Paleogenomics illuminates the evolutionary history of the extinct Holocene \u201chorned\u201d crocodile of Madagascar, Voay robustus

E Hekkala,M Russello,G Amato,R Meredith,M L Aardema,M Norell,A Narechania,S Montanari,C Brochu,E Jensen,J Gatesy

doi:10.1038/s42003-021-02017-0

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.

Highlights

Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions
In 1872, the earliest description of the species by Grandidier and Vaillant[27] noted differences between sub-fossil cranial and postcranial material excavated from Holocene deposits near Amboulisatre and extant crocodiles (C. niloticus) in Madagascar
Molecular and combined data uniformly position Voay as sister to Crocodylus and outside of the clade comprised of Osteolaemus and Mecistops (Figs. 3, 4; Supplementary Data 2)

Summary

Introduction

Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. 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. Explorers to Madagascar noted that Malagasy peoples consistently referred to two types of extant crocodiles on the island, a large robust crocodile and a more gracile form with a preference for rivers[24] This suggests that both types persisted until very recently[24,25], but only the gracile form, recognized as an isolated population of the Nile crocodile (Crocodylus niloticus), currently is found on the island[26]. Based on the robustness of available skeletal features, including vertebral, dental and cranial elements and snout shape,

Methods

Results

Conclusion