Cytochrome b (Cyt-b) gene sequence analysis in six flatfish species (Teleostei, Pleuronectidae), with phylogenetic and taxonomic insights

Kartavtsev, Yuri; Park, T.-J.; Vinnikov, K. A.; Ivankov, V. N.; Sharina, Svetlana N.; Lee, J.-S.

doi:10.1007/s00227-007-0726-9

Cited by 40 publications

(23 citation statements)

References 36 publications

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“…2). Thus, our findings support a barcoding value of Co-1 gene marker for most current taxa, as also shown in many previous observations (Hebert et al 2004, Ward et al 2005, Kartavtsev & Lee 2006, Kartavtsev et al 2007a,b, 2008, Rock et al 2007, Ward & Holmes 2007, Hubert et al 2008.…”

Section: Discussionsupporting

confidence: 91%

“…The interpretation of nucleotide bias is that it reflects the hydrophobic properties of the encoded proteins (Naylor et al 1995). However, taxonomic differences, when found, are more relevant to the evolution of lineages and might reflect their separate divergence (Kartavtsev et al 2007a). …”

Section: Discussionmentioning

confidence: 99%

“…Finally, this mode forecasts the species formation and later independent evolution of species themselves and consequent divergence of representatives in higher lineages or phyletic evolution (Dobzhansky 1955, Bush 1975, Templeton 1981, Mayr 1982, King 1993, Harrison 1998. Recently, the geographic mode of speciation has been substantiated for many other animals and for a wider list of rank categories including subspecies, semispecies, sibling species, morphologically distinct species and genera (Johns & Avise 1998, Avise 2000, Kartavtsev 2005, Ward et al 2005, Kartavtsev & Lee 2006, Kartavtsev et al 2007a,b, 2008, Ward & Holmes 2007. In these, more than 24 000 species are listed for different comparison groups or taxa.…”

Section: Discussionmentioning

confidence: 99%

“…for Co-1 or Cyt-b, are a useful tool for species discrimination (as DNA barcoding tags) and very helpful for phylogenetic reconstructions, including numerous fish taxa (Avise 2000, Hebert et al 2004, Kim et al 2004, Ward et al 2005, Kartavtsev & Lee 2006. Pooling data such as p-distances (Nei & Kumar 2000), or their derivates, across different taxon levels gives repetitive support for an increase of genetic diversity starting at the intraspecies level and up to higher taxonomic ranks (Johns & Avise 1998, Hebert et al 2004, Kartavtsev 2005, Ward et al 2005, Kartavtsev & Lee 2006, Kartavtsev et al 2007a. This positive and proportional distance score increase along with a taxon rank increase may be used as a helpful attribute in searching for the most common speciation mode, a geographic mode (Ayala et al 1974, Avise 2000.…”

Section: Introductionmentioning

confidence: 99%

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Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan

Kartavtsev¹,

Sharina²,

Goto³

et al. 2009

Aquat. Biol.

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Mitochondrial DNA of the Co-1 gene region was sequenced for 8 fish species (in total 17 sequences of at least 532 bp) from the far east of Russia and compared to 3 other perciform sequences, altogether comprising 20 perch-like fish sequences and 2 outgroup sequences (Cypriniformes). The analysis of the protein-coding Co-1 gene revealed a statistically substantiated bias in the (T+C):(A+G) content, confirming the basic findings on the pyrimidines-prunes ratio. The average scores of p-distances for different scales of the evolutionary history of the Co-1 gene revealed a pattern of increased nucleotide diversity at 4 different levels: (1) intraspecies, (2) intragenus, (3) intrafamily and (4) intraorder. The scores of the average p-distances of the 4 categories of comparison were: (1) 0.11 ± 0.04%, (2) 1.87 ± 0.68%, (3) 12.67 ± 0.28%, and (4) 16.52 ± 0.10%, respectively (mean ± SE). These data support the concept that speciation in the order Perciformes in most cases follows a geographic mode through accumulation of numerous small genetic changes over a long time. The phylogenetic trees for 18 and 21 sequences of perch-like fishes together with 2 other fishes belonging to the ray-finned fishes (Actinopterygii) were developed using the Co-1 gene and 4 different analytical approaches: neighbour-joining (NJ), maximum likelihood (ML), Bayesian (BA) and maximum parsimony (MP). The analysis revealed a monophyletic origin for the representatives of the Stichaeidae, which was the principal percoid family investigated (86, 96 and 100% support in our NJ, ML and BA analyses, respectively). Species identification on a per individual basis or Co-1-based DNA barcoding was high.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan

Kartavtsev¹,

Sharina²,

Goto³

et al. 2009

Aquat. Biol.

View full text Add to dashboard Cite

show abstract

“…These mitochondrial regions have been reported as appropriate for identification of many different kind of organisms (Akasaki, Yanagimoto, Yamakami, Tomonaga, & Sato, 2006;Blanco et al, 2008;Kartavtsev et al, 2007;Lin, Shiau, & Hwang, 2005; McVeigh, due to its mutation rate, and it being a mitochondrial DNA marker, it is expected to a high number of copies per cell, making the PCR amplification easier.…”

Section: Primers and Probe Designmentioning

confidence: 98%

Development of a multiplex PCR–ELISA method for the genetic authentication of Thunnus species and Katsuwonus pelamis in food products

et al. 2015

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Sequence diversity at cytochrome oxidase 1 (Co-1) gene among sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish of Russia Far East with phylogenetic and taxonomic insights

et al. 2009

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Mitochondrial DNA (mtDNA) at Co-1 gene region was sequenced for 7 scorpion fish species (in total, 16 sequences of at least 552 bp) from the Far East of Russia and compared with 15 other sequences of Scorpaeniformes comprising altogether 29 scorpion-like fish sequences and two outgroup sequences (Cypriniformes). The analysis of the protein-coding Co-1 gene revealed statistically substantiated bias in the (T + C) : (A + G) content, proving basic findings. The average scores of p-distances for different scales of the evolutionary history at Co-1 gene revealed a clear pattern of increased nucleotide diversity at four different levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. The scores of average p-distances for the compared fish groups were: (1) 1.00 ± 0.20%, (2) 3.80 ± 0.20%, (3) 12.40 ± 1.20%, and (4) 18.00 ± 0.38%, respectively (mean ± SE). These data support the concept that speciation in the order Scorpaeniformes, in most cases, follows a geographic mode through accumulation of numerous small genetic changes over a long period of time. However, intraspecies diversity was surprisingly high among scorpionfish. Phylogenetic trees for 29 sequences of scorpionfish and 2 other fishes belonging to ray-finned fishes (Actinopterigii) were developed using Co-1 gene and four different analytical approaches: Bayesian (BA), maximum likelihood (ML), neighbour-joining (NJ), and maximum parsimony (MP). The analysis revealed a monophyletic origin for the representatives of Cottidae, which is the principal scorpionfish family investigated (100, 96, 98% support level in our BA, MP, and NJ analyses). Similarly, the monophyletic origin of up to the three compared scorpion-like fish genera was supported by molecular phylogenetic data. Species identification on individual basis (barcoding tagging) was high. A few taxonomic complications arose during the analysis and they are discussed here in.

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Cytochrome b (Cyt-b) gene sequence analysis in six flatfish species (Teleostei, Pleuronectidae), with phylogenetic and taxonomic insights

Cited by 40 publications

References 36 publications

Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan

Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan

Development of a multiplex PCR–ELISA method for the genetic authentication of Thunnus species and Katsuwonus pelamis in food products

Sequence diversity at cytochrome oxidase 1 (Co-1) gene among sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish of Russia Far East with phylogenetic and taxonomic insights

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