Cited by 1,960Genomics and Phylogenetic StudiesRNA and protein synthesis mechanismsEvolution and Genetic Dynamics

The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.

A codon-based model of nucleotide substitution for protein-coding DNA sequences.

Nick Goldman, Ziheng Yang·1994·Molecular Biology and Evolution

DOI 10.1093/oxfordjournals.molbev.a040153

Open this paper in CoChat — free account

Abstract

A codon-based model for the evolution of protein-coding DNA sequences is presented for use in phylogenetic estimation. A Markov process is used to describe substitutions between codons. Transition/transversion rate bias and codon usage bias are allowed in the model, and selective restraints at the protein level are accommodated using physicochemical distances between the amino acids coded for by the codons. Analyses of two data sets suggest that the new codon-based model can provide a better fit to data than can nucleotide-based models and can produce more reliable estimates of certain biologically important measures such as the transition/transversion rate ratio and the synonymous/nonsynonymous substitution rate ratio.

Integrity signals

Registry

Crossref · 10.1093/oxfordjournals.molbev.a040153

Cites

31 of 31 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
Nei, M., & Gojobori, T. (1986) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040410 · Cited by 4,904
The Theory of Stochastic Processes
Cox, D. R., Miller, H. D., Weiss, G., & Shuler, K. (1966) · Physics Today · doi:10.1063/1.3047872 · Cited by 3,324
Amino Acid Difference Formula to Help Explain Protein Evolution
Grantham, R. L. (1974) · Science · doi:10.1126/science.185.4154.862 · Cited by 2,363
Mitochondrial DNA sequences of primates: tempo and mode of evolution
Brown, W. M., Prager, E. M., Wang, A., & Wilson, A. C. (1982) · Journal of Molecular Evolution · doi:10.1007/bf01734101 · Cited by 1,554
Unbiased estimation of the rates of synonymous and nonsynonymous substitution
Li, W. (1993) · Journal of Molecular Evolution · doi:10.1007/bf02407308 · Cited by 1,088
Estimating the pattern of nucleotide substitution
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00178256 · Cited by 1,076
Self-citation

Show all 31 references

Sorted by citations

Items 401–500 of 1,002

Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum
Plotkin, J. B., Dushoff, J. G., & Fraser, H. B. (2004) · Nature · doi:10.1038/nature02458 · Cited by 96
Genome-Wide Identification of Na+/H+ Antiporter (NHX) Genes in Sugar Beet (Beta vulgaris L.) and Their Regulated Expression under Salt Stress
Wu, G.-Q., Wang, J., & Li, S. (2019) · Genes · doi:10.3390/genes10050401 · Cited by 93
Rapid Evolution of the Family of CONSTANS LIKE Genes in Plants
Lagercrantz, U., & Axelsson, T. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026249 · Cited by 93
Estimating Absolute Rates of Synonymous and Nonsynonymous Nucleotide Substitution in Order to Characterize Natural Selection and Date Species Divergences
Seo, T. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh088 · Cited by 94
JOINT RECONSTRUCTION OF DIVERGENCE TIMES AND LIFE-HISTORY EVOLUTION IN PLACENTAL MAMMALS USING A PHYLOGENETIC COVARIANCE MODEL
Lartillot, N., & Delsuc, F. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01558.x · Cited by 92
Molecular evolution of synonymous codon usage in Populus
Ingvarsson, P. K. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-307 · Cited by 92
Why Do Paralogs Persist? Molecular Evolution of CYCLOIDEA and Related Floral Symmetry Genes in Antirrhineae (Veronicaceae)
Hileman, L. C. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg063 · Cited by 92
Genome-wide diversity and selective pressure in the human rhinovirus
Kistler, A. L., Webster, D. R., Rouskin, S., Magrini, V. J., Credle, J. J., Schnurr, D. P., Boushey, H. A., Mardis, E. R., Li, H., & DeRisi, J. L. (2007) · Virology Journal · doi:10.1186/1743-422x-4-40 · Cited by 92
Clonal analysis reveals high rate of structural mutations in fimbrial adhesins of extraintestinal pathogenic Escherichia coli
Weissman, S. J., Chattopadhyay, S., Aprikian, P., Obata‐Yasuoka, M., Yarova‐Yarovaya, Y., Stapleton, A. E., Ba‐Thein, W., Dykhuizen, D. E., Johnson, J. R., & Sokurenko, E. V. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04985.x · Cited by 91
Comparative Genomics of Hemiascomycete Yeasts: Genes Involved in DNA Replication, Repair, and Recombination
Richard, G., Kerrest, A., Lafontaine, I., & Dujon, B. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi083 · Cited by 95
Dynamics of genome evolution in facultative symbionts of aphids
Degnan, P. H., Leonardo, T. E., Cass, B. N., Hurwitz, B. L., Stern, D. L., Gibbs, R. A., Richards, S., & Moran, N. A. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02085.x · Cited by 90
The Evolution of the Heat-Shock Protein GroEL from Buchnera, the Primary Endosymbiont of Aphids, Is Governed by Positive Selection
Fares, M. A., Barrio, E., Sabater‐Muñoz, B., & Moyá, A. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004174 · Cited by 90
Phylogenomics of the benzoxazinoid biosynthetic pathway of Poaceae: gene duplications and origin of the Bx cluster
Dutartre, L., Hilliou, F., & Feyereisen, R. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-64 · Cited by 92
Rates of nucleotide substitution in sexual and anciently asexual rotifers
Welch, D., & Meselson, M. S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.111144598 · Cited by 90
Estimating the distribution of fitness effects from DNA sequence data: Implications for the molecular clock
Piganeau, G., & Eyre‐Walker, A. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1833064100 · Cited by 92
Evolution of the multifaceted eukaryotic akirin gene family
Macqueen, D. J., & Johnston, I. A. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-34 · Cited by 89
Mutationism and the dual causation of evolutionary change
Stoltzfus, A. (2006) · Evolution & Development · doi:10.1111/j.1525-142x.2006.00101.x · Cited by 89
Gene-rich UV sex chromosomes harbor conserved regulators of sexual development
Carey, S. B., Jenkins, J. W., Lovell, J. T., Maumus, F., Sreedasyam, A., Payton, A. C., Shu, S., Tiley, G. P., Fernández‐Pozo, N., Healey, A. L., et al. (2021) · Science Advances · doi:10.1126/sciadv.abh2488 · Cited by 90
A Dirichlet process model for detecting positive selection in protein-coding DNA sequences
Huelsenbeck, J. P., Jain, S., Frost, S. D. W., & Pond, S. L. K. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0508279103 · Cited by 89
Evidence for purifying selection acting on silent sites in BRCA1
Hurst, L. D., & Pál, C. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(00)02173-9 · Cited by 89
A Dependent-Rates Model and an MCMC-Based Methodology for the Maximum-Likelihood Analysis of Sequences with Overlapping Reading Frames
Pedersen, A.-M. K., & Jensen, J. L. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003859 · Cited by 89
The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and ConstraintPreprint
Castillo-Davis, C. I., Kondrashov, F. A., Hartl, D. L., & Kulathinal, R. J. (2004) · Genome Research · doi:10.1101/gr.2195604 · Cited by 89
The quest for natural selection in the age of comparative genomics
Anisimova, M. O., & Liberles, D. A. (2007) · Heredity · doi:10.1038/sj.hdy.6801052 · Cited by 89
Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs
Doud, M. B., Ashenberg, O., & Bloom, J. D. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv167 · Cited by 94
EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics
Barker, M. S., Dlugosch, K. M., Dinh, L., Challa, R. S., Kane, N. C., King, M. G., & Rieseberg, L. H. (2010) · Evolutionary Bioinformatics · doi:10.4137/ebo.s5861 · Cited by 88
Unresolved direction of host transfer of Plasmodium vivax v. P. simium and P. malariae v. P. brasilianum
Tazi, L., & Ayala, F. J. (2010) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2010.08.007 · Cited by 92
Incorporating indel information into phylogeny estimation for rapidly emerging pathogens
Redelings, B. D., & Suchard, M. A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-40 · Cited by 88
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
Spielman, S. J., & Wilke, C. O. (2015) · PLoS ONE · doi:10.1371/journal.pone.0139047 · Cited by 88
Adaptive Evolution ofMRG, a Neuron-Specific Gene Family Implicated in NociceptionPreprint
Choi, S. S., & Lahn, B. T. (2003) · Genome Research · doi:10.1101/gr.1431603 · Cited by 89
Mitogenomics reveals two cryptic species in Ciona intestinalis
Iannelli, F., Pesole, G., Sordino, P., & Gissi, C. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.07.001 · Cited by 86
Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency
Baele, G., & Lemey, P. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt340 · Cited by 87
Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae
Gu, Z., David, L., Petrov, D. A., Jones, T., Davis, R. W., & Steinmetz, L. M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409159102 · Cited by 89
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomesPreprint
Lin, M. F., Kheradpour, P., Stefan Washietl, A., Parker, B. J., Pedersen, J. S., & Kellis, M. (2011) · Genome Research · doi:10.1101/gr.108753.110 · Cited by 88
Maximum Likelihood Estimation of Ancestral Codon Usage Bias Parameters in Drosophila
Nielsen, R., DuMont, V. L. B., Hubisz, M. J., & Aquadro, C. F. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl146 · Cited by 85
Comparative Evolutionary Genomics of Androgen-Binding Protein GenesPreprint
Emes, R. D., Riley, M. C., Laukaitis, C. M., Goodstadt, L., Karn, R. C., & Ponting, C. P. (2004) · Genome Research · doi:10.1101/gr.2540304 · Cited by 85
Mutation Patterns of Mitochondrial H- and L-Strand DNA in Closely Related Cyprinid Fishes
Bielawski, J. P., & Gold, J. R. (2002) · Genetics · doi:10.1093/genetics/161.4.1589 · Cited by 84
Comparative analysis of protein coding sequences from human, mouse and the domesticated pig
Jørgensen, F. G., Hobolth, A., Hornshøj, H., Bendixen, C., Fredholm, M., & Schierup, M. H. (2005) · BMC Biology · doi:10.1186/1741-7007-3-2 · Cited by 84
Spatial Covariation of Mutation and Nonsynonymous Substitution Rates in Vertebrate Mitochondrial Genomes
Broughton, R. E., & Reneau, P. C. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl013 · Cited by 84
A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection
Lemey, P., Minin, V. N., Bielejec, F., Pond, S. L. K., & Suchard, M. A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts580 · Cited by 86
Computing Ka and Ks with a consideration of unequal transitional substitutions
Zhang, Z., Li, J., & Yu, J. M. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-44 · Cited by 84
Reciprocally Retained Genes in the Angiosperm Lineage Show the Hallmarks of Dosage Balance Sensitivity
Tasdighian, S., Bel, M. V., Li, Z., de Peer, Y. V., Carretero‐Paulet, L., & Maere, S. (2017) · The Plant Cell · doi:10.1105/tpc.17.00313 · Cited by 84
Antarctic fish hemoglobins: Evidence for adaptive evolution at subzero temperature
Bargelloni, L., Marcato, S., & Patarnello, T. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.15.8670 · Cited by 84
Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis
He, P., Huang, S., Xiao, G., Zhang, Y., & Yu, J. (2016) · BMC Plant Biology · doi:10.1186/s12870-016-0944-8 · Cited by 83
Synonymous mutations and the molecular evolution of SARS-CoV-2 origins
Wang, H., Pipes, L., & Nielsen, R. (2020) · Virus Evolution · doi:10.1093/ve/veaa098 · Cited by 83
A Proteomics and Transcriptomics Investigation of the Venom from the Barychelid Spider Trittame loki (Brush-Foot Trapdoor)
Undheim, E. A. B., Sunagar, K., Herzig, V., Kely, L., Low, D. H. W., Jackson, T., Jones, A., Kurniawan, N. D., King, G. F., Ali, S. A., et al. (2013) · Toxins · doi:10.3390/toxins5122488 · Cited by 83
Natural Selection on Synonymous and Nonsynonymous Mutations Shapes Patterns of Polymorphism in Populus tremula
Ingvarsson, P. K. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp255 · Cited by 83
Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12DrosophilagenomesPreprint
Alvarez‐Ponce, D., Aguadé, M., & Rozas, J. (2009) · Genome Research · doi:10.1101/gr.084038.108 · Cited by 84
Evolution, diversification, and expression of KNOX proteins in plants
Gao, J., Yang, X. Q., Zhao, W., Lang, T., & Samuelsson, T. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.00882 · Cited by 82
Transcriptome Analysis of the Oil-Rich Tea Plant, Camellia oleifera, Reveals Candidate Genes Related to Lipid Metabolism
Xia, E., Jiang, J., Huang, H., Zhang, L., Zhang, H., & Gao, L. (2014) · PLoS ONE · doi:10.1371/journal.pone.0104150 · Cited by 82
Estimating the Frequency of Events That Cause Multiple-Nucleotide Changes
Whelan, S., & Goldman, N. (2004) · Genetics · doi:10.1534/genetics.103.023226 · Cited by 83
Self-citation
GenomeHistory: a software tool and its application to fully sequenced genomes
Conant, G. C. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf449 · Cited by 82
A Codon-Based Model of Host-Specific Selection in Parasites, with an Application to the Influenza A Virus
Forsberg, R. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg149 · Cited by 81
Models of coding sequence evolution
Delport, W., Scheffler, K., & Seoighe, C. (2008) · Briefings in Bioinformatics · doi:10.1093/bib/bbn049 · Cited by 82
Molecular Population Genetics of Accessory Gland Protein Genes and Testis-Expressed Genes in Drosophila mojavensis and D. arizonae
Wagstaff, B. J., & Begun, D. J. (2005) · Genetics · doi:10.1534/genetics.105.043372 · Cited by 81
Characterization of S3Pvac Anti-Cysticercosis Vaccine Components: Implications for the Development of an Anti-Cestodiasis Vaccine
Rassy, D., Bobes, R. J., Rosas, G., Anaya-Muñoz, V. H., Brehm, K., Hernández, B., Cervantes, J., Pedraza, S., Morales, J., Villalobos, N., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011287 · Cited by 80
Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis
Hughes, D. A., Jastroch, M., Stoneking, M., & Klingenspor, M. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-4 · Cited by 81
Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs
Aagaard, J. E., Yi, X., MacCoss, M. J., & Swanson, W. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603125103 · Cited by 80
Molecular evolution of the hepatitis B virus genome
Yang, Z., Lauder, I. J., & Lin, H. J. (1995) · Journal of Molecular Evolution · doi:10.1007/bf00175817 · Cited by 79
Self-citation
The Highly Reduced Plastome of MycoheterotrophicSciaphila(Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection
Lam, V. K. Y., Gomez, M. S., & Graham, S. W. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv134 · Cited by 79
Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak
Ueno, S., Provost, G. L., Léger, V., Klopp, C., Noirot, C., Frigerio, J.-M., Salin, F., Salse, J., Abrouk, M., Murat, F., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-650 · Cited by 84
Natural attenuation of dengue virus type-2 after a series of island outbreaks: A retrospective phylogenetic study of events in the South Pacific three decades ago
Steel, A., Gubler, D. J., & Bennett, S. N. (2010) · Virology · doi:10.1016/j.virol.2010.05.033 · Cited by 79
Using models of nucleotide evolution to build phylogenetic trees
Bos, D. H., & Posada, D. (2004) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2004.07.007 · Cited by 81
Rate Asymmetry After Genome Duplication Causes Substantial Long-Branch Attraction Artifacts in the Phylogeny of Saccharomyces Species
Fares, M. A., Byrne, K. P., & Wolfe, K. H. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj027 · Cited by 81
Adaptive Evolution of Sperm Bindin Tracks Egg Incompatibility in Neotropical Sea Urchins of the Genus Echinometra
McCartney, M. A., & Lessios, H. A. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh071 · Cited by 80
Evolution of the Insect Desaturase Gene Family with an Emphasis on Social Hymenoptera
Helmkampf, M., Cash, E. I., & Gadau, J. R. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu315 · Cited by 79
Substitution Rates in Drosophila Nuclear Genes: Implications for Translational Selection
Dunn, K. A., Bielawski, J. P., & Yang, Z. (2001) · Genetics · doi:10.1093/genetics/157.1.295 · Cited by 79
Self-citation
Evolutionary conservation and divergence of the human brain transcriptome
Pembroke, W. G., Hartl, C., & Geschwind, D. H. (2021) · Genome biology · doi:10.1186/s13059-020-02257-z · Cited by 78
Models of protein sequence evolution and their applications
Thorne, J. L. (2000) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(00)00142-8 · Cited by 78
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes
Yandell, M. D., Mungall, C., Smith, C., Prochnik, S. E., Kaminker, J. S., Hartzell, G., Lewis, S., & Rubin, G. M. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020015 · Cited by 81
Comparison of Three Methods for Estimating Rates of Synonymous and Nonsynonymous Nucleotide Substitutions
Tzeng, Y.-H. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh242 · Cited by 77
Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections
Lam, T. T., Hon, C.-C., & Tang, J. W.-T. (2010) · Critical Reviews in Clinical Laboratory Sciences · doi:10.3109/10408361003633318 · Cited by 83
Rapid Evolution of Immune Proteins in Social Insects
Viljakainen, L., Evans, J. D., Hasselmann, M., Rueppell, O., Tingek, S., & Pamilo, P. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp086 · Cited by 77
A Phylogenetic Codon Substitution Model for Antibody Lineages
Hoehn, K. B., Lunter, G. A., & Pybus, O. G. (2017) · Genetics · doi:10.1534/genetics.116.196303 · Cited by 78
Dracula's children: Molecular evolution of vampire bat venom
Low, D. H. W., Sunagar, K., Undheim, E. A. B., Ali, S. A., Alagon, A. C., Ruder, T., Jackson, T., Pineda, S. S., King, G. F., Jones, A., et al. (2013) · Journal of Proteomics · doi:10.1016/j.jprot.2013.05.034 · Cited by 76
Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography
Bielejec, F., Lemey, P., Baele, G., Rambaut, A., & Suchard, M. A. (2014) · Systematic Biology · doi:10.1093/sysbio/syu015 · Cited by 82
The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land
Biscotti, M. A., Gerdol, M., Canapa, A., Forconi, M., Olmo, E., Pallavicini, A., Barucca, M., & Schartl, M. (2016) · Scientific Reports · doi:10.1038/srep21571 · Cited by 76
Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum
Vanneste, K., Sterck, L., Myburg, A. A., de Peer, Y. V., & Mizrachi, E. (2015) · The Plant Cell · doi:10.1105/tpc.15.00157 · Cited by 76
Recombination and Its Impact on the Genome of the Haplodiploid Parasitoid Wasp Nasonia
Niehuis, O., Gibson, J. D., Rosenberg, M. S., Pannebakker, B. A., Koevoets, T., Judson, A. K., Desjardins, C. A., Kennedy, K., Duggan, D. J., Beukeboom, L. W., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008597 · Cited by 75
Tracking Viral Evolution during a Disease Outbreak: the Rapid and Complete Selective Sweep of a Circovirus in the Endangered Echo Parakeet
Kundu, S., Faulkes, C. G., Greenwood, A. G., Jones, C. G., Kaiser, P., Lyne, O. D., Black, S. A., Chowrimootoo, A., & Groombridge, J. J. (2012) · Journal of Virology · doi:10.1128/jvi.06504-11 · Cited by 75
Assessing the performance of Ks plots for detecting ancient whole genome duplications
Tiley, G. P., Barker, M. S., & Burleigh, J. G. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy200 · Cited by 75
Rapid evolution of BRCA1 and BRCA2in humans and other primates
Lou, D. I., McBee, R. M., Le, U. Q., Stone, A. C., Wilkerson, G. K., Demogines, A. M., & Sawyer, S. L. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-155 · Cited by 74
Evidence of Positively Selected Sites in Mammalian α-Defensins
Lynn, D. J., Lloyd, A. T., Fares, M. A., & O’Farrelly, C. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh084 · Cited by 74
The origin and evolution of geminivirus-related DNA sequences in Nicotiana
Murad, L., Bielawski, J. P., Matyášek, R., Kovařı́k, A., Nichols, R. A., Leitch, A. R., & Lichtenstein, C. P. (2004) · Heredity · doi:10.1038/sj.hdy.6800431 · Cited by 76
R2R3-MYB gene pairs in Populus: evolution and contribution to secondary wall formation and flowering time
Chai, G., Wang, Z., Tang, X., Li, Y., Qi, G., Wang, D., Yan, X., Kong, Y., & Zhou, G. (2014) · Journal of Experimental Botany · doi:10.1093/jxb/eru196 · Cited by 74
Gene expression and feeding ecology: evolution of piscivory in the venomous gastropod genusConus
Duda, T. F., & Palumbi, S. R. (2004) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2004.2708 · Cited by 74
AN EVOLUTIONARY EXPRESSED SEQUENCE TAG ANALYSIS OF DROSOPHILA SPERMATHECA GENES
Prokupek, A., Hoffmann, F. G., Eyun, S., Moriyama, E. N., Zhou, M., & Harshman, L. G. (2008) · Evolution · doi:10.1111/j.1558-5646.2008.00493.x · Cited by 74
Big Data Analysis of Korean Travelers’ Behavior in the Post-COVID-19 Era
Sung, Y.-A., Kim, K. W., & Kwon, H.-J. (2020) · Sustainability · doi:10.3390/su13010310 · Cited by 73
Natural Selection and Adaptive Evolution of Leptin in the Ochotona Family Driven by the Cold Environmental Stress
Yang, J., Wang, Z. L., Zhao, X. Q., Wang, D. P., Qi, D. L., Xu, B. H., Ren, Y., & Tian, H. F. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001472 · Cited by 75
An Asian Origin for Subtype IV BK Virus Based on Phylogenetic Analysis
Nishimoto, Y., Zheng, H.-Y., Zhong, S., Ikegaya, H., Chen, Q., Sugimoto, C., Kitamura, T., & Yogo, Y. (2007) · Journal of Molecular Evolution · doi:10.1007/s00239-006-0269-6 · Cited by 73
Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution
Gu, X., & Li, W. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.11.5899 · Cited by 73
Lipid-binding surfaces of membrane proteins: Evidence from evolutionary and structural analysis
Adamian, L., Naveed, H., & Liang, J. (2010) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2010.12.008 · Cited by 72
Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes
Wang, D., Liu, F., Wang, L., Huang, S., & Yu, J. M. (2011) · Biology Direct · doi:10.1186/1745-6150-6-13 · Cited by 73
Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae
Smith, D. R., Arrigo, K. R., Alderkamp, A., & Allen, A. E. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.10.018 · Cited by 72
On transition bias in mitochondrial genes of pocket gophers
Xia, X., Hafner, M. S., & Sudman, P. D. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02352297 · Cited by 72
Auxin response factor gene family in Brassica rapa: genomic organization, divergence, expression, and evolution
Mun, J., Yu, H., Shin, J. Y., Oh, M., Hwang, H., & Chung, H. (2012) · Molecular Genetics and Genomics · doi:10.1007/s00438-012-0718-4 · Cited by 73
PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
Sipos, B., Massingham, T., Jordan, G. E., & Goldman, N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-104 · Cited by 72
Self-citation
Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
Ho, S. Y. W., & Lanfear, R. (2010) · Mitochondrial DNA · doi:10.3109/19401736.2010.494727 · Cited by 72
Diversity of the cassiicolin gene in Corynespora cassiicola and relation with the pathogenicity in Hevea brasiliensis
Déon, M., Fumanal, B., Gimenez, S., Bieysse, D., de Oliveira, R. R., Shuib, S. S., Breton, F., Sunderasan, E., Vida, J. B., Séguin, M., et al. (2013) · Fungal Biology · doi:10.1016/j.funbio.2013.10.011 · Cited by 72
Coalescent Simulation of Intracodon Recombination
Arenas, M., & Posada, D. (2009) · Genetics · doi:10.1534/genetics.109.109736 · Cited by 73
CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences
Delport, W., Scheffler, K., Botha, G., Gravenor, M. B., Muse, S. V., & Pond, S. L. K. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000885 · Cited by 72

Authors: Goldman, N., & Yang, Z.
Affiliations: National Institute for Medical Research (GB)
ORCID: Nick Goldman
Ziheng Yang
Venue: Molecular Biology and Evolution
Publisher: Oxford University Press (OUP)
Published: 1994-09
Volume: 11
Issue: 5
Pages: 725-36
ISSN: 0737-4038 (ISSN-L)
1537-1719
DOI: 10.1093/oxfordjournals.molbev.a040153
OpenAlex: W1920973730
Cited by: 1,960
References: 31
Citations by year: 2026: 18 · 2025: 42 · 2024: 51 · 2023: 43 · 2022: 61 · 2021: 65 · 2020: 60 · 2019: 74 · 2018: 71 · 2017: 60 · 2016: 69 · 2015: 68 · 2014: 107 · 2013: 97 · 2012: 89
FWCI: 2.27
Type: journal article
Language: en
Open access: closed
Locations: Molecular Biology and Evolution (publishedVersion)
PubMed (publishedVersion)
Funders: National Eye Institute
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords: Markov processes, codon usage bias, selective constraint, synonymous substitution rate, nonsynonymous substitution rate, phylogenetic estimation, nucleotide substitution models
MeSH terms: Animals, Chemistry, Physical, Codon, DNA, Genes, Globins, Mammals, Markov Chains, Models, Genetic, Nucleotidyltransferases, Phylogeny, Proteins, Likelihood Functions, Point Mutation, Glucose-1-Phosphate Adenylyltransferase, Chemical Phenomena

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

A codon-based model of nucleotide substitution for protein-coding DNA sequences.

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks