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Rates of Conservative and Radical Nonsynonymous Nucleotide Substitutions in Mammalian Nuclear Genes

https://doi.org/10.1007/s002399910007
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Evolution of Cysteine Proteinases in Eukaryotes
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Adaptive evolution in the rat olfactory receptor gene family
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Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory
inferredcites →https://doi.org/10.1007/bf00167113openalex-snapshot
New methods for estimating the numbers of synonymous and nonsynonymous substitutions
inferredcites →https://doi.org/10.1007/bf01731581openalex-snapshot
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
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Two types of amino acid substitutions in protein evolution
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Patterns of nucleotide substitution in pseudogenes and functional genes
inferredcites →https://doi.org/10.1007/bf02100628openalex-snapshot
Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications
inferredcites →https://doi.org/10.1007/bf02407308openalex-snapshot
Unbiased estimation of the rates of synonymous and nonsynonymous substitution
inferredcites →https://doi.org/10.1007/pl00006223openalex-snapshot
Mutation Pattern Variation Among Regions of the Primate Genome
inferredcites →https://doi.org/10.1007/pl00006320openalex-snapshot
Synonymous and nonsynonymous rate variation in nuclear genes of mammals
inferredcites →https://doi.org/10.1016/b978-1-4832-2734-4.50017-6openalex-snapshot
Evolutionary Divergence and Convergence in Proteins
inferredcites →https://doi.org/10.1016/b978-1-4832-3211-9.50009-7openalex-snapshot
Evolution of Protein Molecules
inferredcites →https://doi.org/10.1038/210025a0openalex-snapshot
Role of the Amino-Acid ‘Code’ and of Selection for Conformation in the Evolution of Proteins
inferredcites →https://doi.org/10.1038/215355a0openalex-snapshot
Non-randomness of Ammo-acid Changes in the Evolution of Homologous Proteins
inferredcites →https://doi.org/10.1038/228159a0openalex-snapshot
Selective Constraints on Amino-acid Substitutions during the Evolution of Proteins
inferredcites →https://doi.org/10.1073/pnas.95.7.3708openalex-snapshot
Positive Darwinian selection after gene duplication in primate ribonuclease genes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025743openalex-snapshot
Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040056openalex-snapshot
Theoretical foundation of the minimum-evolution method of phylogenetic inference.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040140openalex-snapshot
Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040343openalex-snapshot
A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040410openalex-snapshot
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040626openalex-snapshot
Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040715openalex-snapshot
Coevolution of the vertebrate integrin alpha- and beta-chain genes.
inferredcites →https://doi.org/10.1126/science.153.3734.420openalex-snapshot
Genetic Code: Aspects of Organization
inferredcites →https://doi.org/10.1146/annurev.ecolsys.23.1.263openalex-snapshot
The Nearly Neutral Theory of Molecular Evolution

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inferred← citeshttps://doi.org/10.1073/pnas.0701256104openalex-snapshot
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inferred← citeshttps://doi.org/10.1073/pnas.080071397openalex-snapshot
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Computational Molecular Evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.002.0004openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.002.0005openalex-snapshot
Dedication
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.002.0006openalex-snapshot
Preface
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0001openalex-snapshot
Models of nucleotide substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0002openalex-snapshot
Models of amino acid and codon substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0003openalex-snapshot
Phylogeny reconstruction: overview
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0004openalex-snapshot
Maximum likelihood methods
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0005openalex-snapshot
Bayesian methods
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0006openalex-snapshot
Comparison of methods and tests on trees
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0007openalex-snapshot
Molecular clock and estimation of species divergence times
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0008openalex-snapshot
Neutral and adaptive protein evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0009openalex-snapshot
Simulating molecular evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0010openalex-snapshot
Perspectives
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.005.0001openalex-snapshot
Appendices
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.001.0001openalex-snapshot
Molecular Evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.002.0003openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.002.0004openalex-snapshot
Foreword
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.002.0005openalex-snapshot
Preface
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0001openalex-snapshot
Models of nucleotide substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0002openalex-snapshot
Models of amino acid and codon substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0003openalex-snapshot
Phylogeny reconstruction: overview
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0004openalex-snapshot
Maximum likelihood methods
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0005openalex-snapshot
Comparison of phylogenetic methods and tests on trees
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0006openalex-snapshot
Bayesian theory
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0007openalex-snapshot
Bayesian computation (MCMC)
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0008openalex-snapshot
Bayesian phylogenetics
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0009openalex-snapshot
Coalescent theory and species trees
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0010openalex-snapshot
Molecular clock and estimation of species divergence times
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0011openalex-snapshot
Neutral and adaptive protein evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0012openalex-snapshot
Simulating molecular evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0013openalex-snapshot
Appendices
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq532openalex-snapshot
Characterizing molecular adaptation: a hierarchical approach to assess the selective influence of amino acid properties
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty261openalex-snapshot
An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins
inferred← citeshttps://doi.org/10.1093/biolinnean/blaa173openalex-snapshot
Oxytocin amino acid variation within Neotropical primates: new genetic variants in hormone and receptor sequences and evidence for evolutionary forces driving this unexpected diversity
inferred← citeshttps://doi.org/10.1093/evolut/qpad107openalex-snapshot
An investigation of the sex-specific genetic architecture of fitness in Drosophila melanogaster
inferred← citeshttps://doi.org/10.1093/gbe/evag052openalex-snapshot
Evidence of Relaxed Selection in the Mitochondrial Genomes of Phototrophic Paulinella Lineages
inferred← citeshttps://doi.org/10.1093/gbe/evt054openalex-snapshot
Functional and Evolutionary Analysis of the Genome of an Obligate Fungal Symbiont
inferred← citeshttps://doi.org/10.1093/gbe/evt083openalex-snapshot
Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds
inferred← citeshttps://doi.org/10.1093/gbe/evu099openalex-snapshot
Efficient Purging of Deleterious Mutations in Plants with Haploid Selfing
inferred← citeshttps://doi.org/10.1093/gbe/evu294openalex-snapshot
A Simple Method for Estimating the Strength of Natural Selection on Overlapping Genes
inferred← citeshttps://doi.org/10.1093/gbe/evv216openalex-snapshot
Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex
inferred← citeshttps://doi.org/10.1093/gbe/evx189openalex-snapshot
Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families
inferred← citeshttps://doi.org/10.1093/gbe/evx235openalex-snapshot
Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System
inferred← citeshttps://doi.org/10.1093/genetics/165.3.1279openalex-snapshot
Patterns of Nucleotide Polymorphism and Divergence in the Odorant-Binding Protein Genes OS-E and OS-F: Analysis in the Melanogaster Species Subgroup of Drosophila
inferred← citeshttps://doi.org/10.1093/genetics/iyab083openalex-snapshot
Population dynamics of GC-changing mutations in humans and great apes
inferred← citeshttps://doi.org/10.1093/hmg/10.21.2319openalex-snapshot
Understanding human disease mutations through the use of interspecific genetic variation
inferred← citeshttps://doi.org/10.1093/hmg/ddh183openalex-snapshot
Rapid evolution of primate antiviral enzyme APOBEC3G
inferred← citeshttps://doi.org/10.1093/hr/uhag166openalex-snapshot
Identification and characterization of PsFwC9 conferring Fusarium wilt resistance in pea
inferred← citeshttps://doi.org/10.1093/jhered/esp111openalex-snapshot
The α Glycerophosphate Cycle in Drosophila melanogaster VI. Structure and Evolution of Enzyme Paralogs in the Genus Drosophila
inferred← citeshttps://doi.org/10.1093/molbev/msaa028openalex-snapshot
Phenotypic Convergence Is Not Mirrored at the Protein Level in a Lizard Adaptive Radiation
inferred← citeshttps://doi.org/10.1093/molbev/msaa200openalex-snapshot
Are Nonsynonymous Transversions Generally More Deleterious than Nonsynonymous Transitions?
inferred← citeshttps://doi.org/10.1093/molbev/msg021openalex-snapshot
Positive Selection on an Acrosomal Sperm Protein, M7 Lysin, in Three Species of the Mussel Genus Mytilus
inferred← citeshttps://doi.org/10.1093/molbev/msg060openalex-snapshot
Signal Sequence Conservation and Mature Peptide Divergence Within Subgroups of the Murine beta-Defensin Gene Family
inferred← citeshttps://doi.org/10.1093/molbev/msg083openalex-snapshot
Adaptive Diversification of Bitter Taste Receptor Genes in Mammalian Evolution
inferred← citeshttps://doi.org/10.1093/molbev/msg113openalex-snapshot
Patterns of Transitional Mutation Biases Within and Among Mammalian Genomes
inferred← citeshttps://doi.org/10.1093/molbev/msh048openalex-snapshot
Dramatic Diversity of Ciliate Histone H4 Genes Revealed by Comparisons of Patterns of Substitutions and Paralog Divergences Among Eukaryotes
inferred← citeshttps://doi.org/10.1093/molbev/msh068openalex-snapshot
Genetic Evidence for the Coexistence of Pheromone Perception and Full Trichromatic Vision in Howler Monkeys
inferred← citeshttps://doi.org/10.1093/molbev/msh158openalex-snapshot
A Universal Evolutionary Index for Amino Acid Changes
inferred← citeshttps://doi.org/10.1093/molbev/msh193openalex-snapshot
Average Allozyme Heterozygosity in Vertebrates Correlates with Ka/Ks Measured in the Human-Mouse Lineage
inferred← citeshttps://doi.org/10.1093/molbev/msh236openalex-snapshot
Duplication and Diversifying Selection Among Termite Antifungal Peptides
inferred← citeshttps://doi.org/10.1093/molbev/msi027openalex-snapshot
Evolution of Bitter Taste Receptors in Humans and Apes
inferred← citeshttps://doi.org/10.1093/molbev/msj043openalex-snapshot
A New Method for Estimating Nonsynonymous Substitutions and Its Applications to Detecting Positive Selection
inferred← citeshttps://doi.org/10.1093/molbev/msl066openalex-snapshot
Accelerated Evolution and Loss of a Domain of the Sperm–Egg–Binding Protein SED1 in Ancestral Primates
inferred← citeshttps://doi.org/10.1093/molbev/msm152openalex-snapshot
The Nonsynonymous/Synonymous Substitution Rate Ratio versus the Radical/Conservative Replacement Rate Ratio in the Evolution of Mammalian Genes
inferred← citeshttps://doi.org/10.1093/molbev/msn065openalex-snapshot
Evolutionary Patterns of MHC Class II B in Owls and Their Implications for the Understanding of Avian MHC Evolution
inferred← citeshttps://doi.org/10.1093/molbev/msn177openalex-snapshot
The Legacy of Domestication: Accumulation of Deleterious Mutations in the Dog Genome
inferred← citeshttps://doi.org/10.1093/molbev/msp142openalex-snapshot
Rapid Sequence Evolution of Transcription Factors Controlling Neuron Differentiation in Caenorhabditis
inferred← citeshttps://doi.org/10.1093/molbev/msp216openalex-snapshot
Adaptive Evolution of Digestive RNASE1 Genes in Leaf-Eating Monkeys Revisited: New Insights from Ten Additional Colobines
inferred← citeshttps://doi.org/10.1093/molbev/msq225openalex-snapshot
Elevated Evolutionary Rate in Genes with Homopolymeric Amino Acid Repeats Constituting Nondisordered Structure
inferred← citeshttps://doi.org/10.1093/molbev/msr097openalex-snapshot
Fixation of Deleterious Mutations at Critical Positions in Human Proteins
inferred← citeshttps://doi.org/10.1093/molbev/msr211openalex-snapshot
Mitochondrial–Nuclear Interactions and Accelerated Compensatory Evolution: Evidence from the Primate Cytochrome c Oxidase Complex
inferred← citeshttps://doi.org/10.1093/molbev/msr315openalex-snapshot
Independent Domestication of Asian Rice Followed by Gene Flow from japonica to indica
inferred← citeshttps://doi.org/10.1093/molbev/mss219openalex-snapshot
Purifying Selection in Mammalian Mitochondrial Protein-Coding Genes Is Highly Effective and Congruent with Evolution of Nuclear Genes
inferred← citeshttps://doi.org/10.1093/molbev/msu130openalex-snapshot
Why Human Disease-Associated Residues Appear as the Wild-Type in Other Species: Genome-Scale Structural Evidence for the Compensation Hypothesis
inferred← citeshttps://doi.org/10.1093/molbev/msu306openalex-snapshot
Mutational Signatures Indicative of Environmental Stress in Bacteria
inferred← citeshttps://doi.org/10.1093/molbev/msv234openalex-snapshot
Disentangling Sources of Selection on Exonic Transcriptional Enhancers
inferred← citeshttps://doi.org/10.1093/molbev/msv274openalex-snapshot
On the Causes of Evolutionary Transition:Transversion Bias
inferred← citeshttps://doi.org/10.1093/molbev/msw033openalex-snapshot
Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes
inferred← citeshttps://doi.org/10.1093/molbev/msw191openalex-snapshot
Evolution of Digestive Enzymes and RNASE1 Provides Insights into Dietary Switch of Cetaceans
inferred← citeshttps://doi.org/10.1093/molbev/msx251openalex-snapshot
Evidence for the Selective Basis of Transition-to-Transversion Substitution Bias in Two RNA Viruses
inferred← citeshttps://doi.org/10.1093/molbev/msz003openalex-snapshot
Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations
inferred← citeshttps://doi.org/10.1093/molbev/msz033openalex-snapshot
Does Adaptive Protein Evolution Proceed by Large or Small Steps at the Amino Acid Level?
inferred← citeshttps://doi.org/10.1093/molbev/msz108openalex-snapshot
Molecular Evolution in Large Steps—Codon Substitutions under Positive Selection
inferred← citeshttps://doi.org/10.1093/nar/gkh935openalex-snapshot
Identification of genes with fast-evolving regions in microbial genomes
inferred← citeshttps://doi.org/10.1093/nar/gni003openalex-snapshot
A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003745openalex-snapshot
Evaluation of Methods for Determination of a Reconstructed History of Gene Sequence Evolution
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a004005openalex-snapshot
Episodic Positive Selection in Ape Cytochrome c Oxidase Subunit IV
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a004039openalex-snapshot
Quantifying the Slightly Deleterious Mutation Model of Molecular Evolution
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a004092openalex-snapshot
Phosphoglucose Isomerases of Hagfish, Zebrafish, Gray Mullet, Toad, and Snake, with Reference to the Evolution of the Genes in Vertebrates
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a004099openalex-snapshot
Diversifying Selection of the Tumor-Growth Promoter Angiogenin in Primate Evolution
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a004161openalex-snapshot
Ratios of Radical to Conservative Amino Acid Replacement are Affected by Mutational and Compositional Factors and May Not Be Indicative of Positive Darwinian Selection
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026307openalex-snapshot
An Unusual Form of Purifying Selection in a Sperm Protein
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026425openalex-snapshot
Positive Selection in the Evolution of Mammalian Interleukin-2 Genes
inferred← citeshttps://doi.org/10.1093/plcell/koac053openalex-snapshot
The origin and evolution of a plant resistosome
inferred← citeshttps://doi.org/10.1094/mpmi-09-12-0221-ropenalex-snapshot
The AAA+ ATPases and HflB/FtsH Proteases of ‘Candidatus Phytoplasma mali’: Phylogenetic Diversity, Membrane Topology, and Relationship to Strain Virulence
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