The genetic consequences of captive breeding, environmental change and human exploitation in the endangered peninsular pronghorn

Endangered species with small population sizes are susceptible to genetic erosion, which can be detrimental to long-term persistence. Consequently, monitoring and mitigating the loss of genetic diversity are key to successful conservation. The peninsular pronghorn ( Antilocapra americana peninsularis ) is an endangered pronghorn subspecies that is almost entirely held in captivity. Captive breeding has increased the number of pronghorns from 25 founders in 1997 to around 700 individuals today, but it is unclear how the genetic diversity of the captive herd may have changed over time. We therefore generated and analysed microsatellite data spanning 2009–2021. We found a decline in heterozygosity and an increase in the proportion of inbred individuals over time. However, these trends appear to have abated in response to a genetically informed selective breeding attempt undertaken in 2018. We also reconstructed the recent demographic history of the peninsular pronghorn, revealing two sequential population declines putatively linked to the desertification of the Baja California peninsula around 6,000 years ago, and hunting and habitat loss around 500 years ago. Our results provide insights into the genetic diversity of an endangered antelope and highlight the potential for selective breeding to have positive conservation outcomes.