The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR) was common during much of the twentieth century, declining rapidly since the 1970s, and now only two post-reproductive individuals remain. Despite this species's conservation status, it lacks a genetic assessment of its demographic history. We therefore sampled 232 individuals from extant and museum sources and analysed ten microsatellite loci and the mtDNA control region. Both marker types reliably partitioned the species into SWR and NWR, with moderate nuclear genetic diversity and only three mtDNA haplotypes for the species, including historical samples. We detected ancient interglacial demographic declines in both populations. Both populations may also have been affected by recent declines associated with the colonial expansion for the SWR, and with the much earlier Bantu migrations for the NWR. Finally, we detected post-divergence secondary contact between NWR and SWR, possibly occurring as recently as the last glacial maximum. These results suggest the species was subjected to regular periods of fragmentation and low genetic diversity, which may have been replenished upon secondary contact during glacial periods. The species's current situation thus reflects prehistoric declines that were exacerbated by anthropogenic pressure associated with the rise of late Holocene technological advancement in Africa. Importantly, secondary contact suggests a potentially positive outcome for a hybrid rescue conservation strategy, although further genome-wide data are desirable to corroborate these results.

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

Cardiff School of Biosciences Cardiff University Sir Martin Evans Building Museum Avenue Cardiff CF10 3AX UK Sustainable Places Research Institute Cardiff University Cardiff CF10 3BA UK

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

Department of Zoology University of Venda University Road Thohoyandou 0950 Republic of South Africa

Department of Zoology University of Venda University Road Thohoyandou 0950 Republic of South Africa National Zoological Garden South African National Biodiversity Institute PO Box 754 Pretoria 0001 South Africa

Genetics Division San Diego Zoo Institute for Conservation Research San Diego Zoo Global Escondido CA USA

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

Konrad Lorenz Institute for Ethology Department of Integrative Biology and Evolution University of Veterinary Medicine 1A Savoyen Street 1160 Vienna Austria Wildlife Conservation Society 2300 Southern Blvd 10460 Bronx USA

Leibniz Institut for Zoo and Wildlife Research Alfred Kowalke Straße 17 10315 Berlin Germany

National Zoological Garden South African National Biodiversity Institute PO Box 754 Pretoria 0001 South Africa Department of Genetics University of the Free State 205 Nelson Mandela Drive West Park Bloemfontein 9300 South Africa

Zoo Dvůr Králové Štefánikova 1029 Dvůr Králové nad Labem 54401 Czech Republic

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