Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data
Open accessAbstract
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.
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The analysis of mitochondrial genomes aligns with previously dated phylogenies of Crocodylia.
“Our analysis of mitochondrial genomes (figure 1) aligns with previously dated phylogenies of Crocodylia [35,48], supporting and consolidating our picture of crocodilian evolution.”
From Mitogenomic Crocodylia phylogeny and population structure of <i>Crocodylus porosus</i> including the extinct Seychelles crocodile (2026) · cites this paper as [35]
The available passages are from the reference list (page unavailable). They name earlier mitogenomic and time-calibrated Crocodylia studies, but do not compare this paper’s results with those phylogenies. Searches for divergence times and agreement with previous studies did not retrieve a passage that establishes the claimed alignment. (LLM, conf=0.72)
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Cites
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Agne, S., Arnold, P., Belle, B., Straube, N., Hofreiter, M., & Glaw, F. (2026) · Royal Society Open Science · doi:10.1098/rsos.251546 · Cited by 1 · see citing works
- Authors
- Pan, T., Miao, J.-S., Zhang, H.-B., Yan, P., Lee, P.-S., Jiang, X.-Y., Ouyang, J.-H., Deng, Y.-P., Zhang, B.-W., & Wu, X.-B.
- Affiliations
- Anhui Normal University (CN)
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University , Wuhu, Anhui, China
- School of Life Sciences, Anhui University , Hefei, Anhui, China
- ORCID
- Yan, Peng
- Venue
- Zoological Journal of the Linnean Society
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-07-08
- Volume
- 191
- Issue
- 4
- Pages
- 1075-1089
- ISSN
- 0024-4082 (ISSN-L)
- 1096-3642
- OpenAlex
- W3040777464
- Cited by
- 53
- References
- 1
- Citations by year
- 2026: 8 · 2025: 11 · 2024: 13 · 2023: 7 · 2022: 5 · 2021: 6 · 2020: 3
- FWCI
- 1.71
- Type
- journal article
- Language
- en
- Open access
- green
- zenodo.org
- Locations
- Zoological Journal of the Linnean Society (publishedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion)
- Funders
- National Natural Science Foundation of China (31872253)
- Natural Science Foundation of Anhui Province (1908085QC127)
- Anhui Normal University (751865)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Paleontology and Evolutionary Biology
- Keywords
- crocodilians, phylogeny, mitochondrial genome, Alligatoridae, crocodiles, Gavialidae, Melanosuchus niger, Caiman yacare, divergence time estimation, diversification rates, speciation, climate change, Cretaceous origin, reptile evolution
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