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. 2021 Apr 27;4(1):505.
doi: 10.1038/s42003-021-02017-0.

Paleogenomics illuminates the evolutionary history of the extinct Holocene "horned" crocodile of Madagascar, Voay robustus

E Hekkala  1   2 , J Gatesy  3 , A Narechania  3 , R Meredith  3   4 , M Russello  5 , M L Aardema  3   4 , E Jensen  5   6 , S Montanari  3 , C Brochu  7 , M Norell  3 , G Amato  3
Affiliations

Paleogenomics illuminates the evolutionary history of the extinct Holocene "horned" crocodile of Madagascar, Voay robustus

E Hekkala et al. Commun Biol. .

Erratum in

Abstract

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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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Subfossil skull of Voay robustus (AMNH FR-3102) from southwestern Madagascar.
A skull of Voay robustus collected at Ampoza (44° 42.3’ E, 22° 18.9’ S, 570 m elevation) during the joint Mission Franco-Anglo-American expedition from 1927–1930 (White, 1930).
Fig. 2
Fig. 2. Prior cladistic and Bayesian analyses supporting a grouping of Voay robustus (red) with the genus Osteolaemus (dwarf crocodiles).
Four representative phylogenetic hypotheses are shown (A–D). Both morphology (A, B) and combined analyses of morphology plus molecules (C, D) place Voay with Osteolaemus and extinct African osteolaemines to the exclusion of Crocodylus (true crocodiles). The tip-dated tree in (C) is from a Bayesian reanalysis of morphological data from Brochu (2013) in combination with DNA sequence data (Lee and Yates, 2018). Support scores at nodes are parsimony bootstrap percentages (A) or Bayesian posterior probabilities (B–D). Robust support for Voay + Osteolaemus is highlighted in red.
Fig. 3
Fig. 3. Phylogenetic relationships of Voay robustus based on partial mitochondrial (mt) genomes support a sister group relationship between Voay and a monophyletic Crocodylus (true crocodiles).
The tree shown is based on ML analysis (partitioned by gene) and includes data from all four builds of the Voay mt genome. Bootstrap scores at each node are (from top to bottom): all four builds of Voay mt genome with partitioned ML analysis, Voay AMNH FR-3101 C. porosus reference build with partitioned ML analysis, Voay AMNH FR-3101 Osteolaemus reference build with partitioned ML analysis, Voay AMNH FR-3103 C. porosus reference build with partitioned ML analysis, Voay AMNH FR-3103 Osteolaemus reference build with partitioned ML analysis, and all four builds of Voay mt genome with equally-weighted parsimony analysis. Bootstrap scores for the two internodes that bound the branching point of Voay are highlighted in red. All trees were rooted with bird, turtle, and lizard outgroups (not shown). Higher level taxa are delimited by brackets to the right of species names. Paintings of crocodylians are by C. Buell, and photo of Voay (AMNH FR-3101) is by E. Hekkala.
Fig. 4
Fig. 4. Tip-dated Bayesian timetree showing the phylogenetic relationships of Voay robustus relative to extant and extinct crocodylids with a mapping of geographic distributions (colored squares at tips of branches).
Bayesian posterior probabilities are at nodes; support scores for the two internodes that bound the branching point of Voay are highlighted (red). Optimization of geographic regions to internal nodes (colored circles) is based on equally-weighted parsimony and implies an African ancestry for the overall clade with minimally two migrations to Australia/Asia, two to the New World, and two to Madagascar. An identical mapping of ancestral areas results for minimum area change (MAC) parsimony analysis. The Voay AMNH FR-3101 C. porosus mt genome build (partitioned by 1st, 2nd, 3rd codons) was employed in combination with morphological characters and stratigraphic data from Lee and Yates (2018). Taxa that are distantly related to Voay are pruned from the figure; for the complete timetree, see Supplementary Data 2. Paintings of crocodylians are by C. Buell; photo of Voay (AMNH FR-3101) is by E. Hekkala.
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