Fast phylogenetic DNA barcoding - PubMed (original) (raw)

Fast phylogenetic DNA barcoding

Kasper Munch et al. Philos Trans R Soc Lond B Biol Sci. 2008.

Abstract

We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria for determining the taxonomic level at which a particular DNA sequence can be assigned.

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Figures

Figure 1

Figure 1

Histogram showing the difference in probabilities of assignment to the correct species estimated using the neighbour joining and MCMC.

Figure 2

Figure 2

Estimated probabilities of assignment to the correct species using neighbour joining are plotted against the estimate obtained using MCMC.

Figure 3

Figure 3

ROC curves summarizing the trade-off between sensitivity and specificity in the range of most to least stringent assignment criteria used. Sensitivity is the fraction of all sequences that are correctly assigned and specificity is the fraction of assignments that are correct. Vertical bars represent confidence intervals of the sensitivity statistic. Triangles, NJ; circles, MCMC.

Figure 4

Figure 4

Histogram illustrating the agreement in terms of rank order obtained by sorting the set of homologues by the assignment probability associated obtained neighbour joining with bootstrapping and maximum likelihood and MCMC. The histograms show the average difference in rank order for neighbour joining and BLAST from the one obtained using MCMC.

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References

    1. Abdo Z, Golding G.B. A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups. Syst. Biol. 2007;56:44–56. doi:10.1080/10635150601167005 - DOI - PubMed
    1. Alfaro M.E, Zoller S, Lutzoni F. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 2003;20:255–266. doi:10.1093/molbev/msg028 - DOI - PubMed
    1. Dawnay N, Ogden R, McEwing R, Carvalho G.R, Thorpe R.S. Validation of the barcoding gene COI for use in forensic genetic species identification. Forensic Sci. Int. 2007;173:1–6. doi:10.1016/j.forsciint.2006.09.013 - DOI - PubMed
    1. Desper R, Gascuel O. Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 2004;21:587–598. doi:10.1093/molbev/msh049 - DOI - PubMed
    1. Douady C.J, Delsuc F, Boucher Y, Ford Doolittle W, Douzery E.J.P. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 2003;20:248–252. doi:10.1093/molbev/msg042 - DOI - PubMed

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