Affiliations 

  • 1 Globe Institute, University of Copenhagen, Copenhagen, Denmark
  • 2 Cardiff School of Biosciences, Cardiff University, Cardiff, UK
  • 3 Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
  • 4 Department of Zoology, Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
  • 5 Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
  • 6 Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
  • 7 Department of Biological Sciences, University of Venda, Thohoyandou, Republic of South Africa
Mol Biol Evol, 2023 Sep 01;40(9).
PMID: 37561011 DOI: 10.1093/molbev/msad180

Abstract

The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.