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The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny.

Cheng Y, Wang R, Sun Y, Xu T - Genet. Mol. Biol. (2012)

Bottom Line: An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data.The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae.L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China.

ABSTRACT
To understand the phylogenetic position of Larimichthys polyactis within the family Sciaenidae and the phylogeny of this family, the organization of the mitochondrial genome of small yellow croaker was determined herein. The complete, 16,470 bp long, mitochondrial genome contains 37 mitochondrial genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes), as well as a control region (CR), as in other bony fishes. Comparative analysis of initiation/termination codon usage in mitochondrial protein-coding genes of Percoidei species, indicated that COI in Sciaenidae entails an ATG/AGA codon usage different from other Percoidei fishes, where absence of a typical conserved domain or motif in the control regions is common. Partitioned Bayesian analysis of 618 bp of COI sequences data were used to infer the phylogenetic relationships within the family Sciaenidae. An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data. The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae. L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.

No MeSH data available.


Related in: MedlinePlus

Consensus trees of Sciaenidae constructed using Bayesian analysis based on P2 partition-strategies. The accession numbers of species are those listed in Figure 1.
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f2-gmb-35-1-191: Consensus trees of Sciaenidae constructed using Bayesian analysis based on P2 partition-strategies. The accession numbers of species are those listed in Figure 1.


The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny.

Cheng Y, Wang R, Sun Y, Xu T - Genet. Mol. Biol. (2012)

Consensus trees of Sciaenidae constructed using Bayesian analysis based on P2 partition-strategies. The accession numbers of species are those listed in Figure 1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3313511&req=5

f2-gmb-35-1-191: Consensus trees of Sciaenidae constructed using Bayesian analysis based on P2 partition-strategies. The accession numbers of species are those listed in Figure 1.
Bottom Line: An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data.The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae.L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China.

ABSTRACT
To understand the phylogenetic position of Larimichthys polyactis within the family Sciaenidae and the phylogeny of this family, the organization of the mitochondrial genome of small yellow croaker was determined herein. The complete, 16,470 bp long, mitochondrial genome contains 37 mitochondrial genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes), as well as a control region (CR), as in other bony fishes. Comparative analysis of initiation/termination codon usage in mitochondrial protein-coding genes of Percoidei species, indicated that COI in Sciaenidae entails an ATG/AGA codon usage different from other Percoidei fishes, where absence of a typical conserved domain or motif in the control regions is common. Partitioned Bayesian analysis of 618 bp of COI sequences data were used to infer the phylogenetic relationships within the family Sciaenidae. An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data. The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae. L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.

No MeSH data available.


Related in: MedlinePlus