Genomic landscapes of natural selection in great apes

Abstract Background Great apes are a primate clade with unique biological features. The different species and subspecies have adapted to their respective habitats and followed various evolutionary trajectories influencing their diversity. Hence, studying patterns of natural selection across this clade is an important aspect in understanding their biology. Results We analyze a curated panel of genomic diversity for bonobos, chimpanzees, eastern and western gorillas, and Bornean and Sumatran orangutans to explore their selection landscapes. A genome-wide screen conducted for recent positive and long-term balancing selection reveals candidate loci potentially related to sensory and immune systems, environmental pressures such as diet or altitude, and reproductive strategies in these species. In addition, the distribution of fitness effects is determined, along with the correlations of distribution of fitness effects across lineages. Conclusions We interpret the potential biological meaning of the landscapes of recent positive and long-term balancing selection in our closest living relatives, revealing novel lineage-specific candidate genes and gene categories, as well as recurrent targets across lineages. Our investigation of the deleterious distribution of fitness effects indicates that most non-synonymous mutations fall into either the nearly neutral or strongly deleterious categories, with high correlations between closely related lineages.