Over-representation of sperm-associated deleterious mutations across wild and ex situ cheetah (Acinonyx jubatus) populations

As purifying selection becomes less effective and inbreeding increases, small populations frequently develop an increased load of genome-wide deleterious mutations. Reflecting this pattern, deleterious mutations in genes associated with fertility and immunity have previously been identified in the cheetah (Acinonyx jubatus), which has had a low effective population size for at least the last 10,000 years. However, the distribution of deleterious mutations across cheetah populations is currently unknown. Here, we analysed novel whole genome resequencing data from 30 ex situ and 9 wild cheetahs. We investigated variation in genetic diversity, genomic measures of inbreeding, and the distribution of deleterious mutations across cheetah populations. South Sudanese and Tanzanian cheetahs showed higher inbreeding and realized load, while Namibian cheetahs had a higher proportion of population-specific deleterious mutations. Genes containing high- or moderate-impact deleterious mutations were significantly enriched for sperm-related functions, highlighting putative causative loci associated with poor sperm quality in cheetahs. Similar levels of genetic diversity and inbreeding were observed in ex situ cheetahs compared to their wild counterparts, providing empirical evidence of the efficacy of captive breeding programmes in maintaining genetic variation in ex situ populations.