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.

曾经多样化的犀牛科只剩下五种，这使得重建它们的进化历史成为达尔文以来生物学家面临的挑战。我们对来自五个犀牛物种（三个灭绝和两个活着）的基因组进行了测序，我们将其与来自其余三个现存物种和一系列外群的现有数据进行了比较。我们确定了现存非洲和欧亚血统之间的早期分歧，解决了关于现存犀牛系统发育的关键辩论。这个早期的中新世（约 1600 万年前 [mya]）在非洲 - 阿拉伯和欧亚大陆之间的陆桥形成之后发生了分裂。我们的分析还表明，虽然犀牛基因组总体上表现出低水平的全基因组多样性，但现代物种的杂合性最低，近亲繁殖最高。