Phylogenetic analysis of Altai osmans of the genus Oreoleuciscus (Pisces, Cyprinidae, Leuciscinae), based on the analysis of the cytochrome oxidase 1 gene (Co-1) sequence

Батищева, Н. М.; Kartavtsev, Yuri; Bogutskaya, Nina G.

doi:10.1134/s1022795411100036

Cited by 14 publications

(7 citation statements)

References 19 publications

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“…The results presented in this work confirm that COI can be reliably used from a barcode perspective to distinguish between specimens of the African Cyprinidae in a dataset of 315 specimens representing 14 out of the 24 (58 %) recognised genera in Africa. For example, a significant barcode gap was found irrespective of the methods used, and this has also been reported for Cyprinidae of other geographic regions (e.g., Batishchevaa et al 2011). Our results (79.4 %-92.1 %) from the distance-based method showed a pattern similar to the 90 % to 99 % discriminatory power reported for ornamental cyprinid fish species also mostly from Cyprininae and Danioninae and a catostomid (Collins et al 2012).…”

Section: Discussionsupporting

confidence: 87%

“…2013) as well as the recent development of new generation sequencing techniques (e.g., Taylor and Harris 2012), the marker COI still remains useful for identification purposes (Batishchevaa et al 2011;Collins et al 2012;Van der Bank et al 2013). For example, the high level of COI discrimination is further supported by the test of species monophyly, a test that resulted in strongly supported clades based on Rosenberg (2007)'s probability of reciprocal monophyly on the NJ tree (see also Collins et al 2012).…”

Section: Discussionmentioning

confidence: 99%

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Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Adeoba¹,

Kabongo²,

Bank³

et al. 2018

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Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for comparative phylogenetic analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Adeoba¹,

Kabongo²,

Bank³

et al. 2018

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show abstract

Section: Discussionsupporting

confidence: 86%

“…Nodes in red are strongly supported nodes, indicating species monophyly. 2013) as well as the recent development of new generation sequencing techniques (e.g., Taylor and Harris 2012), the marker COI still remains useful for identification purposes (Batishchevaa et al 2011;Collins et al 2012;Van der Bank et al 2013). For example, the high level of COI discrimination is further supported by the test of species monophyly, a test that resulted in strongly supported clades based on Rosenberg (2007)'s probability of reciprocal monophyly on the NJ tree (see also Collins et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Adeoba¹,

Kabongo²,

Bank³

et al. 2018

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Citation: Adeoba MI, Kabongo R, Van der Bank H, Yessoufou K (2018) Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). ZooKeys 746: 105-121. https://doi. AbstractSpecimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae. A peer-reviewed open-access journalMariam I. Adeoba et al. / ZooKeys 746: 105-121 (2018) 106

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“…The cytochrome c oxidase subunit I gene (COI) appears to be the most conservative protein coding genes in the mitochondria] genome, and it commonly been used in molecular phylogenetic or taxonomic studies [12][13][14]. COI has been proposed as the univer sal DNA barcode for animals [15], and it provides a practical means to differentiate among morphospecies of naked lobose amoeba [16].…”

Section: Introductionmentioning

confidence: 99%

Further resolving the phylogeny of Myxogastria (slime molds) based on COI and SSU rRNA genes

2015

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To date, molecular systematics of Myxogastria has been based primarily on small subunit riboso mal RNA (SSU rRNA) and elongation factor 1 alpha (EF 1α) genes. To establish a natural classification sys tem for the organisms, we examined phylogenetic relationships among myxogastrian species using cyto chrome c oxidase subunit I (COI) and SSU rRNA genes. Twenty new sequences were obtained, including 10 COI and 10 SSU rRNA sequences, were compared with sequences of related species from GenBank in order to construct phylogenic trees. The analysis of the two data sets supported the modern phylogeny of myxogastria: orders Liceida and Trichiida formed a sister group at the most basal clade, while orders Ste monitida and Physarida formed a close group, and order Echinostelida was a sister group to Stemonitida and Physarida. However, the partial COI sequences were too conserved to resolve of the branches in Stemonitida and Physarida. In addition, we also deemed the specific edited mRNA events of COI sequences in myxogas trian species.

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Phylogenetic analysis of Altai osmans of the genus Oreoleuciscus (Pisces, Cyprinidae, Leuciscinae), based on the analysis of the cytochrome oxidase 1 gene (Co-1) sequence

Cited by 14 publications

References 19 publications

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Further resolving the phylogeny of Myxogastria (slime molds) based on COI and SSU rRNA genes

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