Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification

Abstract

Summary1. DNA barcoding studies use Kimura's two-parameter substitution model (K2P) as the de facto standard for constructing genetic distance matrices. Distances generated under this model then provide the basis for most downstream analyses, but uncertainty in model choice is rarely explored and could potentially affect how reliably DNA barcodes discriminate species. 2. Using information-theoretic approaches for a data set comprising 14 472 DNA barcodes from 14 published studies, we tested whether the K2P model was a good fit at the species level and whether applying a better fitting model biased error rates or changed overall identification success. 3. We report that the K2P was a poorly fitting model at the species level; it was never selected as the best model and very rarely selected as a credible alternative model. Despite the lack of support for the K2P model, differences in distance between best model and K2P model estimates were usually minimal, and importantly, identification success rates were largely unaffected by model choice even when interspecific threshold values were reassessed. 4. Although these conclusions may justify using the K2P model for specimen identification purposes, we found simpler metrics such as p distance performed equally well, perhaps obviating the requirement for model correction in DNA barcoding. Conversely, when incorporating genetic distance data into taxonomic studies, we advocate a more thorough examination of model uncertainty.

DNA barcoding confirms the occurrence of Rhamdia branneri and Rhamdia voulezi (Siluriformes: Heptapteridae) in the Iguaçu River Basin

“…The expectation of this method is that individuals of the same species have lower genetic distance (intraspecific variation) compared to individuals of other species (interspecific variation) (Hebert et al, 2003a), based on chosen threshold. The optimum threshold (OT; Collins et al, 2012) was calculated using the localMinima function, using the R package SPIDER (Species IDentity and Evolution; Brown et al, 2012). SPIDER is a R package implementing a number of useful analyses for DNA barcode studies and research into species delimitation and speciation, with functions essential for generating statistics from DNA barcode data, allowing optimizing divergence threshold limits based on the concept of the barcoding gap (Meyer, Paulay, 2005).…”

A Community of Clones: Snow Algae Are Diverse Communities of Spatially Structured Clones

“…A1-A3 available online), the differences between the two algae were similar but not as strong. It should be noted that the use of K2P to generate genetic distances might not provide the best data to investigate DNA bar-code sequences (Collins et al 2012;Collins and Cruickshank 2013) such as those analyzed here.…”

Six new species of Afrotropical Allodia (Diptera: Mycetophilidae): DNA barcodes indicate recent diversification with a single origin

“…The Neighbor joining (NJ; Saitou & Nei 1987) analysis was computed using the p-distance method (Nei & Kumar 2000), with bootstrap test using 1000 replicates (Felsenstein 1985). The p-distance method was selected based on the results of Sivathsan andMeier (2011), andCollins et al (2012), as the Kimura-2-parameter model gave qualitatively the same result. Additionally, the interspecific p-distances (between group distances) were calculated.…”