The 82nd Annual Meeting of the American Association of Physical Anthropologists (2013)


DNA mini-barcodes as a tool for primate applied diagnostics and species identification

TIMOTHY G. E. ROBBINS1,2 and VINCENT NIJMAN1.

1Faculty of Humanities and Social Sciences, Oxford Brookes University, 2Faculty of Health and Life Sciences, Oxford Brookes University

Thursday All day, Clinch Concourse Add to calendar

Increasingly identification of primate samples relies on molecular techniques. DNA barcoding, focussing on the mitochondrial cytochrome c oxidase subunit I, gains popularity as a universal species-identifier. Problems with conventional DNA barcoding include degradation in archival specimens and processed material (food products) and samples stored in DNA-unfriendly preservatives (formalin), preventing the recovery of PCR fragments >200 bp. Mini-barcodes may resolve these problems.

We test the validity of mini-barcodes as a way of identifying (archaic) human and non-human primates, based on 540 sequences of 87 species deposited in GenBank. A 648 bp section was selected and a series of mini-barcodes (108 to 324 bp) were generated. Neighbour-joining trees were compiled for each mini-barcode, relying on bootstrap values to assess accuracy of species identification. The full sequence provided unambiguous support (bootstrap values ≥99%) for 68 (78.2%) species. Efficiency of mini-barcodes reached a maximum of 96.8% (mean 96±1.11%) for the 324 bp barcodes, 84.8% (mean 80.6±3.41%) for the 162 bp barcodes, and 78.8% (mean 67%±6.54%) for the 108 bp barcodes. Problem taxa, which did not provide unambiguous identification for any length of barcode, included those that frequently hybridise in nature, those close in evolutionary terms and those who have seen recent taxonomic change. The terminal 3’ end performed marginally better than the proximal 5’ end

We conclude that mini-barcodes in the order of 160-300 bp can be effective in identifying primates, especially when focussing on the terminal end. Mini-barcodes provide a feasible option for DNA barcode analysis of museum samples and applied diagnostics.

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