Abstract
BackgroundDNA barcoding has recently been proposed as a promising tool for the rapid species identification in a wide range of animal taxa. Two broad methods (distance and monophyly-based methods) have been used. One method is based on degree of DNA sequence variation within and between species while another method requires the recovery of species as discrete clades (monophyly) on a phylogenetic tree. Nevertheless, some issues complicate the use of both methods. A recently applied new technique, the character-based DNA barcode method, however, characterizes species through a unique combination of diagnostic characters.Methodology/Principal FindingsHere we analyzed 108 COI and 102 16S rDNA sequences of 40 species of Neogastropoda from a wide phylogenetic range to assess the performance of distance, monophyly and character-based methods of DNA barcoding. The distance-based method for both COI and 16S rDNA genes performed poorly in terms of species identification. Obvious overlap between intraspecific and interspecific divergences for both genes was found. The “10× rule” threshold resulted in lumping about half of distinct species for both genes. The neighbour-joining phylogenetic tree of COI could distinguish all species studied. However, the 16S rDNA tree could not distinguish some closely related species. In contrast, the character-based barcode method for both genes successfully identified 100% of the neogastropod species included, and performed well in discriminating neogastropod genera.Conclusions/SignificanceThis present study demonstrates the effectiveness of the character-based barcoding method for species identification in different taxonomic levels, especially for discriminating the closely related species. While distance and monophyly-based methods commonly use COI as the ideal gene for barcoding, the character-based approach can perform well for species identification using relatively conserved gene markers (e.g., 16S rDNA in this study). Nevertheless, distance and monophyly-based methods, especially the monophyly-based method, can still be used to flag species.
Highlights
DNA barcoding has been proposed as a method that will make species identification faster and more accessible using a small fragment of DNA sequence, in species with complex accessible morphology [1,2,3,4,5,6]
Other 45 c oxidase subunit I (COI) and 44 16S rDNA sequences were obtained from our previous studies [49]
The ‘‘barcoding gap’’ between levels of intraspecific variation and interspecific divergence does not exist in either analysis of COI or 16S rDNA sequences
Summary
DNA barcoding has been proposed as a method that will make species identification faster and more accessible using a small fragment of DNA sequence, in species with complex accessible morphology [1,2,3,4,5,6]. One (distance-based) is based on degree of DNA sequence variation within and between species Another (monophyly-based) requires the recovery of species as discrete clades (monophyly) on a phylogenetic tree [2]. The distance-based approach converts DNA sequences into genetic distances and uses these distances to establish identification schemes. This approach defines a similarity threshold below which a DNA barcode is assigned to a known or a new species. The monophyly-based approach uses monophyly on a phylogenetic tree to assign unknown taxa to a known or new species. One method is based on degree of DNA sequence variation within and between species while another method requires the recovery of species as discrete clades (monophyly) on a phylogenetic tree. A recently applied new technique, the character-based DNA barcode method, characterizes species through a unique combination of diagnostic characters
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