Data from: Bushmeat genetics: setting up a reference framework for the DNA-typing of African forest bushmeat

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 – DNAbushmeat – that
shall permit the automated identification of African forest bushmeat
items.