Ancient and modern genomes unravel the evolutionary history of the rhinoceros family
Shanlin Liu, Michael V. Westbury, Nicolás 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, Yoshan Moodley, Kees Rookmaaker, Michael W. Bruford, Oliver A. Ryder, Cynthia Steiner, Linda G.R. Bruins-van Sonsbeek, Sergey Vartanyan, Chunxue Guo, Alan Cooper, П. А. Косинцев, Irina Kirillova, Adrian M. Lister, Tomàs Marquès‐Bonet, Shyam Gopalakrishnan, Robert R. Dunn, Eline D. Lorenzen, Beth Shapiro, Guojie Zhang, Pierre‐Olivier Antoine, Love Dalén, M. Thomas P. Gilbert
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 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.