Paleogenomics illuminates the evolutionary history of the extinct Holocene ‘horned’ crocodile of Madagascar, Voay robustus
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Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens ( n = 2) of the extinct “horned” crocodile, Voay robustus , collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.
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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 [48]
The Results (page not provided) say the mitochondrial analyses corroborate previously supported relationships among the nine extant crocodylian genera. But they also say the mitochondrial trees contradict earlier analyses that placed Voay with osteolaemines; the paper does not establish general agreement with previously dated phylogenies. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThis consistency between molecular clock estimates reinforces the hypothesis that Voay represents a sister lineage to the crown Crocodylus, diverging around the Oligocene-Miocene boundary.
“This consistency between molecular clock estimates reinforces the hypothesis that Voay represents a sister lineage to the crown Crocodylus, diverging around the Oligocene-Miocene boundary.”
From Mitogenomic Crocodylia phylogeny and population structure of <i>Crocodylus porosus</i> including the extinct Seychelles crocodile (2026) · cites this paper as [48]
Our estimated node age of 24.54 Ma for the Crocodylus crown group is consistent with the divergence between Voay robustus and Crocodylus at approximately 24.9 Ma reported by Hekkala et al. [48].
“Our estimated node age of 24.54 Ma for the Crocodylus crown group is consistent with the divergence between Voay robustus and Crocodylus at approximately 24.9 Ma reported by Hekkala et al. [48].”
From Mitogenomic Crocodylia phylogeny and population structure of <i>Crocodylus porosus</i> including the extinct Seychelles crocodile (2026) · cites this paper as [48]
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- Authors
- Hekkala, E., Gatesy, J., Narechania, A., Meredith, R., Russello, M., Aardema, M. L., Jensen, E., Montanari, S., Brochu, C., Norell, M., & Amato, G.
- Affiliations
- American Museum of Natural History (US)
- University of British Columbia (CA)
- University of Iowa (US)
- Corresponding author
- Hekkala, E.
- ORCID
- Venue
- Communications Biology
- Published
- 2021-04-27
- Volume
- 4
- Issue
- 1
- Pages
- 505-505
- ISSN
- 2399-3642 (ISSN-L)
- PMC
- PMC8079395
- OpenAlex
- W3159277718
- Cited by
- 39
- References
- 105
- Citations by year
- 2026: 6 · 2025: 5 · 2024: 6 · 2023: 9 · 2022: 7 · 2021: 6
- FWCI
- 5.26
- Type
- journal article
- Language
- en
- Update notices
- correction (2021-05-25)
- Open access
- gold
- doi.org
- Locations
- Communications Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Science Foundation (1725932, 1931213, 1556701)
- Fordham University
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Paleontology and Evolutionary Biology
- Keywords
- Madagascar, mitochondrial genome, ancient DNA, Crocodylus, biogeography, extinction, tip-dating
- MeSH terms
- DNA, Ancient, Alligators and Crocodiles, Animals, Biological Evolution, Fossils, Madagascar, Paleontology, Phylogeny, Genomics, Extinction, Biological
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