DNA-typing surveillance of the bushmeat in Côte d'Ivoire: a multi-faceted tool for wildlife trade management in West Africa

Surveying and quantifying the bushmeat crisis in Africa requires up-front, reliable species-level identification. We conducted a comprehensive survey of 31 trading places where bushmeat are sold in Côte d’Ivoire (West Africa) and two seizures from Europe, using a multi-gene DNA-typing approach and a dedicated species-assignment pipeline (DNAbushmeat). We identified 47 wild and five domestic species-level taxa from 348 collected carcasses, including mammals (15 Cetartiodactyla, 10 Rodentia, seven Carnivora, seven Primates, two Pholidota, two Lagomorpha, one Hyracoidea, one Chiroptera), reptiles (two Squamata), birds (one Bucerotiformes, one Galliformes, one Otidiformes) and fish (one Perciformes). Our DNA-based approach allowed the detection of two separate lineages of red-flanked duikers (Cephalophus rufilatus), a yet unreferenced cane rat (but possibly Thryonomys gregorianus) and two cryptic species of Gambian rat (Cricetomys). We also observed important levels of intraspecific diversity in several mammals and squamates, suggesting additional cryptic diversity within bushmeat species from Côte d’Ivoire. More than half of the bushmeat carcasses were inaccurately identified, with European customs peaking at 100% inaccuracy. Our study also explored the use of diversity indices among bushmeat markets to identify ‘hotspot’ market places where biodiversity would be the most impacted. Overall, 12 protected species (including pangolins, crocodiles, primates and antelopes) were impacted by the bushmeat trade in Côte d’Ivoire, indicating weak law enforcement related to game protection. We suggest that the recognition of the bushmeat sector by the state and its DNA-based surveillance is necessary to reach a sustainable management of the bushmeat trade in Côte d’Ivoire.