Fast phylogenetic DNA barcoding

Kasper Munch; Wouter Boomsma; Eske Willerslev; Rasmus Nielsen

doi:10.1098/rstb.2008.0169

Fast phylogenetic DNA barcoding

Kasper Munch^*, Wouter Boomsma, Eske Willerslev, Rasmus Nielsen

^*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

61 Citations (Scopus)

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.

Original language	English
Journal	Philosophical Transactions of the Royal Society B: Biological Sciences
Volume	363
Issue	1512
Pages (from-to)	3997-4002
Number of pages	6
ISSN	0962-8436
DOIs	https://doi.org/10.1098/rstb.2008.0169
Publication status	Published - 27 Dec 2008

Keywords

Assignment
Barcoding
Neighbour joining
Phylogenetics

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10.1098/rstb.2008.0169

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AU - Munch, Kasper

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AU - Willerslev, Eske

AU - Nielsen, Rasmus

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N2 - 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.

AB - 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.

KW - Assignment

KW - Barcoding

KW - Neighbour joining

KW - Phylogenetics

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JO - Philosophical Transactions of the Royal Society B: Biological Sciences

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Fast phylogenetic DNA barcoding

Abstract

Keywords

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