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Identification of differentially evolved genes: an alternative approach to detection of accelerated molecular evolution from genome-wide comparative data.

Kim KW, Burt DW, Kim H, Cho S - Evol. Bioinform. Online (2013)

Bottom Line: We compared devogs with a branch model method using virtual data and a varying ω ratio, in which parameters were obtained from real data.Devogs showed greater positive predictive value, whereas the branch model method had greater sensitivity.In a working example using devogs, a group of human RNA polymerase II-related genes, which are important in mediating alternative splicing, were significantly accelerated compared to four other mammals.

View Article: PubMed Central - PubMed

Affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea.

ABSTRACT
One of the most important measures for detecting molecular adaptations between species/lineages at the gene level is the comparison of relative fixation rates of synonymous (dS) and non-synonymous (dN) mutations. This study shows that the branch model is sensitive to tree topology and proposes an alternative approach, devogs, which does not require phylogenetic topology for analysis. We compared devogs with a branch model method using virtual data and a varying ω ratio, in which parameters were obtained from real data. The positive predictive value, sensitivity, and specificity of the branch model were affected by the phylogenic tree topology. Devogs showed greater positive predictive value, whereas the branch model method had greater sensitivity. In a working example using devogs, a group of human RNA polymerase II-related genes, which are important in mediating alternative splicing, were significantly accelerated compared to four other mammals.

No MeSH data available.


Branch length for generating virtual data.
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Related In: Results  -  Collection


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f2-ebo-9-2013-285: Branch length for generating virtual data.

Mentions: To compare the two methods under real conditions, we constructed virtual data using real parameters, including tree topology (excluding ω, which is the variable being manipulated). A total of 30 orthologous gene sets, which reduced the computational burden, were selected randomly from the genomes of human, mouse, rat, dog, and opossum obtained from ENSEMBL15 to choose parameter values, including codon usage, substitutions per codon, and sequence length. Test DNA sequences from the five species were generated using the evolver program in PAML4.2 (kappa = 2.0, tree length = 0) based on the actual parameters.18 The phylogenetic tree and branch lengths converted to species divergence times, as required by the evolver program, were obtained from a previous report (Fig. 2).19 In addition, the branch lengths were rescaled based on the average number of substitutions per codon between mice and humans. We included an accelerated branch with a higher ω ratio to compare human, mouse, rat, dog, and opossum branches when generating data. Differences in the ω ratio between the accelerated branch and other branches ranged from 0 to 1.2 (steps of 0.1).


Identification of differentially evolved genes: an alternative approach to detection of accelerated molecular evolution from genome-wide comparative data.

Kim KW, Burt DW, Kim H, Cho S - Evol. Bioinform. Online (2013)

Branch length for generating virtual data.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3733729&req=5

f2-ebo-9-2013-285: Branch length for generating virtual data.
Mentions: To compare the two methods under real conditions, we constructed virtual data using real parameters, including tree topology (excluding ω, which is the variable being manipulated). A total of 30 orthologous gene sets, which reduced the computational burden, were selected randomly from the genomes of human, mouse, rat, dog, and opossum obtained from ENSEMBL15 to choose parameter values, including codon usage, substitutions per codon, and sequence length. Test DNA sequences from the five species were generated using the evolver program in PAML4.2 (kappa = 2.0, tree length = 0) based on the actual parameters.18 The phylogenetic tree and branch lengths converted to species divergence times, as required by the evolver program, were obtained from a previous report (Fig. 2).19 In addition, the branch lengths were rescaled based on the average number of substitutions per codon between mice and humans. We included an accelerated branch with a higher ω ratio to compare human, mouse, rat, dog, and opossum branches when generating data. Differences in the ω ratio between the accelerated branch and other branches ranged from 0 to 1.2 (steps of 0.1).

Bottom Line: We compared devogs with a branch model method using virtual data and a varying ω ratio, in which parameters were obtained from real data.Devogs showed greater positive predictive value, whereas the branch model method had greater sensitivity.In a working example using devogs, a group of human RNA polymerase II-related genes, which are important in mediating alternative splicing, were significantly accelerated compared to four other mammals.

View Article: PubMed Central - PubMed

Affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea.

ABSTRACT
One of the most important measures for detecting molecular adaptations between species/lineages at the gene level is the comparison of relative fixation rates of synonymous (dS) and non-synonymous (dN) mutations. This study shows that the branch model is sensitive to tree topology and proposes an alternative approach, devogs, which does not require phylogenetic topology for analysis. We compared devogs with a branch model method using virtual data and a varying ω ratio, in which parameters were obtained from real data. The positive predictive value, sensitivity, and specificity of the branch model were affected by the phylogenic tree topology. Devogs showed greater positive predictive value, whereas the branch model method had greater sensitivity. In a working example using devogs, a group of human RNA polymerase II-related genes, which are important in mediating alternative splicing, were significantly accelerated compared to four other mammals.

No MeSH data available.