The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species' once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide genetic structure of historic and modern populations using the largest and most geographically representative sample of black rhinoceroses ever assembled. Using both mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species' mitochondrial genetic variation, including the most ancestral lineages that are now absent from modern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad, Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historic range of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southern Kenya, where a handful of individuals survive in the Masai Mara. We also identify conservation units that will help maintain evolutionary potential. Our results suggest a complete re-evaluation of current conservation management paradigms for the black rhinoceros.

Cardiff School of Biosciences Sir Martin Evans Building Cardiff University Museum Avenue Cardiff CF10 3AX United Kingdom

Department of Biological Sciences Thomas Building University of Chester Chester CH1 4BJ United Kingdom

Department of Biology University of Copenhagen Ole Maaløes Vej 5 Copenhagen N DK 2200 Denmark

Department of Genetics University of the Free State 205 Nelson Mandela Drive West Park Bloemfontein 9300 South Africa

Department of Zoology Faculty of Science University of South Bohemia Branišovská 1760 České Budějovice 37005 Czech Republic

Department of Zoology Jomo Kenyatta University of Agriculture and Technology Kenyatta Avenue Nairobi 00200 Kenya

Department of Zoology University of Venda Private Bag X5050 Thohoyandou 0950 Republic of South Africa

Konrad Lorenz Institute of Ethology Department of Integrative Biology and Evolution University of Veterinary Medicine Vienna Austria Savoyenstr 1A 1160 Austria

National Zoological Gardens of South Africa 232 Boom Street Pretoria 0001 South Africa

Swedish Museum of Natural History Frescativägen 40 Stockholm 10405 Sweden

Vienna Museum of Natural History Burgring 7 1010 Vienna Austria

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Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum)