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Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (Dicerorhinus sumatrensis)

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Abstract

The Sumatran rhinoceros (Dicerorhinus sumatrensis) is the smallest and one of the most endangered rhinoceros species, with less than 100 individuals estimated to live in the wild. It was originally divided into three subspecies but only two have survived, D. sumatrensis sumatrensis (Sumatran subspecies), and D. s. harrissoni (Bornean). Questions regarding whether populations of the Sumatran rhinoceros should be treated as different management units to preserve genetic diversity have been raised, particularly in light of its severe decline in the wild and low breeding success in captivity. This work aims to characterize genetic differentiation between Sumatran rhinoceros subspecies using complete mitochondrial genomes, in order to unravel their maternal evolutionary history and evaluate their status as separate management units. We identified three major phylogenetic groups with moderate genetic differentiation: two distinct haplogroups comprising individuals from both the Malay Peninsula and Sumatra, and a third group from Borneo. Estimates of divergence time indicate that the most recent common ancestor of the Sumatran rhinoceros occurred approximately 360,000 years ago. The three mitochondrial haplogroups showed a common divergence time about 80,000 years ago corresponding with a major biogeographic event in the Sundaland region. Patterns of mitochondrial genetic differentiation may suggest considering Sumatran rhinoceros subspecies as different conservation units. However, the management of subspecies as part of a metapopulation may appear as the last resource to save this species from extinction, imposing a conservation dilemma.

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Acknowledgements

This work was possible thanks to the contribution of Julie Fronczek, Marisa Korody, and Suellen Charter generating the Sumatran rhinoceros fibroblast cell lines. Inclusion of the rhinoceros samples from Sabah, D. s. harrisoni, was made possible through BORA (Bornean Rhino Alliance) and the Leibnitz Institute of Zoo and Wildlife Medicine. We thank Alfred Roca and Jessica Brandt for helpful discussion and comments on the manuscript. Funding was obtained from an anonymous donor to San Diego Zoo Global.

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  1. San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, 15600 San Pasqual Valley Road, Escondido, CA, 92027, USA

    Cynthia C. Steiner, Marlys L. Houck & Oliver A. Ryder

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  1. Cynthia C. Steiner
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Correspondence to Cynthia C. Steiner.

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Steiner, C.C., Houck, M. & Ryder, O.A. Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Conserv Genet 19, 397–408 (2018). https://doi.org/10.1007/s10592-017-1011-1

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