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      Molecular evolution of the ent-kaurenoic acid oxidase gene in Oryzeae

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          Abstract

          We surveyed the substitution patterns in the ent-kaurenoic acid oxidase (KAO) gene in 11 species of Oryzeae with an outgroup in the Ehrhartoidaea. The synonymous and non-synonymous substitution rates showed a high positive correlation with each other, but were negatively correlated with codon usage bias and GC content at third codon positions. The substitution rate was heterogenous among lineages. Likelihood-ratio tests showed that the non-synonymous/synonymous rate ratio changed significantly among lineages. Site-specific models provided no evidence for positive selection of particular amino acid sites in any codon of the KAO gene. This finding suggested that the significant rate heterogeneity among some lineages may have been caused by variability in the relaxation of the selective constraint among lineages or by neutral processes.

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          The origins of genome complexity.

          Michael Lynch, John Conery (2003)
          Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size. According to this model, much of the restructuring of eukaryotic genomes was initiated by nonadaptive processes, and this in turn provided novel substrates for the secondary evolution of phenotypic complexity by natural selection. The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies.
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            The 'effective number of codons' used in a gene.

            F. Wright (1990)
            A simple measure is presented that quantifies how far the codon usage of a gene departs from equal usage of synonymous codons. This measure of synonymous codon usage bias, the 'effective number of codons used in a gene', Nc, can be easily calculated from codon usage data alone, and is independent of gene length and amino acid (aa) composition. Nc can take values from 20, in the case of extreme bias where one codon is exclusively used for each aa, to 61 when the use of alternative synonymous codons is equally likely. Nc thus provides an intuitively meaningful measure of the extent of codon preference in a gene. Codon usage patterns across genes can be investigated by the Nc-plot: a plot of Nc vs. G + C content at synonymous sites. Nc-plots are produced for Homo sapiens, Saccharomyces cerevisiae, Escherichia coli, Bacillus subtilis, Dictyostelium discoideum, and Drosophila melanogaster. A FORTRAN77 program written to calculate Nc is available on request.
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              Statistical methods for detecting molecular adaptation.

              Michael Bielawski, K Bielawski, Yang Yang (2000)
              The past few years have seen the development of powerful statistical methods for detecting adaptive molecular evolution. These methods compare synonymous and nonsynonymous substitution rates in protein-coding genes, and regard a nonsynonymous rate elevated above the synonymous rate as evidence for darwinian selection. Numerous cases of molecular adaptation are being identified in various systems from viruses to humans. Although previous analyses averaging rates over sites and time have little power, recent methods designed to detect positive selection at individual sites and lineages have been successful. Here, we summarize recent statistical methods for detecting molecular adaptation, and discuss their limitations and possible improvements.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genet Mol Biol
                Journal ID (iso-abbrev): Genet. Mol. Biol
                Journal ID (publisher-id): GMB
                Title: Genetics and Molecular Biology
                Publisher: Sociedade Brasileira de Genética (Ribeirão Preto, SP, Brazil )
                ISSN (Print): 1415-4757
                ISSN (Electronic): 1678-4685
                Publication date (Print): Apr-Jun 2012
                Publication date (Electronic): 16 February 2012
                Volume: 35
                Issue: 2
                Pages: 448-454
                Affiliations
                [1 ]Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
                [2 ]State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
                Author notes
                Send correspondence to Yanhua Yang. Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, 212013 Zhenjiang, Jiangsu Province, P.R. China. E-mail: yanhuayang@ 123456126.com .
                Article
                Publisher ID: gmb-35-2-448
                DOI: 10.1590/S1415-47572012005000020
                PMC ID: 3389533
                PubMed ID: 22888294
                SO-VID: 90d6613d-22bc-4c7b-9607-ca2c663ccd05
                Copyright © Copyright © 2012, Sociedade Brasileira de Genética.
                License:

                License information: This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 21 July 2011
                Date accepted : 09 November 2011
                Categories
                Subject: Plant Genetics
                Subject: Research Article

                ScienceOpen disciplines: Molecular biology
                Keywords: ent-kaurenoic acid oxidase (kao),rate heterogeneity,codon usage bias,positive selection,substitution rate
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: ent-kaurenoic acid oxidase (kao), rate heterogeneity, codon usage bias, positive selection, substitution rate

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