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Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates

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Abstract

The creation and use of a globally available database of DNA sequences from a standardized gene region has been proposed as a tool for species identification, assessing genetic diversity and monitoring the legal and illegal trade in wildlife species. Here, we contribute to the Barcode of Life Data System and test whether a short region of the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene would reliably distinguish among a suite of commonly hunted African and South American mammal and reptile species. We used universal primers to generate reference barcode sequences of 645 bp for 23 species from five vertebrate families (Crocodilidae, Alligatoridae, Bovidae, Suidae and Cercopithecidae). Primer cocktails yielded high quality barcode sequences for 179 out of 204 samples (87.7%) from all species included in the study. For most taxa, we sequenced multiple individuals to estimate intraspecific sequence variability and document fixed diagnostic characters for species identification. Polymorphism in the COX1 fragment was generally low (mean = 0.24%), while differences between congeneric species averaged 9.77%. Both fixed character differences and tree-based maximum likelihood distance methods unambiguously identified unknown and misidentified samples with a high degree of certainty. Barcode sequences also differentiated among newly identified lineages of African crocodiles and identified unusually high levels of genetic diversity in one species of African duiker. DNA barcoding offers promise as an effective tool for monitoring poaching and commercial trade in endangered species, especially when investigating semi-processed or morphologically indistinguishable wildlife products. We discuss additional benefits of barcoding to ecology and conservation.

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Acknowledgments

This work was supported by the Alfred P. Sloan Foundation and the Richard Lounsbery Foundation. The National Science Foundation and the American Museum of Natural History’s Research Experience for Undergraduates Program supported the laboratory work of GLM. The AMNH sponsored Aritra Datta and Arlene Amador to extract and sequence the USFWS crocodile skin products and we thank them for their efforts. Field support was provided to MJE by the Wildlife Conservation Society’s Congo and Gabon programs, the National Geographic Society, the Rufford Foundation, Lincoln Park Zoo’s Asia & Africa Fund and the Mac-Arthur Program of the University of Minnesota. MJE thanks Paul and Sarah Elkan (WCS-Congo), Debora Pires, and Congo field assistants Yamba Flavien, Bienvenu Kimbembe and Rufin Lekana. New World crocodilian samples were collected by Peter Brazaitis, Carlos Yamashita (IBAMA, Brazil) and George Rebelo (INPA, Brazil) and provided by G. J. Watkins-Colwell of the Peabody Museum. Ellen Bean and three anonymous reviewers greatly improved the clarity and scope of this manuscript.

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Authors and Affiliations

  1. Department of Ecology and Evolutionary Biology, N122 Ramaley, University of Colorado, Boulder, CO, 80309, USA

    Mitchell J. Eaton & Andrew P. Martin

  2. Department of Environmental Science, Barnard College, 3009 Broadway, 404 Altschul Hall, New York, NY, 10027, USA

    Greta L. Meyers

  3. Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA

    Sergios-Orestis Kolokotronis, Matthew S. Leslie & George Amato

  4. Patuxent Wildlife Research Center, US Geological Survey, 12100 Beech Forest Road, Laurel, MD, 20708-4017, USA

    Mitchell J. Eaton

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  1. Mitchell J. Eaton
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Correspondence to Mitchell J. Eaton.

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Eaton, M.J., Meyers, G.L., Kolokotronis, SO. et al. Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates. Conserv Genet 11, 1389–1404 (2010). https://doi.org/10.1007/s10592-009-9967-0

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