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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.

Non-threatened primates are often overlooked in conservation efforts despite their increasing vulnerability to local extirpation. Campbell’s ( Cercopithecus campbelli ) and green monkeys ( Chlorocebus sabaeus ) are sympatric medium-sized West African guenons (tribe Cercopithecini) whose intraspecific genetic diversity remains understudied in most of their distribution. Both species are ecological generalists and are globally considered non-threatened. In Guinea–Bissau, C. campbelli and Chl. sabaeus are considered the most abundant of the ten extant primate species and are the most frequently hunted for meat. Their populations are thought to be decreasing and but up-to-date data on their occurrence in the country hinders their conservation status assessment. We aimed to update occurrence data and estimate the country-wide mitochondrial (mtDNA) genetic diversity for both species in Guinea–Bissau. From 2008–2022, we conducted surveys in four mainland protected areas and on the islands of the Bijagós Archipelago. We identified C. campbelli populations outside their known distribution. We found high mtDNA diversity for both species on the mainland and lower diversity in insular populations. Our results show significant signals of geographically induced mtDNA differentiation, particularly in C. campbelli . In Chl. Sabaeus , we found divergent haplotypes at geographically close locations. We identified differentiated haplogroups with an estimated divergence time of 1.53 million years ago (Ma) in C. campbelli and 1.16 Ma in Chl. sabaeus, possibly linked to Pleistocene climatic fluctuations. Given the local presence of differentiated mtDNA haplogroups across these and other primate species, we suggest that Guinea–Bissau should be considered as an important region for primate conservation in West Africa.