Genetic typing and in silico assignment of smoked and fresh bushmeat sold on markets and restaurants in west-central Cte dIvoire

Abstract

Poachers and bushmeat traders most of the time modify the wildlife materials before commercialization. Therefore, the morphological identification of species is no longer possible. However, accurate identification of the sale wildlife materials is essential for species identification, quantification and better conservation management. The aim of this study is to take advantages of specific gene sequences and in silico analysis to identify smoked and decapitated wildlife materials encountered on bushmeat markets and traditional restaurants in Center-Western Cote d’Ivoire. DNA from 352 bushmeat samples comprising 123 decapitated and smoked specimens was extracted, amplified by polymerase chain reaction (PCR) using the Cytb and COI primers and analyzed in silico. Up to 98.37% of the DNA from smoked bushmeat was successfully amplified. Assignment of Cytb and COI query sequences with reference sequences in the NCBI Genbank allowed to correct three misidentifications by traders. Thus, specimens identified as Heliosciurus sp, Phacochoerus aethiopicus africanus and Dendrohyrax dorsalis sylvestris by traders were assigned to Funisciurus sp, Tragelaphus scriptus, Crossarchus obscurus with 84.94, 100, 98.76% similarity respectively. Morphologically unidentifiable sample coded IP3CS1O was assigned to species Eidolon helvum with 99.53% similarity.  The study shows the interest of DNA-based identification of bushmeat to circumvent misidentification for better management of wildlife biodiversity.   Key words: smoked bushmeat, misidentification, genetic typing, in silico analysis, identification, biodiversity, wildlife conservation.