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bioRxiv · 10.1101/2025.08.29.673040

Genomic Landscapes of Natural Selection in Great Apes

Huang, X.·Chen, S.·Han, S.·Kuhlwilm, M.
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Abstract

BackgroundGreat 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. ResultsWe analyzed 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 was conducted for recent positive and long-term balancing selection, revealing 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 (DFE) was determined, along with the correlations of DFEs across lineages. ConclusionsWe 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 DFE indicates that most non-synonymous mutations fall into either the nearly neutral or strongly deleterious categories, with high correlations between closely related lineages.

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Huang, X., Chen, S., Han, S., Kuhlwilm, M.. 2025-08-29. Genomic Landscapes of Natural Selection in Great Apes. https://doi.org/10.1101/2025.08.29.673040

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