Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

Cell. 2021 Sep 16;184(19):4874-4885.e16. doi: 10.1016/j.cell.2021.07.032. Epub 2021 Aug 24.


Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.

Keywords: Rhinoceros, Perissodactyl, Conservation genomics, Phylogenomics, Genomic diversity..

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Demography
  • Evolution, Molecular*
  • Gene Flow
  • Genetic Variation
  • Genome*
  • Geography
  • Heterozygote
  • Homozygote
  • Host Specificity
  • Markov Chains
  • Mutation / genetics
  • Perissodactyla / genetics*
  • Phylogeny
  • Species Specificity
  • Time Factors