Abstract
DNA barcoding shows enormous promise for the rapid identification of organisms at the species level. There has been much recent debate, however, about the need for longer barcode sequences, especially when these sequences are used to construct molecular phylogenies. Here, we have analysed a set of fungal mitochondrial sequences — of various lengths — and we have monitored the effect of reducing sequence length on the utility of the data for both species identification and phylogenetic reconstruction. Our results demonstrate that reducing sequence length has a profound effect on the accuracy of resulting phylogenetic trees, but surprisingly short sequences still yield accurate species identifications. We conclude that the standard short barcode sequences (∼600 bp) are not suitable for inferring accurate phylogenetic relationships, but they are sufficient for species identification among the fungi.
Highlights
DNA barcoding has been promoted as a potentially powerful method for the efficient, accurate and high throughput assignment of unknown specimens to known species
As we found that protein-guided DNA sequence alignment was more accurate, we used these aligned five gene-DNA sequences and DNA barcode sequences and compared the trees constructed by different methods including NJ with Kimura 2parameter (K2P) model, Jukes-Cantor model, Tajima-Nei model and LogDet model (Kumar et al 2004); maximum parsimony with close-neighbour-interchange (CNI) search method and min-mini heuristic search method (Kumar et al 2004); and maximum likelihood (Guindon et al 2005)
The resulting tree topologies are in good agreement with accepted fungal phylogeny (Bullerwell et al 2003a, b; Kouvelis et al 2004), and the majority of the internal nodes are supported by bootstrap analysis
Summary
DNA barcoding has been promoted as a potentially powerful method for the efficient, accurate and high throughput assignment of unknown specimens to known species. It has been tested in a number of animal taxa, including birds (Hebert et al 2004b), fishes (Ward et al 2005), and Lepidopteran insects (Hebert et al 2004a; Hajibabaei et al 2006a). In all of these studies, a 648-bp region of the mitochondrial cytochrome c oxidase I (COI or cox1) has been evaluated and used as a ‘biological barcode’ for species identification.
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