(Q33303674)

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Ancestral inference and the study of codon bias evolution: implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup

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scholarly article

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Europe PubMed Central

25 July 2017

Ancestral inference and the study of codon bias evolution: implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup (English)

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Europe PubMed Central

25 July 2017

Drosophila melanogaster

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1 reference

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author name string

Hiroshi Akashi

1

1 reference

Europe PubMed Central

25 July 2017

Piyush Goel

2

1 reference

Europe PubMed Central

25 July 2017

Anoop John

3

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Europe PubMed Central

25 July 2017

language of work or name

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publication date

24 October 2007

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Europe PubMed Central

25 July 2017

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Europe PubMed Central

25 July 2017

2

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Europe PubMed Central

25 July 2017

10

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Europe PubMed Central

25 July 2017

e1065

1 reference

Europe PubMed Central

25 July 2017

copyright license

Creative Commons Attribution 4.0 International

24 October 2007

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April 2022 Public Data File from Crossref

copyright status

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Patterns of molecular variation and evolution in Drosophila americana and its relatives

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Phylogenetic incongruence in the Drosophila melanogaster species group

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Strong regional heterogeneity in base composition evolution on the Drosophila X chromosome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Molecular evolution in the Drosophila melanogaster species subgroup: frequent parameter fluctuations on the timescale of molecular divergence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Recombination enhances protein adaptation in Drosophila melanogaster

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Simultaneous inference of selection and population growth from patterns of variation in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Reconstructing large regions of an ancestral mammalian genome in silico

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Patterns of selection on synonymous and nonsynonymous variants in Drosophila miranda

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Bayesian estimation of ancestral character states on phylogenies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

DNA variability and divergence at the notch locus in Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Effect of misoriented sites on neutrality tests with outgroup.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Compositional evolution of noncoding DNA in the human and chimpanzee genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Vanishing GC-rich isochores in mammalian genomes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Molecular population genetics of Xdh and the evolution of base composition in Drosophila.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Evolution of synonymous codon usage in metazoans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Codon bias differentiates between the duplicated amylase loci following gene duplication in Drosophila.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Population, evolutionary and genomic consequences of interference selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Directional selection and the site-frequency spectrum.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Gene expression and molecular evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Nucleotide polymorphism at the RpII215 gene in Drosophila subobscura. Weak selection on synonymous mutations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Fluctuating mutation bias and the evolution of base composition in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Local recombination and mutation effects on molecular evolution in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Synonymous rates at the RpII215 gene of Drosophila: variation among species and across the coding region

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

PAML: a program package for phylogenetic analysis by maximum likelihood

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Codon usage bias and tRNA abundance in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Long term trends in the evolution of H(3) HA1 human influenza type A

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Episodic adaptive evolution of primate lysozymes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Contingency tests of neutrality using intra/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Historical selection, amino acid polymorphism and lineage-specific divergence at the G6pd locus in Drosophila melanogaster and D. simulans.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

A new method of inference of ancestral nucleotide and amino acid sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

DNA sequence evolution: the sounds of silence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

On the use of nucleic acid sequences to infer early branchings in the tree of life

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Codon usage and tRNA content in unicellular and multicellular organisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Confidence interval for the number of selectively neutral amino acid polymorphisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Codon preferences in free-living microorganisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Adaptive protein evolution at the Adh locus in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Translational accuracy and the fitness of bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

28 July 2018

Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Recent selection on synonymous codon usage in Drosophila.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

The frequency distribution of nucleotide variation in Drosophila simulans

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

The evolution of codon preferences in Drosophila: a maximum-likelihood approach to parameter estimation and hypothesis testing.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Evidence for a high ancestral GC content in Drosophila

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Nucleotide polymorphism in the RpII215 gene region of the insular species Drosophila guanche: reduced efficacy of weak selection on synonymous variation.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Analysis of a shift in codon usage in Drosophila.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

The compositional evolution of the murid genome.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Reconstruction of ancestral nucleotide sequences and estimation of substitution frequencies in a star phylogeny.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Inaccurate reconstruction of ancestral GC levels creates a "vanishing isochores" effect

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Selection on codon usage in Drosophila americana.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Molecular phylogeny of the Drosophila melanogaster species subgroup

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Empirical and hierarchical Bayesian estimation of ancestral states.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Step matrices and the interpretation of homoplasy

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Context dependence, ancestral misidentification, and spurious signatures of natural selection.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

The cost of inbreeding in Arabidopsis.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Adaptive evolution of non-coding DNA in Drosophila

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Problems with Parsimony in Sequences of Biased Base Composition

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Patterns of Base Composition Within the Genes of Drosophila melanogaster

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001065

21 January 2018

Hitchhiking under positive Darwinian selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

31 October 2018

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

31 October 2018

Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2020436

31 October 2018

Mapping mutations on phylogenies

1 reference

https://pubmed.ncbi.nlm.nih.gov/17957249

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods

1 reference

https://pubmed.ncbi.nlm.nih.gov/17957249

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A method for detecting positive selection at single amino acid sites

1 reference

https://pubmed.ncbi.nlm.nih.gov/17957249

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A new method for locating changes in a tree reveals distinct nucleotide polymorphism vs. divergence patterns in mouse mitochondrial control region

1 reference

https://pubmed.ncbi.nlm.nih.gov/17957249

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1371/JOURNAL.PONE.0001065

1 reference

Europe PubMed Central

25 July 2017

2007PLoSO...2.1065A

0 references

1 reference

Europe PubMed Central

25 July 2017

1 reference

Europe PubMed Central

25 July 2017

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