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 af dette arbejde

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

50 Citationer (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.

Originalsprog	Engelsk
Tidsskrift	Philosophical Transactions of the Royal Society B: Biological Sciences
Vol/bind	363
Nummer	1512
Sider (fra-til)	3997-4002
Antal sider	6
ISSN	0962-8436
DOI	https://doi.org/10.1098/rstb.2008.0169
Status	Udgivet - 27 dec. 2008

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Citationsformater

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AU - Munch, Kasper

AU - Boomsma, Wouter

AU - Willerslev, Eske

AU - Nielsen, Rasmus

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Y1 - 2008/12/27

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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M3 - Journal article

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EP - 4002

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

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

IS - 1512

ER -

Fast phylogenetic DNA barcoding

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