Estimating the effective population size across space and time in the critically endangered western chimpanzee in Guinea-Bissau: Challenges and implications for conservation management

Ferreira da Silva, Maria Joana, Borges, Filipa, Gerini, Federica, Sá, Rui M., Silva, Francisco, Maie, Tiago, Hernández-Alonso, Germán, Ramos-Madrigal, Jazmín, Gopalakrishnan, Shyam, Aleixo Pais, Isa, Djaló, Mohamed, Fernandes, Nelson, Camará, Idrissa, Regalla, Aissa, Casanova, Catarina, Costa, Malfada, Colmonero Marques Costeira, Ivo, Fernandes, Carlos Rodríguez, Chikhi, Lounès, Minhós, Tânia and Bruford, Michael W. ORCID: https://orcid.org/0000-0001-6357-6080 2025. Estimating the effective population size across space and time in the critically endangered western chimpanzee in Guinea-Bissau: Challenges and implications for conservation management. Evolutionary Applications 18 (10) , e70162. 10.1111/eva.70162

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Abstract

The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau (GB), the subspecies is increasingly threatened, but there is a lack of understanding regarding the degree of genetic threat faced by populations. This hinders the development of targeted conservation strategies and the prioritization of efforts by national agencies. In this study, we use microsatellite data from four parks located in southern GB and five whole-genome sequences to estimate the effective population size (Ne) and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss the strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10,000–15,000 years ago. After that, a change in connectivity, a real decrease in size, or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: ~10,000 decreasing to 1,000–6,000 breeding individuals), possibly indicating a fragmentation into coastal and inland subpopulations. In the most recent past, contemporary Ne is close to 500 (GONE: 395–583, NeEstimator: 107–549), suggesting a high risk of extinction. The populations located at the coastal parks may have been small or isolated for several generations and are at higher risk, whereas the ones located inland exhibit higher long-term Ne and can be considered a stronghold for chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we tried to overcome the limitations of obtaining high-quality DNA samples from wild threatened populations and estimated Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Schools > Biosciences
Publisher:	Wiley
ISSN:	1752-4563
Date of First Compliant Deposit:	16 September 2025
Date of Acceptance:	8 September 2025
Last Modified:	13 Oct 2025 14:22
URI:	https://orca.cardiff.ac.uk/id/eprint/181132

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