Likelihood-ratio tests for positive selection of human and mouse duplicate genes reveal nonconservative and anomalous properties of widely used methods

scientific article published on 03 August 2006

Likelihood-ratio tests for positive selection of human and mouse duplicate genes reveal nonconservative and anomalous properties of widely used methods is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1016/J.YMPEV.2006.07.015
P698PubMed publication ID16959502

P50authorAustin L. HughesQ107333432
P2093author name stringRobert Friedman
P2860cites workCLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceQ24286950
Structure of the human class I histocompatibility antigen, HLA-A2Q24297966
Gapped BLAST and PSI-BLAST: a new generation of protein database search programsQ24545170
The evolutionary fate and consequences of duplicate genesQ27861065
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary modelsQ28144403
Evolution of synonymous codon usage in metazoansQ28214982
On Some Principles Governing Molecular EvolutionQ28776018
Bayes empirical bayes inference of amino acid sites under positive selectionQ29547692
Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selectionQ29616615
Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selectionQ33835136
Adaptive protein evolution in DrosophilaQ34116884
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sitesQ34569737
Enhanced immunological surveillance in mice heterozygous at the H-2 gene complexQ43880398
Preponderance of synonymous changes as evidence for the neutral theory of molecular evolutionQ44492208
False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virusQ45667557
Large-scale search for genes on which positive selection may operateQ48064461
Accelerated evolution in the reactive centre regions of serine protease inhibitorsQ48348346
The evolution of functionally novel proteins after gene duplication.Q55065818
The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigensQ59092174
Tests for positive selection on immune and reproductive genes in closely related species of the murine genus musQ73069252
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolutionQ74258476
Frequent false detection of positive selection by the likelihood method with branch-site modelsQ79763451
Differential loss of ancestral gene families as a source of genomic divergence in animalsQ79968253
Variation in the pattern of synonymous and nonsynonymous difference between two fungal genomesQ81474733
P433issue2
P1104number of pages6
P304page(s)388-393
P577publication date2006-08-03
P1433published inMolecular Phylogenetics and EvolutionQ4248868
P1476titleLikelihood-ratio tests for positive selection of human and mouse duplicate genes reveal nonconservative and anomalous properties of widely used methods
P478volume42

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cites work (P2860)
Q28648310Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga)
Q21145221Gene family evolution across 12 Drosophila genomes
Q38696679Lineage-specific duplications of Muroidea Faim and Spag6 genes and atypical accelerated evolution of the parental Spag6 gene
Q34648294Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level
Q33316586Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids
Q35044415Molecular adaptation of telomere associated genes in mammals
Q92180163Molecular evolution of mammalian genes with epistatic interactions in fertilization
Q42594425Molecular evolution of the CPP-like gene family in plants: insights from comparative genomics of Arabidopsis and rice
Q37193352Near neutrality: leading edge of the neutral theory of molecular evolution
Q36857726Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
Q36935355The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC
Q42590484Uncorrected nucleotide bias in mtDNA can mimic the effects of positive Darwinian selection.

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