“COI-like” Sequences Are Becoming Problematic in Molecular Systematic and DNA Barcoding Studies

Buhay, Jennifer E.

doi:10.1651/08-3020.1

Cited by 303 publications

(282 citation statements)

References 57 publications

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“…They have been found in a wide range of crustacean taxa including calanoid copepods (Bucklin et al, 1999(Bucklin et al, , 2000Machida and Lin, 2017) and diaptomid calanoids (Thum and Harrison, 2009;Marrone et al, 2013). The aberrant sequences found in this study do not contain any stop codons or frame shifts, and therefore do not resemble classical nuclear mitochondrial pseudogenes (so called numts) that often contain InDels (Insertion/Deletions) and mutations at any codon position (Song et al, 2008;Buhay, 2009;Calvignac et al, 2011). Still, the pronounced nucleotide diversity of the sequences may indicate a recent translocation of a COI copy to the nucleus.…”

Section: Discussionmentioning

confidence: 66%

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Population genetic structure of Calanoides natalis (Copepoda, Calanoida) in the eastern Atlantic Ocean and Benguela upwelling system

Höring¹,

Cornils²,

Auel³

et al. 2017

Journal of Plankton Research

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The population genetic structure of Calanoides natalis (ex Calanoides carinatus; Copepoda, Calanoida), an ecologically important component of African upwelling systems, was studied in order to (i) search for potential cryptic species, (ii) describe spatial patterns in the distribution of genetic variance and (iii) identify potential barriers to gene flow. Samples were obtained in the eastern Atlantic Ocean from the Iberian Peninsula to Namibia. Analysis of mitochondrial (cytochrome c oxidase subunit I; COI) and nuclear (citrate synthase; CS) marker genes revealed a genetically cohesive population of C. natalis with a prevalent shift in allele frequencies. The discovery of a deep split solely present in the mitochondrial dataset does not point to cryptic speciation, but rather suggests the occurrence of nuclear mitochondrial pseudogenes or incomplete reproductive isolation upon secondary contact. Genetic differentiation between the northern and southern hemisphere was significant, which may point to a potential, but permeable barrier close to the equator. No vertical genetic structuring was detected in the northern Benguela implying that horizontal differentiation was more pronounced than vertical structuring. Retention mechanisms and the oxygen minimum zone did not have a strong impact on genetic differentiation of C. natalis in the Benguela region.

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Section: Discussionmentioning

confidence: 66%

“…COI-like sequences have often been reported as a problematic feature in molecular genetics (Buhay, 2009) Significant results in bold, significance level *(P < 0.05), **(P < 0.01) and ***(P < 0.001). Significant results are indicated with *(P < 0.05), **(P < 0.01) and ***(P < 0.001).…”

Section: Discussionmentioning

confidence: 99%

Population genetic structure of Calanoides natalis (Copepoda, Calanoida) in the eastern Atlantic Ocean and Benguela upwelling system

Höring¹,

Cornils²,

Auel³

et al. 2017

Journal of Plankton Research

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“…Numts have been observed from several crustacean species (Buhay, 2009;Bybee et al, 2011;da Silva et al, 2011), the main cause being false diversity in certain species. During this study, the sequencing data was manually checked and approximately 10% of the sequencing results were excluded due to low quality chromatograms that appeared randomly in all studied populations.…”

Section: Figure 2 Maximum Likelihood (Ml) -Tree Of the Sequenced Coi-mentioning

confidence: 99%

Mitochondrial cytochrome oxidase I gene analysis indicates a restricted genetic background in Finnish noble crayfish(Astacus astacus)stocks

Makkonen

Kokko

Jussila

2015

Knowl. Manag. Aquat. Ecosyst.

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Key-words:noble crayfish, native species, population decline, genetic diversity, cytochrome oxidase IThe IUCN Red List indexes the noble crayfish (Astacus astacus) as vulnerable, with a declining population trend. The main threats to the species are the crayfish plague caused by the oomycete Aphanomyces astaci and the introduced North American crayfish that act as the carriers of this disease. In Finland, the noble crayfish is considered as a native species, which original distribution area covers the southern part of the country, but the species distribution has been dispersed to cover almost the whole country. The aim of this study was to survey the genetic diversity among the Finnish noble crayfish populations. The mitochondrial cytochrome oxidase I (COI)-gene was sequenced from 742 individuals representing 59 populations from Finland and Estonia. As a result, only a single haplotype was found. Based on these results, the genetic diversity of noble crayfish in its Northern distribution range is remarkably low. The observed lack of variation can result from several mechanisms including small size of the founder population and the intense spreading of the species by manmade stockings. The restricted diversity can also be caused by eradication of the original populations due to crayfish plague epidemics and spreading of the invasive crayfish species carrying the crayfish plague. It is also possible that all contemporary Finnish noble crayfish populations originate from stockings with no variation in respect to COI-gene. RÉSUMÉ L'analyse du gène mitochondrial du cytochrome oxydase I indique un fond génétique restreint dans les populations finlandaises de l'écrevisse à pattes rouges (Astacus astacus)

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“…In this study, we also assessed the quality of our cox1 data set by evaluating the reproducibility of our DNA sequencing procedure and by using comparative analyses to check for the presence of contaminating nuclearmitochondrial DNA (numts), as both factors have been shown to bias evolutionary genetic analyses severely (Clark and Whittam, 1992;Buhay, 2009). In addition, we applied a new 'Bayesian Skyride' method to infer the demographic history of swarms.…”

Section: Introductionmentioning

confidence: 99%

Swarms of diversity at the gene cox1 in Antarctic krill

et al. 2010

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“COI-like” Sequences Are Becoming Problematic in Molecular Systematic and DNA Barcoding Studies

Cited by 303 publications

References 57 publications

Population genetic structure of Calanoides natalis (Copepoda, Calanoida) in the eastern Atlantic Ocean and Benguela upwelling system

Population genetic structure of Calanoides natalis (Copepoda, Calanoida) in the eastern Atlantic Ocean and Benguela upwelling system

Mitochondrial cytochrome oxidase I gene analysis indicates a restricted genetic background in Finnish noble crayfish(Astacus astacus)stocks

Swarms of diversity at the gene cox1 in Antarctic krill

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