Ancient mitogenomics elucidates diversity of extinct West Indian tortoises

Christian Kehlmaier,Uwe Fritz,Eva Graciá,David W. Steadman,Richard Franz,Nancy A. Albury

doi:10.1038/s41598-021-82299-w

Abstract

We present 10 nearly complete mitochondrial genomes of the extinct tortoise Chelonoidis alburyorum from the Bahamas. While our samples represent morphologically distinct populations from six islands, their genetic divergences were shallow and resembled those among Galápagos tortoises. Our molecular clock estimates revealed that divergence among Bahamian tortoises began ~ 1.5 mya, whereas divergence among the Galápagos tortoises (C. niger complex) began ~ 2 mya. The inter-island divergences of tortoises from within the Bahamas and within the Galápagos Islands are much younger (0.09–0.59 mya, and 0.08–1.43 mya, respectively) than the genetic differentiation between any other congeneric pair of tortoise species. The shallow mitochondrial divergences of the two radiations on the Bahamas and the Galápagos Islands suggest that each archipelago sustained only one species of tortoise, and that the taxa currently regarded as distinct species in the Galápagos should be returned to subspecies status. The extinct tortoises from the Bahamas have two well-supported clades: the first includes one sample from Great Abaco and two from Crooked Island; the second clade includes tortoises from Great Abaco, Eleuthera, Crooked Island, Mayaguana, Middle Caicos, and Grand Turk. Tortoises belonging to both clades on Great Abaco and Crooked Island suggest late Holocene inter-island transport by prehistoric humans.

Highlights

We present 10 nearly complete mitochondrial genomes of the extinct tortoise Chelonoidis alburyorum from the Bahamas
What we know about the extinct tortoises is derived only from late Quaternary and Holocene fossils, which have been reported from the Bahamian Archipelago, Cuba, Hispaniola, Navassa, Sombrero, and Mona
That the Sawmill Sink fossils should be assessed for ancient DNA, which was successfully extracted and sequenced by Kehlmaier et al.[19], allowing their firm phylogenetic placement in the same clade as the giant tortoises from Galápagos (Chelonoidis niger complex) and a small to medium-sized species from South America (C. chilensis)

Summary

Introduction

We present 10 nearly complete mitochondrial genomes of the extinct tortoise Chelonoidis alburyorum from the Bahamas. The Holocene fossils from Sawmill Sink retained enough collagen to allow radiocarbon dating and stable isotope analyses[17,18] It followed, that the Sawmill Sink fossils should be assessed for ancient DNA (aDNA), which was successfully extracted and sequenced by Kehlmaier et al.[19], allowing their firm phylogenetic placement in the same clade as the giant tortoises from Galápagos (Chelonoidis niger complex) and a small to medium-sized species from South America (C. chilensis). We have discovered tortoise fossils from a variety of late Quaternary localities (flooded sinkholes, dry sinkholes and caves, and archaeological sites) on 14 different islands in the Bahamian (Lucayan) Archipelago (Fig. 1) Many of these fossils are Holocene in age (< 10 ka) and retain enough collagen for Scientific Reports | (2021) 11:3224. We include late Quaternary material from sites in Argentina, Venezuela and the Dominican Republic (Hispaniola) with the aim to place the tortoises from the Bahamas in a comprehensive phylogenetic framework

Methods

Results

Conclusion