属：短吻鳄，凯门鳄，Melanosuchus和Paleosuchus），鳄科（三个属：鳄，Mecistops和Osteolaemus）和Gavialidae（两个属：Gavialis和Tomistoma））。树形拓扑通常类似于先前的研究。分子测年表明，鳄科的第一次分裂可追溯到上白垩纪（约86.75 Mya）。到扬子鳄科的最近共同祖先（TMRCA）的估计时间是53.33 Mya，鳄科和Gavialidae的时间是50.13 Mya，这可能与古新世晚期和始新世早期的气候变化紧密相关。此外，这项研究证明，从晚始新世（约36 Mya）开始，鳄科的多样化率开始增加，并且揭示了鳄科的两个多样化高峰期（0-10 Mya和10-20 Mya），这与通过时间估算鳄鱼物种的丰富度。结合所有这些线索，