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

Understanding the relationships among rhinoceros species and when they diverged has been a question addressed by evolutionary biologists since the dawn of the field. Darwin himself discussed the topic in 1842 as one of a handful of examples in his short treatise on evolution that preceded ‘On the Origin of Species’ in 1859. Our data include the five extant rhinoceros species, represented by four de novo genome assemblies of black (Diceros bicornis), white (Ceratotherium simum), Sumatran (Dicerorhinus sumatrensis) and greater one-horned (Rhinoceros unicornis, also known as Indian) rhinoceroses, and a resequenced genome of a Javan rhinoceros (R. sondaicus). The Javan rhinoceros genome was retrieved from a museum specimen dating to 1838, and resequenced to high coverage (25✕). In addition, we sequenced the genomes of three extinct rhinoceros species from Late Pleistocene fossils that are close to, or beyond, the radiocarbon dating limit of ~50 thousand years ago (kya), specifically a Siberian unicorn, a Merck’s rhinoceros, and a woolly rhinoceros, sequenced to 9✕, 12✕ and 35✕ coverage, respectively.

In brief, the comparison of de novo genomes from the white, black, Sumatran, and greater one-horned rhinoceroses with the genomes of a historic Javan rhinoceros and three extinct Pleistocene species resolves the evolutionary relationships within the Rhinocerotidae family and reveals that low genetic diversity is a long-term feature of rhinoceroses.


  • Analysis of genomes from all five extant and three extinct rhinoceros species

  • Strong phylogenomic support for the geographical hypothesis of rhinoceros evolution

  • Basal split between African and Eurasian lineages in the early Miocene (~16 mya)

  • While all rhinoceroses have low genome diversity, it is lowest in modern-day ones

S. Liu*, M. Westbury, N. Dussex, K. Mitchel, M. Sinding, P. Heintzman, D. Duchêne, J. Kapp, J. Seth, H. Heiniger, F. Sánchez-Barreiro, A. Margaryan, R. André-Olsen, B.Cahsan, G.Meng, C. Yang, L. Chen, T. Valk, Y. Moodley, K. Rookmaaker, M. Bruford, O. Ryder, C. Steiner, L. Sonsbeek, S. Vartanyan, C. Guo, A. Cooper, P. Kosintsev, I. Kirillova, A. Lister, T. Marques-Bonet, S. Gopalakrishnan, R. Dunn, E. Lorenzen, B. Shapiro, G. Zhang, P. Antoine, L. Dalén*, M. Gilbert*, “Ancient and modern genomes unravel the evolutionary history of the rhinoceros family” , Cell, 184, 1-12, DOI: 10.1016/j.cell.2021.07.032

Abstract: 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 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.

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