Non-invasive genomic sampling uncovers novel connectivities and origins of confiscated gorillas

Abstract Background Gorillas are a group of African great apes with two species and four subspecies that are currently critically endangered or endangered. Previous studies analyzing the genetics of wild gorillas from non-invasive samples such as faeces or hair have analysed short mitochondrial or nuclear markers, which may not reflect the wider nuclear genome. Recent technical advances in target capture hybridisation, enrich the endogenous DNA content of non-invasive samples, allowing contiguous genomic regions to be sequenced. Results Here, we generate georeferenced genetic dataset from faecal and hair samples of 280 wild gorillas, sampled from three of the four gorilla subspecies, across large parts of their present-day distributions. With this expanded representation of gorilla genetic diversity in the wild, we detect three population clusters in western lowland gorillas, with the Sangha River and its affluents acting as significant barriers to gene flow. We reconstruct patterns of past population connectivity between western lowland gorillas in the north-eastern distribution range and Cross River gorillas, which may have been facilitated by a migration corridor also used by the Central and Nigeria-Cameroon chimpanzee subspecies. Finally, we predict the geographic origins of wild-born gorillas, achieving a mean prediction error of 65 km, with a population-level resolution for mountain gorillas and some populations of western lowland gorillas. Conclusion Our work characterises fine-scale population structure in western lowland gorillas, which will be informative for future conservation strategies. This proof-of-concept in predicting geographic locations of wild gorillas, will be useful for future applications to geolocalise trafficked or rescued gorillas.

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Journal
Genome biology
Published
2026-10-15
DOI
https://doi.org/10.1186/s13059-026-04305-6
Primary Topic
Genetic diversity and population structure
Type
article
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article

Non-invasive genomic sampling uncovers novel connectivities and origins of confiscated gorillas

Martin Kuhlwilm, Neetha Iyer, Nikki Tagg, Alfred Ngomanda et al.
Genome biology
Genetic diversity and population structure
article

Non-invasive genomic sampling uncovers novel connectivities and origins of confiscated gorillas

Martin Kuhlwilm, Neetha Iyer, Nikki Tagg, Alfred Ngomanda, Claudia Fontsere, Esther Lizano, Javier Prado-Martinez, Barbora Pafčo, Christopher Orbell, Larson Boundenga, Escobar Binyinyi, Emmanuel Ayuk Ayimisin, Joseph Daniel Orkin, Magdalena Bermejo, Sebastián Cuadros-Espinoza, Mimi Arandjelovic, Harvinder Pawar, Bethan Jane Morgan, Ulrich Maloueki, Franck Prugnolle, Juichi Yamagiwa, Hjalmar S. Kühl, Christophe Boesch, Tierra Smiley Evans, Emily Neil, Crickette Sanz, Josephine S. Head, Ron Pinhasi, David Morgan, Veerle Hermans, Julius Nziza, Mattia Bessone, Emmanuel Dilambaka, Richard Muvunyi, Torsten Bohm, Emma Bailey, Donald Mbohli, Jacob Willie, Marina Álvarez-Estapé, Martha M. Robbins, Damien Caillaud, Inaoyom Imong, Olivia Cheronet, Terence Neba Fuh, Klára J. Petrželková, Augustin Kanyunyi Basabose, Harrison J. Ostridge, Ivo Glynne Gut, Germán Illera, Barthélémy Ngoubangoye, Kirsten V. K. Gilardi, Virginie Rougeron, Tobias Deschner, Karine A. Viaud‐Martinez, Irune Ruiz‐Gartzia, Katerina Guschanski, Tomàs Marquès‐Bonet, Miho Inoue‐Murayama, Martine Peeters, Anne‐Céline Granjon, Giovanna Maretti, Paula Dieguez, Sandra Ruibal-Puertas, Pol Alentorn-Moron, Andrew Dunn, Marta Ortova Gut, Etienne François Akomo-Okoue, Kathryn J. Jeffery, Yuji TAKENOSHITA, Urban Ngobobo-As-Ibungu, Kamungu Sebulimbwa, Nadege Wange Njomen, Shiho Fujita, Kevin Lee, Eiji Inoue, Ndelani Nkalla Lambi
article en

Abstract

Abstract Background Gorillas are a group of African great apes with two species and four subspecies that are currently critically endangered or endangered. Previous studies analyzing the genetics of wild gorillas from non-invasive samples such as faeces or hair have analysed short mitochondrial or nuclear markers, which may not reflect the wider nuclear genome. Recent technical advances in target capture hybridisation, enrich the endogenous DNA content of non-invasive samples, allowing contiguous genomic regions to be sequenced. Results Here, we generate georeferenced genetic dataset from faecal and hair samples of 280 wild gorillas, sampled from three of the four gorilla subspecies, across large parts of their present-day distributions. With this expanded representation of gorilla genetic diversity in the wild, we detect three population clusters in western lowland gorillas, with the Sangha River and its affluents acting as significant barriers to gene flow. We reconstruct patterns of past population connectivity between western lowland gorillas in the north-eastern distribution range and Cross River gorillas, which may have been facilitated by a migration corridor also used by the Central and Nigeria-Cameroon chimpanzee subspecies. Finally, we predict the geographic origins of wild-born gorillas, achieving a mean prediction error of 65 km, with a population-level resolution for mountain gorillas and some populations of western lowland gorillas. Conclusion Our work characterises fine-scale population structure in western lowland gorillas, which will be informative for future conservation strategies. This proof-of-concept in predicting geographic locations of wild gorillas, will be useful for future applications to geolocalise trafficked or rescued gorillas.

Genome biology
Université Claude Bernard Lyon 1 (FR), Kagoshima University (JP), Institució Catalana de Recerca i Estudis Avançats (ES), University of Stirling (GB), Universitat Autònoma de Barcelona (ES), Uppsala University (SE), University of Copenhagen (DK), Centre National de la Recherche Scientifique (FR), Toho University (JP), University of Vienna (AT), WWF Colombia (CO), Zoological Society of San Diego (US), Wildlife Conservation Society (US), Panthera Corporation (US), Consejo Superior de Investigaciones Científicas (ES), Okayama University of Science (JP), Inserm (FR), Universitat Pompeu Fabra (ES), Osnabrück University (DE), Illumina (United States) (US), University of Konstanz (DE), Université de Montpellier (FR), Czech Academy of Sciences (CZ), Washington University in St. Louis (US), Kyoto University (JP), German Centre for Integrative Biodiversity Research (DE), Lincoln Park Zoo (US), Ghent University (BE), University of Kinshasa (CD), Arcus Foundation (GB), Royal Zoological Society of Antwerp (BE), Wild Chimpanzee Foundation (DE), Centre International de Recherches Médicales de Franceville (GA), Max Planck Institute of Animal Behavior (DE), Rwanda Development Board (RW), Centre National de la Recherche Scientifique et Technologique (BF), Max Planck Institute for Evolutionary Anthropology (DE), UMR Botanique et Modélisation de l’Architecture des Plantes et des végétations (FR), The Dian Fossey Gorilla Fund International (US), Wildlife Conservation Society Congo (CG), Gorilla Doctors (US), WWF Cameroon (CM), Institut de Biologia Evolutiva (ES), Centro Nacional de Análisis Genómico (ES), Czech Academy of Sciences, Institute of Vertebrate Biology (CZ), Senckenberg Museum für Naturkunde Görlitz (DE), Berkeley Public Health Division (US), International University Institute (IHI) Zittau (DE), Institut Català de Paleontologia Miquel Crusafont (ES), Hochschule Osnabrück (DE), Research Institute for Humanity and Nature (JP), Institute of Parasitology (CZ), Czech Academy of Sciences, Biology Centre (CZ), Institut de Recherche pour le Développement (FR), Wildlife Research Center, Kyoto University (JP), Reconciling Ecological and Human Adaptations for a Biosphere-based Sustainability (ZA), University College London (GB), Arizona State University (US), Université de Montréal (CA), Universitat de Barcelona (ES), Makerere University (UG), Technische Universität Dresden (DE), University of California, Davis (US), Leipzig University (DE), University of California, Berkeley (US), University of Edinburgh (GB), Nelson Mandela University (ZA)
Vienna Science and Technology Fund
Life on land
Openalex Percentile: Top 15%
Genetic diversity and population structure
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