Comparative population genomics reveals evolutionary potential and conservation priorities in three Procapra species.

The genus Procapra, comprising the Mongolian gazelle (P. gutturosa; MG), Przewalski's gazelle (P. przewalskii; PG), and Tibetan gazelle (P. picticaudata; TG), has experienced substantial range contractions and population declines due to anthropogenic disturbance and habitat degradation. Effective conservation of these species requires a clearer understanding of how distinct demographic histories have shaped their current evolutionary potential and genetic risks. Here, we assembled chromosome-level genomes for all three Procapra species and conducted population genomic analyses using whole-genome resequencing data from 93 individuals. Our findings show that MG underwent substantial historical population expansion and retained the highest genetic diversity and lowest levels of inbreeding. In contrast, TG currently has a relatively large census size, but its historically small effective population size may have contributed to elevated inbreeding and reduced genetic diversity. Despite having the smallest census size among the three species, PG retained intermediate genetic diversity, consistent with its historically larger effective population size, whereas severe contemporary habitat fragmentation is associated with elevated inbreeding and a pronounced demographic decline. Collectively, our results demonstrate that census size alone does not reliably predict genetic risk in closely related Procapra species and highlight the importance of demographic history in shaping evolutionary potential and species-specific conservation needs. Given the escalating anthropogenic fragmentation affecting PG, targeted conservation actions are urgently needed to limit further inbreeding and erosion of genetic diversity and to safeguard its long-term viability.