• Boé
• Gene flow
• Hunting
• Non-invasive sampling
• Population genetics
• Primates
• Sex-biased dispersal

Investigating patterns of gene flow across the same landscape for primates with different socio-ecological requirements can improve the ability to identify barriers to dispersal (e.g. rivers, villages) or the landscape features facilitating gene flow (e.g. ecological corridors). Such information is important to draw-up conservation plans to maintain genetic exchange among sub-populations in the long-term. We investigated the genetic diversity, population structure and gene flow of two co-distributed primates - Pan troglodytes verus (the Western chimpanzee) and Papio papio (the Guinean baboon), that are both threatened by hunting and habitat loss in a human-dominated landscape in southern Guinea-Bissau. We collected 231 faecal samples (105 for Pan troglodytes verus and 126 for Papio papio) in three protected areas (Boé NP, Cufada Lagoons NP and Dulombi NP). Samples were genotyped using between 14 to 21 autosomal microsatellite loci. The sex of the individuals was determined using molecular protocols. The three populations are not significantly distinct in terms of genetic diversity estimated for both species. Results from individual-based Bayesian clustering suggest a weaker population structure in Pan troglodytes verus than in Papio papio and that Boé NP population is a genetically distinct unit for both species. The Corubal river does not seem to constitute a significant barrier to gene flow for both species. The population of Guinea baboon show signs of a demographic bottleneck. Dispersal in Pan troglodytes verus and Papio papio seems to be mediated by both sexes in GB, which constitute an exception from what is known in literature and it could be due to anthropic disturbance. Our findings should be considered by governmental agencies when managing the network of protected areas. Law enforcement should be improved along the corridors connecting the protected areas as these are important dispersing routes.