Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

Bonobos (<i>Pan paniscus</i>), an endangered species, have for decades been genetically understudied, partly due to difficulties in obtaining high-quality samples. The study of their genome is important not only for understanding their evolution, but also for improving conservation efforts, including population management, diversity and inbreeding assessment, and tracking rescued individuals to combat illegal wildlife trafficking. Here, we use chromosome 21 target capture data from 156 non-invasively collected faecal samples from wild bonobos to perform a comprehensive analysis of their population structure. We confirm the existence of three previously suggested subpopulations identified here as Western, Central and Eastern bonobos which are defined by natural barriers of gene flow such as the Lomami River. By estimating levels of inbreeding, diversity and differentiation, we find support for isolation of mainly Western and Eastern populations and add information on the dispersal routes of their ancestors. We infer split times and separation of these populations and apply a genetic framework to geolocalize samples of unknown origin, showing that locations of their potential origin can be estimated with a precision of up to a median of ~50 km. Our study provides valuable insight into the evolution and population structure of bonobos and reveals how rivers act as strong barriers between populations. It also offers resources for conservation efforts and highlights the need to monitor bonobo populations more closely, in particular isolated ones.

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Publication Details

Journal
bioRxiv (Cold Spring Harbor Laboratory)
Published
2026-01-09
DOI
https://doi.org/10.64898/2026.01.08.698381
Primary Topic
Primate Behavior and Ecology
Type
article
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article

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

Martin Kuhlwilm, Claudia Fontsere, Esther Lizano, Erin G. Wessling et al.
bioRxiv (Cold Spring Harbor Laboratory)
Primate Behavior and Ecology
article

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

Martin Kuhlwilm, Claudia Fontsere, Esther Lizano, Erin G. Wessling, Sebastián Cuadros-Espinoza, B. Hahn, Sojung Han, Térese B. Hart, Paul M. Sharp, Weimin Liu, Jasmin Giles, Claude Monghiemo, Victor Narat, Christina Hvilsom, Zjef J. J. M. Pereboom, Muzungu Ngofuna, Hjalmar Kuehl, Marina Álvarez Estapé, Colin M. Brand, Aida M. Andrés, Albert Lotana Lokasola, Philippe Helsen, David Fasbender, Jeroen M. G. Stevens, Peter Frandsen, Paula Dieguez, Pol Alentorn-Moron, John A.L. Hart, Alexandra Maria Brumwell Prats, Alexander V. Georgiev, Irune Ruiz-Gartzia, Ilan Gronau, Jo Thompson, Michael Krutzen, Yingying Li, Fabian Leendertz, Nuria Hermosilla, Jean-Bosco Ndjango, Tomas Marques-Bonet, Javier Prado-Martinez, Martin Surbeck, Mar Crego-Walters
article en

Abstract

Bonobos (<i>Pan paniscus</i>), an endangered species, have for decades been genetically understudied, partly due to difficulties in obtaining high-quality samples. The study of their genome is important not only for understanding their evolution, but also for improving conservation efforts, including population management, diversity and inbreeding assessment, and tracking rescued individuals to combat illegal wildlife trafficking. Here, we use chromosome 21 target capture data from 156 non-invasively collected faecal samples from wild bonobos to perform a comprehensive analysis of their population structure. We confirm the existence of three previously suggested subpopulations identified here as Western, Central and Eastern bonobos which are defined by natural barriers of gene flow such as the Lomami River. By estimating levels of inbreeding, diversity and differentiation, we find support for isolation of mainly Western and Eastern populations and add information on the dispersal routes of their ancestors. We infer split times and separation of these populations and apply a genetic framework to geolocalize samples of unknown origin, showing that locations of their potential origin can be estimated with a precision of up to a median of ~50 km. Our study provides valuable insight into the evolution and population structure of bonobos and reveals how rivers act as strong barriers between populations. It also offers resources for conservation efforts and highlights the need to monitor bonobo populations more closely, in particular isolated ones.

bioRxiv (Cold Spring Harbor Laboratory)
Institució Catalana de Recerca i Estudis Avançats (ES), Universitat Autònoma de Barcelona (ES), University of Copenhagen (DK), Centre National de la Recherche Scientifique (FR), Consejo Superior de Investigaciones Científicas (ES), Harvard University (US), Bangor University (GB), Universitat Pompeu Fabra (ES), University of California, San Francisco (US), University of Zurich (CH), Université Paris Cité (FR), German Primate Center (DE), Hvidovre Hospital (DK), Copenhagen Zoo (DK), Senckenberg Research Institute and Natural History Museum Frankfurt/M (DE), Reidman College (IL), Royal Zoological Society of Antwerp (BE), Lukuru Foundation (CD), Odisee, University of Applied Sciences (BE), Territoires (FR), Helmholtz Centre for Infection Research (DE), Helmholtz Institute for RNA-based Infection Research (DE), Centre for Immunity, Infection and Evolution (GB), Inuyama Chuo Hospital (JP), Institut de Biologia Evolutiva (ES), Centro Nacional de Análisis Genómico (ES), Senckenberg Museum für Naturkunde Görlitz (DE), Institut Català de Paleontologia Miquel Crusafont (ES), Musée de l'Homme (FR), Institut Supérieur d'Etudes Sociales (CD), University College London (GB), Université de Kisangani (CD), University of Pennsylvania (US)
European Commission, Vienna Science and Technology Fund, Austrian Science Fund, Universität Wien, European Regional Development Fund, Agencia Estatal de Investigación
Openalex Percentile: Top 94%
Primate Behavior and Ecology
DOIOpen Access PDFOpenAlex
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