Diversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction.

Elisabeth Hempel,Michael Hofreiter,José H Grau,Michael V Westbury,Frieder Mayer,Johanna L A Paijmans,Axel Barlow,Lei Chen,Sergei Kliver,Alexandra Trinks,Faysal Bibi,Johannes Müller,Klaus-Peter Koepfli

doi:10.3390/genes12081236

Abstract

Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11–58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo–Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries.

Highlights

Characterizing the population genetics of species on the verge of extinction is of vital importance, both for guiding conservation efforts as well as gathering baseline data that can be used to guide post-extinction restoration from captive populations
Through the generation of ten mitochondrial genomes from across the addax’s historical range, and, to our knowledge, the first nuclear genome assembly, our study presented baseline information for a highly threatened desert species
The addax seems to have already had low population sizes in historical and prehistoric times before more recent human interference, which is thought to be the reason for its current crisis of severe population decline in the wild

Summary

Introduction

Characterizing the population genetics of species on the verge of extinction is of vital importance, both for guiding conservation efforts as well as gathering baseline data that can be used to guide post-extinction restoration from captive populations. One species that exemplifies this dire situation is the addax, Addax nasomaculatus (de Blainville, 1816), which is critically endangered and may soon be extinct in the wild [1]. It is highly nomadic, surviving in the hyperarid Sahara by tracking sporadic rainfall that leads to fast vegetation growth [2]. The addax is highly adapted to its desert environment and formerly occurred in great numbers across the entire Sahelo–Saharan region west of the Nile [2,3,4,5]. The only documented wild population is in the Réserve Naturelle Nationale du Termit et du Tin Toumma (TTNNR) in eastern Niger, but its status is not well known: The most recent surveys in 2016 and 2017 found only three and six individuals, respectively [1,6,7,8]

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