The research, led by Xin Huang and Martin Kuhlwilm of the Department of Evolutionary Anthropology at the University of Vienna, together with Simon Chen and Sojung Han, addresses a long-standing gap in evolutionary biology. Although individual great ape species have been studied for signs of selection before, few analyses have systematically compared the signals across the full clade using a consistent framework. Great apes are of particular interest because they occupy a remarkable range of environments, from the swampy forests inhabited by bonobos to the high-altitude mountain forests of eastern gorillas, and because their biology, behavior and reproductive strategies differ in ways that may have left measurable traces in their genomes. Understanding where selection has acted, and whether the same genes or gene categories were targeted repeatedly across lineages, offers a window into both the shared and idiosyncratic paths of ape evolution.

Technically, the study employed two complementary population genetic approaches. Recent positive selection, in which a beneficial mutation rises rapidly in frequency and drags nearby genetic variants along with it, was detected through genome-wide screens designed to identify the characteristic patterns of reduced variation and skewed allele frequencies that such sweeps produce. Long-term balancing selection, by contrast, maintains multiple versions of a gene within a population over extended evolutionary periods, often because heterozygotes enjoy an advantage or because varying conditions favor different forms at different times. This leaves a different signature: unusually high levels of genetic diversity clustered around specific loci. By searching for both signals simultaneously across all six lineages, the team could distinguish candidate regions shaped by recent environmental pressures from those under ancient, persistent constraints.

The results revealed a striking diversity of candidate loci. Genes potentially related to sensory systems appeared repeatedly, suggesting that the demands of seeing, hearing, smelling and tasting in different forest environments have driven adaptation in multiple ape lineages. Immune-related genes also featured prominently, consistent with the well-established role of pathogens as powerful selective agents in wild primate populations, where each species and subspecies encounters its own distinctive suite of viruses, bacteria and parasites. Environmental pressures such as diet and altitude left their mark as well, with candidate genes in gorilla lineages potentially reflecting the challenges of life at elevation and others pointing to the divergent dietary specializations that separate, for example, the highly frugivorous orangutans of Borneo and Sumatra from their African cousins.

Reproductive strategies emerged as another recurring theme in the selection landscapes. Great apes exhibit extraordinary variation in their mating systems, ranging from the relatively egalitarian social structure of bonobos to the pronounced sexual competition seen in chimpanzees and gorillas, and the solitary lifestyles of orangutans. Genes implicated in gamete biology, reproductive physiology and related traits showed evidence of selection in patterns that may reflect these differing strategies. The researchers emphasize that these are candidate loci, meaning they represent well-supported hypotheses about the targets of selection rather than definitive proof of adaptation in every case. Nevertheless, the consistent appearance of genes in these functional categories across independent analyses strengthens the biological plausibility of the findings.

Beyond cataloging individual genes, the study ventured into territory rarely explored at this scale across multiple ape species: the distribution of fitness effects, often abbreviated as the DFE. This statistical framework describes the spectrum of fitness consequences that new mutations carry, from lethal to beneficial, and provides a fundamental descriptor of a population’s genetic architecture. The analysis showed that the vast majority of non-synonymous mutations, those that change the amino acid sequence of proteins, fall into either the nearly neutral category, where selection is too weak to matter much, or the strongly deleterious category, where natural selection efficiently removes them from the population. This bimodal pattern suggests a relatively narrow middle ground of mildly deleterious mutations, with important implications for how genetic disease and load are modeled in endangered ape populations.

One of the study’s most intriguing findings concerns the correlations of these fitness-effect distributions across lineages. Closely related species and subspecies showed highly correlated distributions of fitness effects, indicating that the fundamental mutational landscape is shared among kin lineages and shifts gradually with evolutionary distance. Bornean and Sumatran orangutans, for example, diverged relatively recently and display correspondingly similar patterns, while comparisons spanning deeper evolutionary splits, such as between Asian and African apes, reveal greater divergence. This observation provides empirical support for using closely related species as proxies in conservation genomics, where the fitness consequences of mutations in one endangered population might be partly inferred from better-studied relatives.

The comparative dimension of the work also uncovered both novelty and recurrence. Some candidate genes and gene categories were lineage-specific, pointing to adaptations unique to particular species or subspecies and potentially explaining traits found in only one member of the clade. Others represented recurrent targets, selected independently in multiple lineages, which suggests that certain biological functions are repeatedly subject to similar pressures wherever great apes live. Distinguishing between these two modes of evolution is central to understanding whether adaptation proceeds mainly through the innovation of new solutions or through the redeployment of old ones, and the great ape selection landscapes assembled here offer a rich dataset for addressing that question.

The practical implications extend beyond basic science. All six great ape species are threatened with extinction, and several subspecies are critically endangered. Knowing which portions of the genome harbor functionally important variation under selection can inform conservation priorities, helping managers decide which populations to prioritize for protection or translocation to preserve adaptive potential. The finding that most protein-altering mutations are either effectively neutral or strongly harmful also carries a cautionary message: small, isolated ape populations may accumulate strongly deleterious mutations through drift, a process known as genetic erosion, making genetic monitoring an urgent component of species survival plans.

The study relied exclusively on previously published genomic data, requiring no new field sampling, and was made possible by substantial computational resources provided by the Life Science Compute Cluster at the University of Vienna and the Austrian Scientific Computing infrastructure. The work was funded by the Vienna Science and Technology Fund and the Austrian Science Fund. The authors stress that the analysis is a first detailed pass at cross-lineage selection landscapes in great apes, and the accompanying candidate gene lists, published as part of the open-access article along with extensive supplementary materials, are intended as a resource for the wider community. As genomic datasets for wild apes continue to grow in size and geographic coverage, the framework established here can be updated and refined, potentially extending to additional subspecies and to ancient DNA from primate populations that no longer exist.

For evolutionary anthropologists, the study reframes great ape genomes not as static records of shared ancestry but as dynamic documents of adaptation, each lineage’s DNA inscribed with the history of its struggles against pathogens, climates, diets and social pressures. For conservationists, it provides a genomic compass pointing toward the variation that matters most. And for anyone curious about human origins, it offers a crucial comparative backdrop: by understanding how selection has shaped the genomes of our closest relatives, researchers gain a sharper sense of which features of our own genomes are truly exceptional and which are simply the shared inheritance of a remarkable family of primates that once spanned the forests of Africa and Southeast Asia.