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Ancient and modern genomes unravel the evolutionary history of the rhinoceros family
Cell  (IF41.582),  Pub Date : 2021-08-24, DOI: 10.1016/j.cell.2021.07.032
Shanlin Liu, Michael V. Westbury, Nicolas Dussex, Kieren J. Mitchell, Mikkel-Holger S. Sinding, Peter D. Heintzman, David A. Duchêne, Joshua D. Kapp, Johanna von Seth, Holly Heiniger, Fátima Sánchez-Barreiro, Ashot Margaryan, Remi André-Olsen, Binia De Cahsan, Guanliang Meng, Chentao Yang, Lei Chen, Tom van der Valk, M. Thomas P. Gilbert

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.