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

Date: September 01, 2009

Pub: Conservation Genetics. Online. DOI 10.1007/s10592-009-9967-0

Author(s): Eaton, MJ; Meyers, GL; Kolokotronis, S.; Leslie, MS; Martin, AP; Amato, G.

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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