Agriculture affects genetic diversity and functional connectivity in an ecologically flexible West African primate

Land-use changes in West Africa are threatening wildlife viability, yet their impacts on species' genetic diversity and connectivity remain poorly understood. We investigated the environmental drivers of genetic diversity and functional connectivity in the Near Threatened Guinea baboon (Papio papio) by genotyping 243 non-invasively collected faecal samples across its range and applying a landscape genetics framework. We identified distinct genetic clusters, with Gambian populations exhibiting the lowest genetic diversity and highest inbreeding. Genetic diversity was positively associated with shrublands and forest-savannah mosaics, highlighting the importance of these habitats for maintaining viable populations. Rivers, grasslands, and shrublands facilitate functional connectivity and act as dispersal corridors, whereas large waterbodies and intensive croplands serve as strong barriers. Notably, habitats constituted by mosaics of forest and croplands provide more permeable barriers to movement than strict monocultures. Our results suggest that intensive agricultural land use can reduce functional connectivity, whereas heterogeneous natural habitats and riverine networks sustain it. To ensure the long-term survival of Guinea baboons, conservation strategies must prioritize preserving riverine corridors and habitat heterogeneity. Furthermore, replacing monoculture farming with agroecological practices like agroforestry is crucial to support landscape connectivity and mitigate the adverse effects of agricultural expansion.