Bushmeat genetics: setting up a reference framework for theDNAtyping ofAfrican forest bushmeat

Abstract

The bushmeat trade in tropical Africa represents illegal, unsustainable off-takes of millions of tons of wild game - mostly mammals - per year. We sequenced four mitochondrial gene fragments (cyt b, COI, 12S, 16S) in >300 bushmeat items representing nine mammalian orders and 59 morphological species from five western and central African countries (Guinea, Ghana, Nigeria, Cameroon and Equatorial Guinea). Our objectives were to assess the efficiency of cross-species PCR amplification and to evaluate the usefulness of our multilocus approach for reliable bushmeat species identification. We provide a straightforward amplification protocol using a single 'universal' primer pair per gene that generally yielded >90% PCR success rates across orders and was robust to different types of meat preprocessing and DNA extraction protocols. For taxonomic identification, we set up a decision pipeline combining similarity- and tree-based approaches with an assessment of taxonomic expertise and coverage of the GENBANK database. Our multilocus approach permitted us to: (i) adjust for existing taxonomic gaps in GENBANK databases, (ii) assign to the species level 67% of the morphological species hypotheses and (iii) successfully identify samples with uncertain taxonomic attribution (preprocessed carcasses and cryptic lineages). High levels of genetic polymorphism across genes and taxa, together with the excellent resolution observed among species-level clusters (neighbour-joining trees and Klee diagrams) advocate the usefulness of our markers for bushmeat DNA typing. We formalize our DNA typing decision pipeline through an expert-curated query database - DNA BUSHMEAT - that shall permit the automated identification of African forest bushmeat items.

Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification

“…; Gaubert et al . ). Less explored has been the appropriateness of such an approach in the context of genetic variation within widely distributed taxa.…”

“…) on a local, expert‐curated online database dedicated to the identification of African forest mammals (DNA bushmeat ; Gaubert et al . ). Tissue samples were kept in ethanol 75% at 4 °C before laboratory processing.…”

“…; Gaubert & Antunes ; Gaubert et al . ) and completed the remaining gaps by amplifying cyt b fragments (following the same protocol as detailed above) from additional samples and downloading sequences from GenBank (see Table S1, Supporting information).…”

“…This idea is supported by preliminary genetic data suggesting deep phylogenetic structuring within the species (Gaubert & Antunes ; Gaubert et al . ). Moreover, M. tricuspis might represent a valuable biogeographic ‘marker’ to study the influence of Plio‐Pleistocene glaciation cycles on the African rainforest biodiversity given its range encompassing both the Upper and Lower Guinean Blocks (UGB and LGB, respectively), its low dispersal abilities and its dependence on large trees (Gaubert ).…”

Morphometric and genetic differentiation among populations of flat‐headed cusimanse (Crossarchus platycephalus) in Nigeria

“…Flat‐headed cusimanse eat a variety of food products, ranging from plants to animals (Kingdon, ), and the species is considered to be of least concern of extinction (Angelici & Do Linh San, ). However, along with some other carnivora hunted in Africa, it is often encountered in the bush meat market (Angelici & Di Vittorio, ; Gaubert et al., ), suggesting that overhunting could decrease population sizes. Flat‐headed cusimanse is therefore a good model to study the preservation of genetic diversity prior to population decline.…”