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 801–900 of 1,002

Genome-Wide Analysis of theTCPGene Family in Switchgrass (Panicum virgatumL.)
Huo, Y., Xiong, W., Su, K., Li, Y., Yang, Y., Fu, C., Wu, Z., & Sun, Z. (2019) · International Journal of Genomics · doi:10.1155/2019/8514928 · Cited by 39
Cophylogenetic interactions between marine viruses and eukaryotic picophytoplankton
Bellec, L., Clérissi, C., Edern, R., Foulon, E., Simon, N., Grimsley, N. H., & Desdevises, Y. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-59 · Cited by 39
A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes
Sabath, N., Landan, G., & Graur, D. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003996 · Cited by 39
The Rates of Molecular Evolution in Rodent and Primate Mitochondrial DNA
Weinreich, D. M. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010132 · Cited by 39
Cytochrome b evolution in birds and mammals: an evaluation of the avian constraint hypothesis
Stanley, S. E., & Harrison, R. G. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026070 · Cited by 39
Building phylogenies: are the big easy?
Purvis, A., & Quicke, D. L. J. (1997) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(96)30066-9 · Cited by 39
De Novo Genes
Zhao, L., Svetec, N., & Begun, D. J. (2024) · Annual Review of Genetics · doi:10.1146/annurev-genet-111523-102413 · Cited by 38
Observations of Amino Acid Gain and Loss during Protein Evolution Are Explained by Statistical Bias
Goldstein, R. A. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl010 · Cited by 39
Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses
Lucaci, A. G., Zehr, J. D., Enard, D., Thornton, J. W., & Pond, S. L. K. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad150 · Cited by 39
Phylogenetic analysis and systematic revision of Remipedia (Nectiopoda) from Bayesian analysis of molecular data
Hoenemann, M., Humphreys, W. F., Li, D., Neiber, M. T., Koenemann, S., Iliffe, T. M., & Schram, F. R. (2013) · Journal of Crustacean Biology · doi:10.1163/1937240x-00002179 · Cited by 38
Looking for Darwin in Genomic Sequences—Validity and Success of Statistical Methods
Zhai, W., Nielsen, R., Goldman, N., & Yang, Z. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss104 · Cited by 39
Self-citation
Relaxed Selection Among Duplicate Floral Regulatory Genes in Lamiales
Aagaard, J. E., Willis, J. H., & Phillips, P. C. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-005-0306-x · Cited by 38
High Diversity at PRDM9 in Chimpanzees and Bonobos
Groeneveld, L. F., Atencia, R., Garriga, R. M., & Vigilant, L. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039064 · Cited by 42
Gene Family Expansions in Aphids Maintained by Endosymbiotic and Nonsymbiotic Traits
Duncan, R. P., Feng, H., Nguyen, D. M., & Wilson, A. C. C. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw020 · Cited by 39
Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection
Davydov, I. I., Salamin, N., & Robinson‐Rechavi, M. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz048 · Cited by 38
Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes
Legrand, S., Caron, T., Maumus, F., Schvartzman, S., Quadrana, L., Durand, É., Gallina, S., Pauwels, M., Mazoyer, C., Huyghe, L., et al. (2019) · Mobile DNA · doi:10.1186/s13100-019-0171-6 · Cited by 38
Genome-wide identification and classification of Lipoxygenase gene family and their roles in sorghum-aphid interaction
Shrestha, K., Pant, S. R., & Huang, Y. (2021) · Plant Molecular Biology · doi:10.1007/s11103-020-01107-7 · Cited by 38
The Codon-Degeneracy Model of Molecular Evolution
McClellan, D. A. (2000) · Journal of Molecular Evolution · doi:10.1007/s002399910015 · Cited by 38
Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines
Mazumder, R., Hu, Z.-Z., Vinayaka, C. R., Sagripanti, J., Frost, S. D. W., Pond, S. L. K., & Wu, C. H. (2007) · Virus Genes · doi:10.1007/s11262-007-0103-2 · Cited by 38
“Phylogenetic and evolutionary analysis of functional divergence among Gamma glutamyl transpeptidase (GGT) subfamilies”
Verma, V. V., Gupta, R., & Goel, M. (2015) · Biology Direct · doi:10.1186/s13062-015-0080-7 · Cited by 38
Characterization of a Putative Ancestor of Coxsackievirus B5
Gullberg, M., Tolf, C., Jonsson, N., Mulders, M. N., Savolainen‐Kopra, C., Hovi, T., Ranst, M. A. V., Lemey, P., Hafenstein, S. L., & Lindberg, A. M. (2010) · Journal of Virology · doi:10.1128/jvi.00071-10 · Cited by 38
Host-Specific Modulation of the Selective Constraints Driving Human Immunodeficiency Virus Type 1 env Gene Evolution
Bagnarelli, P., Mazzola, F., Menzo, S., Montroni, M., Butini, L., & Clementi, M. (1999) · Journal of Virology · doi:10.1128/jvi.73.5.3764-3777.1999 · Cited by 38
Vertical Transmission of Biosynthetic Plasmids in Aphid Endosymbionts ( Buchnera )
Wernegreen, J. J., & Moran, N. A. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.2.785-790.2001 · Cited by 38
Low‐coverage, whole‐genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery
Gardner, E. M., Johnson, M. G., Ragone, D., Wickett, N. J., & Zerega, N. J. C. (2016) · Applications in Plant Sciences · doi:10.3732/apps.1600017 · Cited by 37
New insights into the origin and evolution of α-amylase genes in green plants
Ju, L., Pan, Z., Zhang, H., Li, Q., Liang, J., Deng, G., Yu, M., & Long, H. (2019) · Scientific Reports · doi:10.1038/s41598-019-41420-w · Cited by 40
Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species
Mugal, C. F., Kutschera, V. E., Botero-Castro, F., Wolf, J. B. W., & Kaj, I. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz203 · Cited by 37
Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes
Lucaci, A. G., Wisotsky, S. R., Shank, S. D., Weaver, S., & Pond, S. L. K. (2021) · PLoS ONE · doi:10.1371/journal.pone.0248337 · Cited by 38
Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci:BuchneraofDiuraphis
Wernegreen, J. J., & Moran, N. A. (2000) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2000.1159 · Cited by 37
Evolutionary rate patterns of genes involved in the Drosophila Toll and Imd signaling pathway
Han, M., Qin, S., Song, X., Li, Y., Jin, P., Chen, L., & Ma, F. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-245 · Cited by 38
Functional and evolutionary analysis of DXL1, a non-essential gene encoding a 1-deoxy-D-xylulose 5-phosphate synthase like protein in Arabidopsis thaliana
Carretero‐Paulet, L., Cairó, A., Talavera, D., Saura, A., Imperial, S., Rodrı́guez-Concepción, M., Campos, N., & Boronat, A. (2012) · Gene · doi:10.1016/j.gene.2012.10.071 · Cited by 39
Quantifying the Impact of Dependent Evolution among Sites in Phylogenetic Inference
Nasrallah, C. A., Mathews, D. H., & Huelsenbeck, J. P. (2010) · Systematic Biology · doi:10.1093/sysbio/syq074 · Cited by 37
The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): high genome plasticity at intra-genus level
Iannelli, F., Griggio, F., Pesole, G., & Gissi, C. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-155 · Cited by 37
Sexual Selection of Protamine 1 in Mammals
Arévalo, L., Tourmente, M., & Roldán, E. R. S. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv209 · Cited by 37
Altered Transcription and Neofunctionalization of Duplicated Genes Rescue the Harmful Effects of a Chimeric Gene in Brassica napus
Xia, S., Wang, Z., Zhang, H., Hu, K., Zhang, Z., Qin, M., Dun, X., Yi, B., Wen, J., Ma, C., et al. (2016) · The Plant Cell · doi:10.1105/tpc.16.00281 · Cited by 37
The human progesterone receptor shows evidence of adaptive evolution associated with its ability to act as a transcription factor
Chen, C., Opazo, J. C., Erez, O., Uddin, M., Santolaya-Forgas, J., Goodman, M., Grossman, L. I., Romero, R. J., & Wildman, D. E. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.12.026 · Cited by 37
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies
Kapli, P., Kotari, I., Telford, M. J., Goldman, N., & Yang, Z. (2023) · Systematic Biology · doi:10.1093/sysbio/syad036 · Cited by 36
Self-citation
Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications
Redelings, B. D., Holmes, I., Lunter, G. A., Pupko, T., & Anisimova, M. O. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae177 · Cited by 38
The evolutionary rate variation among genes of HOG-signaling pathway in yeast genomes
Wu, X., Chi, X., Wang, P., Zheng, D., Ding, R., & Li, Y. (2010) · Biology Direct · doi:10.1186/1745-6150-5-46 · Cited by 36
Characterization of voltage-dependent calcium channel blocking peptides from the venom of the tarantula Grammostola rosea
Ono, S., Kimura, T., & Kubo, T. (2011) · Toxicon · doi:10.1016/j.toxicon.2011.06.006 · Cited by 36
Molecular evolution of rbcL in the mycoheterotrophic coralroot orchids (Corallorhiza Gagnebin, Orchidaceae)
Barrett, C. F., & Freudenstein, J. V. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.02.014 · Cited by 36
Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales
Duchêne, S., Giallonardo, F. D., & Holmes, E. C. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv207 · Cited by 38
A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta)
Johnson, M. G., Malley, C. E., Goffinet, B., Shaw, A. J., & Wickett, N. J. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.01.008 · Cited by 36
The tangled bank of amino acids
Goldstein, R. A., & Pollock, D. D. (2016) · Protein Science · doi:10.1002/pro.2930 · Cited by 36
Widespread signatures of selection for secreted peptidases in a fungal plant pathogen
Krishnan, P., Ma, X., McDonald, B. A., & Brunner, P. C. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1123-3 · Cited by 36
Symbiosis, Selection, and Novelty: Freshwater Adaptation in the Unique Sponges of Lake Baikal
Kenny, N. J., Pleše, B., Riesgo, A., & Itskovich, V. B. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz151 · Cited by 37
Analysis of selection in protein-coding sequences accounting for common biases
Amparo, R. D., Branco, C., Arenas, J., Vicens, A., & Arenas, M. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa431 · Cited by 38
Adaptive Molecular Evolution of HINTW, a Female-Specific Gene in Birds
Ceplitis, H. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg239 · Cited by 36
Rates of nucleotide substitution in Cornaceae (Cornales)—Pattern of variation and underlying causal factors
Xiang, Q., Thorne, J. L., Seo, T., Zhang, W., Thomas, D. T., & Ricklefs, R. E. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.07.010 · Cited by 36
Positive selection in penicillin-binding proteins 1a, 2b, and 2x from Streptococcus pneumoniae and its correlation with amoxicillin resistance development
Stanhope, M. J., Tristan, L., Walsh, S. L., Becker, J. A., Lang, P., Bitar, P. D. P., Miller, L. A., Italia, M. J., & Amrine‐Madsen, H. (2008) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2008.02.001 · Cited by 36
Retrieval of Four Adaptive Lineages in Duiker Antelope: Evidence from Mitochondrial DNA Sequences and Fluorescence in Situ Hybridization
van Vuuren, B. J., & Robinson, T. J. (2001) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.2001.0962 · Cited by 36
Adaptive evolution ofHoxA–11andHoxA–13at the origin of the uterus in mammals
Lynch, V. J., Roth, J. J., Takahashi, K., Dunn, C. W., Nonaka, D. F., Stopper, G. F., & Wagner, G. P. (2004) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2004.2848 · Cited by 37
Suppressors of RNAi from plant viruses are subject to episodic positive selection
Murray, G. G. R., Pond, S. L. K., & Obbard, D. J. (2013) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2013.0965 · Cited by 36
Balancing selection and genetic drift at major histocompatibility complex class II genes in isolated populations of golden snub-nosed monkey (Rhinopithecus roxellana)
Luo, M., Pan, H., Liu, Z., & Li, M. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-207 · Cited by 37
Natural selection in bats with historical exposure to white-nose syndrome
Harazim, M., Horáček, I., Jakešová, L., Luermann, K., Moravec, J., Morgan, S., Pikula, J., Sosı́k, P., Vavrušová, Z., Zahradníková, A., et al. (2018) · BMC Zoology · doi:10.1186/s40850-018-0035-4 · Cited by 36
Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication
Aase-Remedios, M. E., Janßen, R., Leite, D. J., Sumner‐Rooney, L. H., & McGregor, A. P. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad239 · Cited by 35
Amino acid transporter expansions associated with the evolution of obligate endosymbiosis in sap-feeding insects (Hemiptera: sternorrhyncha)
Dahan, R. A., Duncan, R. P., Wilson, A. C. C., & Dávalos, L. M. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0315-3 · Cited by 37
Slow Co-Evolution of the MAGO and Y14 Protein Families Is Required for the Maintenance of Their Obligate Heterodimerization Mode
Gong, P., Zhao, M., & He, C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084842 · Cited by 37
Genome-wide identification and expression analysis of the fatty acid desaturase genes in Medicago truncatula
Zhang, Z., Wei, X., Liu, W., Min, X., Jin, X., Ndayambaza, B., & Wang, Y. (2018) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2018.03.165 · Cited by 35
Benchmarking Tree and Ancestral Sequence Inference for B Cell Receptor Sequences
Davidsen, K., & Matsen, F. A., IV (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02451 · Cited by 35
Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)
Thode, V. A., Lohmann, L., & Sanmartín, I. (2020) · Journal of Systematics and Evolution · doi:10.1111/jse.12579 · Cited by 31
Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa
Rogers, R. L., Grizzard, S. L., Titus‐McQuillan, J. E., Bockrath, K., Patel, S., Wares, J. P., Garner, J. T., & Moore, C. C. (2020) · Molecular Ecology · doi:10.1111/mec.15786 · Cited by 39
The origins and functional effects of postzygotic mutations throughout the human life span
Rockweiler, N. B., Ramu, A., Nagirnaja, L., Wong, W., Noordam, M. J., Drubin, C. W., Huang, N., Miller, B., Todres, E. Z., Vigh‐Conrad, K. A., et al. (2023) · Science · doi:10.1126/science.abn7113 · Cited by 39
Diversity and selective sweep in the OsAMT1;1genomic region of rice
Ding, Z., Wang, C., Chen, S., & Yu, S. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-61 · Cited by 35
The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection
Martens, C., & de Peer, Y. V. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-353 · Cited by 35
A Model of Directional Selection Applied to the Evolution of Drug Resistance in HIV-1
Seoighe, C., Ketwaroo, F., Pillay, V., Scheffler, K., Wood, N. T., Duffet, R., Zvelebil, M., Martinson, N. A., McIntyre, J. A., Morris, L., et al. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm021 · Cited by 36
Identification of physicochemical selective pressure on protein encoding nucleotide sequences
Wong, W. S., Sainudiin, R., & Nielsen, R. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-148 · Cited by 35
The Trouble with Sliding Windows and the Selective Pressure in BRCA1
Schmid, K., & Yang, Z. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003746 · Cited by 35
Self-citation
Sequence Level Analysis of Recently Duplicated Regions in Soybean [Glycine max (L.) Merr.] Genome
Van, K., Kim, D. H., Cai, C. M., Kim, M. Y., Shin, J. H., Graham, M. A., Shoemaker, R. C., Choi, B.-S., Yang, T., & Lee, S. (2008) · DNA Research · doi:10.1093/dnares/dsn001 · Cited by 35
Using GC Content to Compare Recombination Patterns on the Sex Chromosomes and Autosomes of the Guppy, Poecilia reticulata , and Its Close Outgroup Species
Charlesworth, D., Zhang, Y., Bergero, R., Graham, C., Gardner, J., & Yong, L. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa187 · Cited by 35
Toward Assigning Helical Regions in Alignments of Ribosomal RNA and Testing the Appropriateness of Evolutionary Models
Schöniger, M., & von Haeseler, A. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006590 · Cited by 35
Origin and Evolution of the Unique Tetra-Domain Hemoglobin from the Hydrothermal Vent Scale Worm Branchipolynoe
Projecto-Garcia, J., Zorn, N., Jollivet, D., Schaeffer, S. W., Lallier, F. H., & Hourdez, S. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp218 · Cited by 35
Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage (Brassicaceae)
Zhou, D., Zhou, J., Meng, L., Wang, Q., Xie, H., Guan, Y., Ma, Z., Zhong, Y., Chen, F., & Liu, J. (2008) · Gene · doi:10.1016/j.gene.2008.06.024 · Cited by 34
Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria
Schaber, J., Rispe, C., Wernegreen, J. J., Buneß, A., Delmotte, F., Silva, F. J., & Moyá, A. (2005) · Gene · doi:10.1016/j.gene.2005.04.003 · Cited by 34
Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation
Lopes, J. S., Arenas, M., Posada, D., & Beaumont, M. (2013) · Heredity · doi:10.1038/hdy.2013.101 · Cited by 34
Shifting Balance on a Static Mutation–Selection Landscape: A Novel Scenario of Positive Selection
Jones, C. T., Youssef, N., Susko, E., & Bielawski, J. P. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw237 · Cited by 34
Evidence for an ancient whole genome duplication in the cycad lineage
Roodt, D., Lohaus, R., Sterck, L., Swanepoel, R. L., de Peer, Y. V., & Mizrachi, E. (2017) · PLoS ONE · doi:10.1371/journal.pone.0184454 · Cited by 34
Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization
Schirrmann, M. K., Zoller, S., Croll, D., Stukenbrock, E. H., Leuchtmann, A., & Fior, S. (2018) · Molecular Ecology · doi:10.1111/mec.14585 · Cited by 34
Acute Influenza A virus outbreak in an enzootic infected sow herd: Impact on viral dynamics, genetic and antigenic variability and effect of maternally derived antibodies and vaccination
Ryt‐Hansen, P., Pedersen, A. G., Larsen, I., Krog, J. S., Kristensen, C. S., & Larsen, L. E. (2019) · PLoS ONE · doi:10.1371/journal.pone.0224854 · Cited by 34
The Molecular Evolution of Animal Reproductive Tract Proteins: What Have We Learned from Mating-System Comparisons?
Wong, A. (2011) · International Journal of Evolutionary Biology · doi:10.4061/2011/908735 · Cited by 34
Viral cystatin evolution and three-dimensional structure modelling: A case of directional selection acting on a viral protein involved in a host-parasitoid interaction
Serbielle, C., Chowdhury, S. F., Pichon, S., Dupas, S., Lesobre, J., Purisima, E. O., Drezen, J., & Huguet, E. (2008) · BMC Biology · doi:10.1186/1741-7007-6-38 · Cited by 40
SEQUENCE EVOLUTION OF THE SPERM LIGAND ZONADHESIN CORRELATES NEGATIVELY WITH BODY WEIGHT DIMORPHISM IN PRIMATES
Herlyn, H., & Zischler, H. (2007) · Evolution · doi:10.1111/j.1558-5646.2007.00035.x · Cited by 34
Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences
Ngandu, N. K., Scheffler, K., Moore, P. L., Woodman, Z., Martin, D. P., & Seoighe, C. (2008) · Virology Journal · doi:10.1186/1743-422x-5-160 · Cited by 34
Measuring and Detecting Molecular Adaptation in Codon Usage Against Nonsense Errors During Protein Translation
Gilchrist, M. A., Shah, P., & Zaretzki, R. (2009) · Genetics · doi:10.1534/genetics.109.108209 · Cited by 34
Adaptive evolution in GroEL from distantly related endosymbiotic bacteria of insects
Fares, M. A., Moyá, A., & Barrio, E. (2005) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2004.00861.x · Cited by 34
Mutational Signatures Are Critical for Proper Estimation of Purifying Selection Pressures in Cancer Somatic Mutation Data When Using the dN/dS Metric
den Eynden, J. V., & Larsson, E. (2017) · Frontiers in Genetics · doi:10.3389/fgene.2017.00074 · Cited by 34
Variation in synonymous codon use and DNA polymorphism within the Drosophila genome
Bierne, N., & Eyre‐Walker, A. (2005) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2005.00996.x · Cited by 34
Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome
Kosiol, C., Bofkin, L., & Whelan, S. (2005) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2005.08.003 · Cited by 34
SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence?Preprint
Zhan, S. H., Deverman, B. E., & Chan, Y. A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.01.073262 · Cited by 34
Lack of Spatial Immunogenetic Structure among Wolverine (Gulo gulo) Populations Suggestive of Broad Scale Balancing Selection
Rico, Y., Morris‐Pocock, J. A., Zigouris, J., Nocera, J. J., & Kyle, C. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0140170 · Cited by 33
Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations
Weber, C. C., & Whelan, S. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz003 · Cited by 34
Drosophila female reproductive tract gene expression reveals coordinated mating responses and rapidly evolving tissue-specific genes
McDonough-Goldstein, C. E., Borziak, K., Pitnick, S., & Dorus, S. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab020 · Cited by 33
Evolutionary changes of the importance of olfaction in cetaceans based on the olfactory marker protein gene
Kishida, T., & Thewissen, J. G. M. (2011) · Gene · doi:10.1016/j.gene.2011.11.013 · Cited by 33
Jacalin domain in wheat jasmonate-regulated protein Ta-JA1 confers agglutinating activity and pathogen resistance
Ma, Q.-H., Zhen, W.-B., & Liu, Y.-C. (2012) · Biochimie · doi:10.1016/j.biochi.2012.10.014 · Cited by 33
Phylogenetic methods in natural product research
Schmitt, I., & Barker, F. K. (2009) · Natural Product Reports · doi:10.1039/b910458p · Cited by 33
Recent host-shifts in ranaviruses: signatures of positive selection in the viral genome
Abrams, A. J., Cannatella, D. C., Hillis, D. M., & Sawyer, S. L. (2013) · Journal of General Virology · doi:10.1099/vir.0.052837-0 · Cited by 33
Phylogenetic Mixture Models Can Reduce Node-Density Artifacts
Venditti, C., Meade, A., & Pagel, M. D. (2008) · Systematic Biology · doi:10.1080/10635150802044045 · Cited by 33
Increased constraints on MC4R during primate and human evolution
Hughes, D. A., Hinney, A., Brumm, H., Wermter, A., Biebermann, H., Hebebrand, J., & Stoneking, M. (2008) · Human Genetics · doi:10.1007/s00439-008-0591-8 · Cited by 33
Models of RNA virus evolution and their roles in vaccine design
Ojosnegros, S., & Beerenwinkel, N. (2010) · Immunome Research · doi:10.1186/1745-7580-6-s2-s5 · Cited by 33
Selection on the Protein-Coding Genome
Kosiol, C., & Anisimova, M. O. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-585-5_5 · Cited by 32
Criticality in tumor evolution and clinical outcome
Persi, E., Wolf, Y. I., Leiserson, M. D. M., Koonin, E. V., & Ruppin, E. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1807256115 · Cited by 34

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