On the inappropriate use of Kimura‐2‐parameter (K2P) divergences in the DNA‐barcoding literature

Srivathsan, Amrita; Meier, Rudolf

doi:10.1111/j.1096-0031.2011.00370.x

Cited by 348 publications

(230 citation statements)

References 35 publications

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“…The K2P model has been recently criticized as being inappropriate in some cases for divergence estimation and having no evident advantages over uncorrected p-distance (Srivathsan and Meier 2012). Indeed, a comparison of K2P with p-distances in our dataset showed high correlation between both distance metrics (Pearson correlation = 0.9980, P < 2.2e − 16; Additional file 4).…”

Section: Barcoding Gapmentioning

confidence: 83%

DNA barcoding of Palaearctic Ulidiidae (Diptera: Tephritoidea): morphology, DNA evolution, and Markov codon models

et al. 2014

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Background: Here, for the first time, we report a barcoding survey of the dipterian family Ulidiidae (with two subfamilies Ulidiinae and Otitinae) coupled with morphology. To date, this is the first comprehensive analysis of the family that relies on molecular data. To reconstruct probable higher-level phylogenetic relationships between the genera of Ulidiidae, we exploited maximum likelihood and Bayesian inference, and additionally, we utilized a modern Markov model of codon substitutions for protein-coding genes coupled with the maximum likelihood approach to establish more realistic evolutionary scenarios connecting Ulidiinae and Otitinae. Results: Though we found morphological synapomorphic characters that clearly distinguish two groups of genera, formerly relating to two subfamilies, the monophyly of the clade Otitinae was not firmly supported by molecular phylogenetic reconstructions. The subfamily Ulidiinae was recovered as the basal likely paraphyletic group with high reliability. Overall, our results suggest the inclusion of the genera Homalocephala and Seioptera into the tribe Seiopterini (Otitinae). Three genera of Ulidiinae (Physiphora, Timia, Ulidia), eight genera of Otitinae (Ceroxys, Herina, Melieria, Myennis, Otites, Pseudotephritis, Seioptera, Tetanops), and the genus of Homalocephala with still unconfirmed systematic status were included in the analysis.

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Section: Barcoding Gapmentioning

confidence: 83%

DNA barcoding of Palaearctic Ulidiidae (Diptera: Tephritoidea): morphology, DNA evolution, and Markov codon models

et al. 2014

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“…Genetic distance calculations were performed using uncorrected P distance (Srivathsan & Meier 2012).…”

Section: Resultsmentioning

confidence: 99%

The Bupleurum (Apiaceae) feeding species of Trifurcula (Glaucolepis): new species, biology and distribution (Lepidoptera: Nepticulidae)

Laštůvka

Laštůvka²,

Nieukerken

2013

Tijdschr Entomol

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The Bupleurum feeding species of Trifurcula (Glaucolepis) Braun, 1917 are revised. Five species are recognised: T. bupleurella (Chrétien, 1907), T. sanctibenedicti Klimesch, 1979, T. megaphallus van Nieukerken, Z. Laštůvka & A. Laštůvka sp. n. feeding on Bupleurum gibraltarium in southern Spain, T. chretieni Z. Laštůvka, A. Laštůvka & van Nieukerken sp. n. feeding on Bupleurum rigidum in southern France, Spain and Portugal, and T. siciliae Z. Laštůvka, A. Laštůvka & van Nieukerken sp. n. feeding on B. fruticosum in Sicily. The group is restricted to southwestern Europe and northern Africa, the area where most shrubby Bupleurum species occur. A NJ and Bayesian analysis of DNA barcodes of four out of five species suggest a single origin of Bupleurum feeding in the subgenus Glaucolepis.

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“…Nevertheless, its applicability is under debate. According to Srivathsan & Meier (2012) the model did not appear to increase identification success and might not be entirely suitable for closely related COI sequences.…”

Section: Dna Barcodingmentioning

confidence: 99%

Evaluation of criteria for species delimitation of bagworm moths (Lepidoptera: Psychidae)

Chevasco¹,

Elzinga²,

Mappes³

et al. 2014

Eur. J. Entomol.

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Abstract. Accurate identification of species is fundamental for biological research and necessary for species conservation. DNA barcoding is particularly useful when identification using morphological characteristics is laborious and/or unreliable. However, barcodes for species are dependent on the availability of reference sequences from correctly identified specimens. The traditional use of morphology to delimit the species boundaries of Finnish bagworm moths (Lepidoptera: Psychidae: Naryciinae: Dahliciini) is controversial because there is overlap in their morphological characteristics. In addition, there are no suitable molecular markers. We verified the delimitation of seven out of eight previously described taxa, by using the currently standardized COI barcode and phylogenetic inference based on fragments of mitochondrial (COI) and nuclear genes (MDH). Moreover, we compared the results of molecular methods with the outcome of geometric morphometrics. Based on molecular identification, our findings indicate that there are five sexual species (Dahlica and Siederia spp.) and two parthenogenetic species (D. fennicella and D. triquetrella) in Finland. We suggest that molecular methods, together with geometric morphometrics of male genitalia are an effective way of delimiting species of bagworm moths.

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On the inappropriate use of Kimura‐2‐parameter (K2P) divergences in the DNA‐barcoding literature

Cited by 348 publications

References 35 publications

DNA barcoding of Palaearctic Ulidiidae (Diptera: Tephritoidea): morphology, DNA evolution, and Markov codon models

DNA barcoding of Palaearctic Ulidiidae (Diptera: Tephritoidea): morphology, DNA evolution, and Markov codon models

The Bupleurum (Apiaceae) feeding species of Trifurcula (Glaucolepis): new species, biology and distribution (Lepidoptera: Nepticulidae)

Evaluation of criteria for species delimitation of bagworm moths (Lepidoptera: Psychidae)

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