After the following two articles, I got confused and am trying to figure out whether the method of DNA barcoding gap to identify species is suitable or not. How should i treat this method?
Srivathsan, A., & Meier, R. (2012). On the inappropriate use of Kimura‐2‐parameter (K2P) divergences in the DNA‐barcoding literature. Cladistics, 28(2), 190-194. DOI: 10.1111/j.1096-0031.2011.00370.x
Klemen Candek and Matjaz Kuntner. (2015). DNA barcoding gap: reliable species identification over morphological and geographical scales. Molecular Ecology Resources (2015) 15, 268–277. DOI: 10.1111/1755-0998.12304
Barcode Gap is a suitable method to delineate species from a set of aligned sequences as long as you have enough sequences per species. Yet, it is important to remind that Barcode Gap should not be the only criterion! Complementary evidences like other genetic markers, morphology and distribution are necessary to make a decision. I recommend reading the ABGD method, see link attached.
Once you have established a reference dataset with barcode gap then you can be confident with the identification of an unknown specimen through it's barcode sequence.
Hope that helps.
Article ABGD, Automatic Barcode Gap Discovery for primary species delimitation
K2P weighs transitions and transversions differently, while standard uncorrected distances treat all nucleotide transformations as having equal weight. Generally speaking, for closely-related taxa, the number of nucleotide differences over the 640 bp stretch of the COI barcode is so small (like two or three individual changes) that a differential weighting scheme does not make any difference.
Dear Fan.
Before calculating the K2P distances, you always can obtain which is the evolutionary model that best fit to your dataset and use that one for obtaining them. You can also use the uncorrected distances.
Hope this helps.
The K2P nucleotide substitution model is one of most comun models used for phylogeny recostruction, its suppost is transition, and transvertion occur a the same rate, however, no all data set has the same sustitution rate,there are many sustituion models, that include transition rates, change proportion, gamma distribution...among other, then what is the best model to be used in your data set, Modeltest, JModel test are algoritmos than can be used to find the best model. the result of this test can be the best option if you use distances o ML recostruction method.
Those can be implented in MEGA o Jmodeltest
Hope this can help you
https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msn083
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