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

• Type: Article in International Scientific Journal
• Date: 2015

Authors

Gaubert, P (Author) Other; Njiokou, F (Author) Other; Olayemi, A (Author) Other; Pagani, P (Author) Other; Dufour, S (Author) Other; Danquah, E (Author) Other; Nutsuakor, MEK (Author) Other; Ngua, G (Author) Other; Missoup, AD (Author) Other; Tedesco, PA (Author) Other; Dernat, R (Author) Other; Agostinho Antunes (Author) FCUP

Journal

Title: Molecular Ecology Resources

Vol. 15

Pages: 633-651

ISSN: 1755-098X

Publisher: Wiley-Blackwell

Indexing

ISI Web of Knowledge - 39 Citations

Scopus - 46 Citations

Other information

Authenticus ID: P-00A-AX2

DOI: 10.1111/1755-0998.12334

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 19