Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?

Abstract

The ability to discriminate between species using barcoding loci has proved more difficult in plants than animals, raising the possibility that plant species boundaries are less well defined. Here, we review a selection of published barcoding data sets to compare species discrimination in plants vs. animals. Although the use of different genetic markers, analytical methods and depths of taxon sampling may complicate comparisons, our results using common metrics demonstrate that the number of species supported as monophyletic using barcoding markers is higher in animals (> 90%) than plants (~70%), even after controlling for the amount of parsimony-informative information per species. This suggests that more than a simple lack of variability limits species discrimination in plants. Both animal and plant species pairs have variable size gaps between intra- and interspecific genetic distances, but animal species tend to have larger gaps than plants, even in relatively densely sampled genera. An analysis of 12 plant genera suggests that hybridization contributes significantly to variation in genetic discontinuity in plants. Barcoding success may be improved in some plant groups by careful choice of markers and appropriate sampling; however, overall fine-scale species discrimination in plants relative to animals may be inherently more difficult because of greater levels of gene-tree paraphyly.

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

“…A threshold value calculated from genetic distances may be more appropriate than using a single arbitrary 1% or 3% threshold (Meier et al., 2006; Fazekas et al. 2009; Collins & Cruickshank, 2013). In this study, there was little change in the proportion of “correct,” “ambiguous,” and “incorrect” assignments when threshold values of 1%, 3% and a separate calculated threshold for each reference sequence library dataset were used.…”

A DNA barcode for land plants

“…There is little doubt that the approaches used in plant DNA barcoding will be refined in future (22). However, the key foundation step for plant barcoding is in reaching agreement on a standard set of loci to enable large-scale sequencing and the development of a global plant barcoding infrastructure.…”

Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences

“…This study is one of the few that evaluated the efficacy of DNA barcoding among congeneric species (Salvia). Although our sampling was limited to a single genus, dense sampling within a genus and within species is necessary to clarify whether DNA barcoding can successfully delineate species rather than only higher taxonomic levels (e.g., to genus or species groups) (Fazekas et al, 2009;Pettengill and Neel, 2010). In conclusion, our study shows that ITS1 in the nuclear genome is the best DNA barcoding among the considered loci with sufficient variability and high identification efficiency (81.48%).…”