Ancient mtDNA from the extinct Indian cheetah supports unexpectedly deep divergence from African cheetahs

Niraj Rai,Florin Mircea Iliescu,Satya Prakash,Tirupathi Rao Golla,Lalji Singh,Sreenivas Ara,Kailash Chandra,Mukesh Thakur,Kumarasamy Thangaraj,Ajay Gaur,Guy S Jacobs,Sunil Kumar Verma,Wajeeda Tabasum

doi:10.1038/s41598-020-60751-7

Abstract

The Indian cheetah was hunted to extinction by the mid-20th century. While analysis of 139 bp of mitochondrial DNA (mtDNA) has confirmed that the Indian cheetah was part of the Asiatic subspecies (Acinonyx jubatus venaticus), the detailed relationships between cheetah populations remains unclear due to limited genetic data. We clarify these relationships by studying larger fragments of cheetah mtDNA, both from an Indian cheetah museum specimen and two African cheetah, one modern and one historic, imported into India at different times. Our results suggest that the most recent common ancestor of cheetah mtDNA is approximately twice as ancient as currently recognised. The Indian and Southeast African (Acinonyx jubatus jubatus) cheetah mtDNA diverged approximately 72 kya, while the Southeast and Northeast African (Acinonyx jubatus soemmeringii) cheetah mtDNA diverged around 139 kya. Additionally, the historic African cheetah sampled from India proved to have an A. j. jubatus haplotype, suggesting a hitherto unrecognised South African route of cheetah importation into India in the 19th century. Together, our results provide a deeper understanding of the relationships between cheetah subspecies, and have important implications for the conservation of A. j. venaticus and potential reintroduction of cheetahs into India.

Highlights

In 1947, the last three confirmed Indian cheetahs (Asiatic cheetah subspecies, Acinonyx jubatus venaticus) were shot by the Maharaja of the State of Korwai[1]
In the absence of comparable genomic data from other cheetah populations it remains unclear whether this model – of a common ancestor from approximately 24 kya followed by recent isolation and dramatic population decline – is accurate for all cheetah subspecies, including the endangered Asiatic cheetah
We seek to resolve the relationship between cheetah subspecies and address discrepancies between more ancient[9] and more recent[10] Asiatic and African cheetah divergence dates, testing the extent to which previous dating has been hampered by the limited genetic data available

Summary

Introduction

In 1947, the last three confirmed Indian cheetahs (Asiatic cheetah subspecies, Acinonyx jubatus venaticus) were shot by the Maharaja of the State of Korwai[1]. We can highlight two phylogeographic debates – the origin of modern cheetahs, likely resolved as Old World[8], and the time scale of regional isolation, including differentiation between African and Asiatic cheetahs[7,9,10] The latter question is important given current discussion on the potential of re-establishing wild cheetah populations in India through the import of, most realistically, African animals[11,12]. We seek to resolve the relationship between cheetah subspecies and address discrepancies between more ancient[9] and more recent[10] Asiatic and African cheetah divergence dates, testing the extent to which previous dating has been hampered by the limited genetic data available To this end, we report and analyse mtDNA data recovered from a new historical Indian A. j. Our results emphasise the uniqueness of Asiatic cheetah, and the importance of conservation efforts

Methods

Results

Conclusion