Fast phylogenetic DNA barcoding

TY - JOUR

T1 - Fast phylogenetic DNA barcoding

AU - Terkelsen, Kasper Munch

AU - Boomsma, Wouter Krogh

AU - Willerslev, Eske

AU - Nielsen, Rasmus

N1 - KEYWORDS: assignment, barcoding, phylogenetics, neighbour joining

PY - 2008

Y1 - 2008

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.

U2 - 10.1098/rstb.2008.0169

DO - 10.1098/rstb.2008.0169

M3 - Journal article

C2 - 18852104

SN - 0962-8436

VL - 363

SP - 3997

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 -