Statistical tests of models of DNA substitution

1993/02/01 by Nick Goldman · 778 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · Earth and Planetary Sciences · Mathematics · #Artificial intelligence #Bayesian Methods and Mixture Models #Biology #Computer science #Confidence interval #Econometrics #Evolution and Paleontology Studies #Genetics #Genomics and Phylogenetic Studies #Inference #Mathematics #Phylogenetic tree #Sequence (biology) #Statistic #Statistical hypothesis testing #Statistical inference #Statistics #Substitution (logic) #Tree (set theory)

paper · doi:10.1007/bf00166252

published in Journal of Molecular Evolution 36(2), 182-198 (Springer Science+Business Media)

openalex publication_date 1993/02/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Citations

• Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
• Evolutionary trees from DNA sequences: A maximum likelihood approach

Cited by

• Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods
• THE ORIGIN AND DIVERSIFICATION OF GALAPAGOS MOCKINGBIRDS
• PHYLOGEOGRAPHY AND HISTORY OF GIANT GALAPAGOS TORTOISES
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
• PHYLOGENETIC ANALYSIS IN MOLECULAR EVOLUTIONARY GENETICS
• Measuring Fit of Sequence Data to Phylogenetic Model: Gain of Power using Marginal Tests
• PAML 4: Phylogenetic Analysis by Maximum Likelihood
• MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
• Phylogenomic analyses recover a clade of large-bodied decapodiform cephalopods
• The Prevalence and Impact of Model Violations in Phylogenetic Analysis
• Ultrafast Approximation for Phylogenetic Bootstrap
• Phylogeny of carabid beetles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae)
• Phylogenetic relationships of tachinid flies in subfamily Exoristinae (Tachinidae: Diptera) based on 28S rDNA and elongation factor‐1α
• An Evolving View of Species Tree Inference
• Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes
• Phylogenetic reconstruction of carnivore social organizations
• Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): Evidence from the mitochondrial genome
• Molecular phylogeny and historical biogeography of the land snail genus Solatopupa (Pulmonata) in the peri-Tyrrhenian area
• Patterns of Speciation in the Yucca Moths: Parallel Species Radiations within the Tegeticula yuccasella Species Complex
• Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences
• UFBoot2: Improving the Ultrafast Bootstrap Approximation
• Molecular Phylogeny of <I>Conradina</I> and Other Scrub Mints (Lamiaceae) from the Southeastern USA: Evidence for Hybridization in Pleistocene Refugia?
• Phylogenetic Patterns in Northern Hemisphere Plant Geography
• Tramps, narrow endemics and morphologically cryptic species in the epiphyllous liverwort Diplasiolejeunea
• Experimental Design in Caecilian Systematics: Phylogenetic Information of Mitochondrial Genomes and Nuclear rag1
• Identification of domestic cattle hybrids in wild cattle and bison species: a general approach using mtDNA markers and the parametric bootstrap
• Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals
• Biogeography and Floral Evolution of Baobabs Adansonia, Bombacaceae as Inferred From Multiple Data Sets
• Phylogeny and Biogeography of the Arbutoideae (Ericaceae): Implications for the Madrean-Tethyan Hypothesis
• RNA secondary structure: physical and computational aspects
• Phylogenetic relationships, historical biogeography and character evolution of fig-pollinating wasps
• Estimating Synonymous and Nonsynonymous Substitution Rates Under Realistic Evolutionary Models
• Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
• Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics
• Likelihood-Based Tests of Topologies in Phylogenetics
• IS YOUR PHYLOGENY INFORMATIVE? MEASURING THE POWER OF COMPARATIVE METHODS
• THE DYNAMICS OF NATURAL SELECTION AND VICARIANCE IN THE DOMINICAN ANOLE: PATTERNS OF WITHIN-ISLAND MOLECULAR AND MORPHOLOGICAL DIVERGENCE
• piBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios
• Molecular clock-like evolution of human immunodeficiency virus type 1
• Clustering Genes of Common Evolutionary History
• Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. [europepmc]
• Understanding the molecular epidemiology of foot-and-mouth-disease virus. [europepmc]
• Quaternary history and contemporary patterns in a currently expanding species. [europepmc]
• Molecular systematics: A synthesis of the common methods and the state of knowledge. [europepmc]
• Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. [europepmc]
• PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment. [europepmc]
• Return to Beringia: parasites reveal cryptic biogeographic history of North American pikas. [europepmc]
• Detailed genetic analysis of hemagglutinin-neuraminidase glycoprotein gene in human parainfluenza virus type 1 isolates from patients with acute respiratory infection between 2002 and 2009 in Yamagata prefecture, Japan. [europepmc]
• Quantifying limits to detection of early warning for critical transitions. [europepmc]
• Is your phylogeny informative? Measuring the power of comparative methods. [europepmc]
• πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. [europepmc]
• Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations. [europepmc]
• Clustering Genes of Common Evolutionary History. [europepmc]
• Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes. [europepmc]
• UFBoot2: Improving the Ultrafast Bootstrap Approximation. [europepmc]
• Rapid Global Spread of wRi-like Wolbachia across Multiple Drosophila. [europepmc]
• Model selection may not be a mandatory step for phylogeny reconstruction. [europepmc]
• Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Heliconius Butterflies. [europepmc]
• The Prevalence and Impact of Model Violations in Phylogenetic Analysis. [europepmc]
• The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets. [europepmc]
• Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics. [europepmc]
• Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods. [europepmc]
• Inferring the Deep Past from Molecular Data. [europepmc]
• Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data. [europepmc]
• Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications. [europepmc]