On the Demographic History of Chimpanzees and Some Consequences of Integrating Population Structure in Chimpanzees and Other Great Apes

Human Population Genetics and Genomics 2025;5(2):0004 | https://doi.org/10.47248/hpgg2505020004

Original Research Open Access

On the Demographic History of Chimpanzees and Some Consequences of Integrating Population Structure in Chimpanzees and Other Great Apes

Camille Steux ^1,2,3 , Clément Couloigner ^3,4 , Armando Arredondo ^5,6 , Willy Rodríguez ^5,6 , Olivier Mazet ^5,6 , Rémi Tournebize ^1,3,7 , Lounès Chikhi ^1,2,3

1. Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 – Paul Sabatier (UT3), 31062 Toulouse, France
2. Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
3. Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
4. Centre d’Etude de la Forêt, Département de Biologie, Université Laval, G1V 0A6 Québec, Canada
5. Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, 31077 Toulouse, France
6. Institut de Mathématiques de Toulouse; UMR5219. Université de Toulouse, 31062 Toulouse, France
7. UMR DIADE - Diversité, adaptation, développement des plantes, CIRAD, CNRS, IRD, Université de Montpellier, 34394 Montpellier, France

Correspondence: Camille Steux; Lounès Chikhi

Academic Editor(s): Joshua Akey

Received: Jun 17, 2024 | Accepted: Jan 28, 2025 | Published: May 24, 2025

Cite this article: Steux C, Couloigner C, Arredondo A, Rodríguez W, Mazet O, Tournebize R, Chikhi L. On the Demographic History of Chimpanzees and Some Consequences of Integrating Population Structure in Chimpanzees and Other Great Apes. Hum Popul Genet Genom 2025; 5(2):0004. https://doi.org/10.47248/hpgg2505020004

Abstract

Reconstructing the evolutionary history of great apes is of particular importance for our understanding of the demographic history of humans. The reason for this is that modern humans and their hominin ancestors evolved in Africa and thus shared the continent with the ancestors of chimpanzees and gorillas. Common chimpanzees (Pan troglodytes) are our closest relatives with bonobos (Pan paniscus) and most of what we know about their evolutionary history comes from genetic and genomic studies. Most evolutionary studies of common chimpanzees have assumed that the four currently recognised subspecies can be modelled using simple tree models where each subspecies is panmictic and represented by one branch of the evolutionary tree. In addition, one recent genetic study claimed to have detected admixture between bonobos and chimpanzees. However, several studies have identified the existence of significant population structure with evidence of isolation-by-distance (IBD) patterns, both within and between subspecies. This suggests that demographic models integrating population structure may be necessary to improve our understanding of their evolutionary history. Here we propose to use n-island models within each subspecies to infer a demographic history integrating population structure and changes in connectivity (i.e., gene flow). For each subspecies, we use SNIF (Structured non-stationary inference framework), a method developed to infer a piecewise stationary n-island model using PSMC (Pairwise sequentially Markovian coalescent) curves as summary statistics. We then propose a general model integrating the four subspecies as metapopulations within a phylogenetic tree. We find that this model correctly predicts estimates of within subspecies genetic diversity and differentiation, but overestimates genetic differentiation between subspecies as a consequence of the tree structure. We argue that spatial models integrating gene flow between subspecies should improve the prediction of between subspecies differentiation and generate the observed IBD patterns. We also simulated data under a simple spatially structured model for bonobos and chimpanzees (without admixture) and found that it generates potentially spurious signals of admixture between the two species that have been reported and could thus be spurious. This may have implications for our understanding of the evolutionary history of the Homo genus.

Keywords

demographic history, population structure, chimpanzees, connectivity, fragmentation, human evolution, spatial models, admixture

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