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Systematic Biology 2008 57(5):750-757; doi:10.1080/10635150802422316
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© 2008 Society of Systematic Biologists

Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics

Kasper Munch1, Wouter Boomsma2, John P. Huelsenbeck1, Eske Willerslev3 and Rasmus Nielsen4

1 Department of Integrative Biology, University of California Berkeley, California 94720-3140, USA
2 Bioinformatics Centre, University of Copenhagen Ole Maaløes Vej 5, 2200 København N, Denmark
3 Department of Biology and Centre for Ancient Genetics, University of Copenhagen Universitetsparken 15, 2100 København Ø, Denmark
4 Department of Biology, University of Copenhagen, University of Copenhagen Universitetsparken 15, 2100 København Ø, Denmark and Departments of Integrative Biology and Statistics, University of California Berkeley, California 94720-3140, USA


  Abstract

We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all false assignment based on best Blast hit. However, the most important advance of the method is that it provides statistically meaningful measures of confidence. We apply the method to a re-analysis of previously published ancient DNA data and show that, with high statistical confidence, most of the published sequences are in fact of Neanderthal origin. However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA.

Keywords: Assignment; barcoding; Bayesian; phylogenetics

Received December 1, 2007; Revised February 11, 2008; Accepted June 4, 2008
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