Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

Abstract

The genus <i>Crocuta</i> (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (~2.5 Ma) between African and Eurasian <i>Crocuta</i> populations, suggesting that ancestral <i>Crocuta</i> left Africa around the same time as early <i>Homo</i>. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian <i>Crocuta</i> after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.