Genomic evidence resolves diversification and fossil taxonomic ambiguities of endangered East Asian gazelles.

Procapra (East Asian gazelles) is a genus of antelopes endemic to Asia, with three extant species inhabiting both plateau and steppe regions. Previous morphological and limited molecular studies suggested that the uplift of the Tibetan Plateau during the Pleistocene may have driven diversification within this genus. However, due to the lack of comprehensive whole-genomic data, the details of diversification and phylogenetic structure within this genus remain unresolved. In this study, we sequenced whole genomes of both ancient and modern Procapra individuals to explore their evolutionary history and genetic diversity. Our results identified two major divergence events: the first, around 0.5 Ma, leading to the divergence of Tibetan gazelle (Procapra picticaudata, Tib), and the second, around 0.12 Ma, resulting in the separation between Mongolian gazelle (Procapra gutturosa, Mon) and Przewalski's gazelle (Procapra przewalskii, Prz). We also detected post-divergence gene flow among species, which complicated their phylogenetic relationships. This is especially true for the shallow divergence between Prz and Mon in contrast to their current taxonomic separation. Furthermore, demographic analyses revealed that population contractions were possibly linked to climate changes and human impacts. Additionally, ancient DNA analyses suggested that several Late Pleistocene specimens from northeastern China, previously attributed to Prz, are more closely related to Mon. These findings underscore the importance of integrating genomic data when recognizing ancient specimens' identity and evolutionary relationships in Procapra, particularly in the context of shallow divergence and historical gene flow.