Evolutionary trees from DNA sequences: A maximum likelihood approach

1981/11/01 by Joseph Felsenstein · 14,903 citations
Biochemistry, Genetics and Molecular Biology · Mathematics · #Biology #Clade #Combinatorics #Evolutionary biology #Gene #Genetic Mapping and Diversity in Plants and Animals #Genetic diversity and population structure #Genetics #Genomics and Phylogenetic Studies #Mathematics #Maximum likelihood #Maximum parsimony #Phylogenetic tree #Sequence (biology) #Statistics #Tree (set theory) #Tree rearrangement

paper · doi:10.1007/bf01734359

published in Journal of Molecular Evolution 17(6), 368-376 (Springer Science+Business Media)

openalex publication_date 1981/11/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05

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• Automated Tensor-Relational Decomposition for Large-Scale Sparse Tensor Computation
• Phylogenetic estimation with partial likelihood tensors
• The Emergence of Life
• Phylogeny, ancestors, and anagenesis in the hominin fossil record
• A multilocus timescale for the origin of extant amphibians
• Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1
• Experimental Design in Caecilian Systematics: Phylogenetic Information of Mitochondrial Genomes and Nuclear rag1
• Experimental Design in Phylogenetics: Testing Predictions from Expected Information
• Life-history evolution and mitogenomic phylogeny of caecilian amphibians
• Phylogenetics and Biogeography of Alnus (Betulaceae) Inferred from Sequences of Nuclear Ribosomal DNA ITS Region
• Evolutionary origin of Plasmodium and other Apicomplexa based on rRNA genes.
• Small-Subunit Ribosomal RNA Gene Sequences of Phaeodarea Challenge the Monophyly of Haeckel's Radiolaria
• Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset
• Early bioinformatics: the birth of a discipline—a personal view
• Species tree estimation using Neighbor Joining
• A glimpse on the pattern of rodent diversification: a phylogenetic approach
• Evaluating Hypotheses of Deuterostome Phylogeny and Chordate Evolution with New LSU and SSU Ribosomal DNA Data
• Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary
• The bee tree of life: a supermatrix approach to apoid phylogeny and biogeography
• Complete Mitochondrial DNA of the Hagfish, Eptatretus burgeri: The Comparative Analysis of Mitochondrial DNA Sequences Strongly Supports the Cyclostome Monophyly
• Evidence from Nuclear DNA Sequences Sheds Light on the Phylogenetic Relationships of Pinnipedia: Single Origin with Affinity to Musteloidea
• The Baculum was Gained and Lost Multiple Times during Mammalian Evolution
• On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence
• Getting Started in Probabilistic Graphical Models
• Conditionally Site-Independent Neural Evolution of Antibody Sequences
• Phylogenetic Analyses Indicate that the 19′Hexanoyloxy-fucoxanthin-Containing Dinoflagellates Have Tertiary Plastids of Haptophyte Origin
• The complete mitochondrial genome of dhole Cuon alpinus: phylogenetic analysis and dating evolutionary divergence within canidae
• Phylogenetic origins of Lophocereus (Cactaceae) and the senita cactus–senita moth pollination mutualism
• Molecular phylogeny of the genera Digitalis L. and Isoplexis (Lindley) Loudon (Veronicaceae) based on ITS- and trnL-F sequences
• ON PHYLOGENETIC TESTS OF IRREVERSIBLE EVOLUTION
• Diversity and phylogenetic profiling of niche-specific Bacilli from extreme environments of India
• Rhodopechys obsoleta (desert finch): a pale ancestor of greenfinches (Carduelis spp.) according to molecular phylogeny
• The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes
• Mitochondrial Phylogenetics and Evolution of Mysticete Whales
• Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria
• PHYLOGENETIC RELATIONSHIPS AMONG THE DELPHINID CETACEANS BASED ON FULL CYTOCHROME B SEQUENCES
• Агиография и фольклор как средство духовно-нравственного воспитания школьников
• 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
• Typological variation across Mandarin dialects: An areal perspective with a quantitative approach
• Going to Extremes: Contrasting Rates of Diversification in a Recent Radiation of New World Passerine Birds
• Monophyly and relationships of wrens (Aves: Troglodytidae): a congruence analysis of heterogeneous mitochondrial and nuclear DNA sequence data
• c-mos Variation in Songbirds: Molecular Evolution, Phylogenetic Implications, and Comparisons with Mitochondrial Differentiation
• A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequences
• Evolutionary Relationships among Extant Albatrosses (Procellariiformes: Diomedeidae) Established from Complete Cytochrome-B Gene Sequences
• Sexual Dichromatism in the Blue-fronted Amazon Parrot (Amazona aestiva) Revealed by Multiple-angle Spectrometry
• Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group
• Phylogenetic Tree Construction Using Markov Chain Monte Carlo
• The origin of peroxisomes: The possibility of an actinobacterial symbiosis
• Are the Platyhelminthes a monophyletic primitive group? An assessment using 18S rDNA sequences
• The evolutionary diversification of cyanobacteria: Molecular–phylogenetic and paleontological perspectives
• Diversification of almonds, peaches, plums and cherries – Molecular systematics and biogeographic history of Prunus (Rosaceae)
• The Eukaryotic Tree of Life from a Global Phylogenomic Perspective
• Generative Modeling of Discrete Latent Structures via Dynamic Policy Gradients
• Characterization and Pathogenicity ofBotryosphaeriaceaeSpecies Collected from Olive and Other Hosts in Spain and California
• Vampires in the oceans: predatory cercozoan amoebae in marine habitats
• Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution
• Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data
• Complete Sequence and Characterization of the Channel Catfish Mitochondrial Genome
• Spiribacter aquaticus Leon et al. 2017 is a later heterotypic synonym of Spiribacter roseus Leon et al. 2016. Reclassification of Halopeptonella vilamensis Menes et al. 2016 as Spiribacter vilamensis comb. nov.
• Halopeptonella vilamensis gen. nov, sp. nov., a halophilic strictly aerobic bacterium of the family Ectothiorhodospiraceae
• Relationships of the Wollemi Pine (Wollemia nobilis) and a molecular phylogeny of the Araucariaceae
• Hybridization promotes color polymorphism in the aposematic harlequin poison frog,Oophaga histrionica
• Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily
• Phylogenetic Hypotheses for the Monocotyledons Constructed from rbcL Sequence Data
• A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy
• <i>Streptomyces cameroonensis</i> sp. nov., a Geldanamycin Producer That Promotes <i>Theobroma cacao</i> Growth
• Molecular evidence for the inclusion of cetaceans within the order Artiodactyla.
• Phylogenetic relationships among Malagasy lemurs as revealed by mitochondrial DNA sequence analysis
• Phylogenetic Analysis of Section Sinomartagon in Genus Lilium Using Sequences of the Internal Transcribed Spacer Region in Nuclear Ribosomal DNA.
• Shrinking the Violets: Phylogenetic Relationships of Infrageneric Groups in Viola (Violaceae) Based on Internal Transcribed Spacer DNA Sequences
• Phylogeny and Historical Biogeography of the Genus <I>Platanus</I> as Inferred From Nuclear and Chloroplast DNA
• An approximate stationary solution for multi-allele neutral diffusion with low mutation rates
• Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus
• Phylogeny and Evolutionary History of Old World Suboscine Birds (Aves: Eurylaimides)
• Phylogenetic reconstruction of the felidae using 16S rRNA and NADH-5 mitochondrial genes
• PHYLOGENETIC ANALYSIS OF THE FAMILY PECTINIDAE (BIVALVIA) BASED ON MITOCHONDRIAL CYTOCHROME C OXIDASE SUBUNIT I
• Two new cryptic species of the Cyrtodactylus irregularis complex (Squamata: Gekkonidae) from southern Vietnam
• Phylogenetic Relationships and the Radiation of Sigmodontine Rodents in South America: Evidence from Cytochrome b
• Phylogeny of the Hamamelidaceae based on the ITS sequences of nuclear ribosomal DNA
• Cytochrome b and Bayesian inference of whale phylogeny
• Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections
• Revisiting the phylogeny of Cephalopoda using complete mitochondrial genomes
• Reticulate evolution in Thuja inferred from multiple gene sequences: Implications for the study of biogeographical disjunction between eastern Asia and North America
• nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models
• Species status and conservation issues of New Zealand’s endemic Latrodectus spider species (Araneae : Theridiidae)
• Molecular diversification of salamanders of the tropical American genus Bolitoglossa (Caudata: Plethodontidae) and its evolutionary and biogeographical implications
• Using the tangle: a consistent construction of phylogenetic distance matrices for quartets
• Revealing Less Derived Nature of Cartilaginous Fish Genomes with Their Evolutionary Time Scale Inferred with Nuclear Genes
• Morphological evolution and ecological diversification of the forest-dwelling poppies (Papaveraceae: Chelidonioideae) as deduced from a molecular phylogeny of the ITS region
• Molecular genetics of the most endangered canid: the Ethiopian wolf Canis simensis
• Phylogeography of the Golden Jackal (Canis aureus) in India
• Molecular Phylogenetics of the Leafy Cactus Genus <I>Pereskia</I> (Cactaceae)
• Slow worm, Anguis fragilis (Reptilia: Anguidae) as a species complex: Genetic structure reveals deep divergences
• A new species of the genus Oxymycterus (Mammalia: Rodentia: Cricetidae) from the vanishing Yungas of Argentina
• A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals
• Phylogenetic relationships of otters (Carnivora: Mustelidae) based on mitochondrial cytochrome b sequences
• A chloroplast phylogeny of Arisaema (Araceae) illustrates Tertiary floristic links between Asia, North America, and East Africa
• Microbial diversity in hydrothermal surface to subsurface environments of Suiyo Seamount, Izu-Bonin Arc, using a catheter-type in situ growth chamber
• Molecular analysis of a 11 700‐year‐old rodent midden from the Atacama Desert, Chile
• Likelihood-Based Tests of Topologies in Phylogenetics
• Inferring Epidemiological Dynamics with Bayesian Coalescent Inference: The Merits of Deterministic and Stochastic Models
• Modelling Trait-dependent Speciation with Approximate Bayesian Computation
• Origin and evolutionary relationships of giant Galápagos tortoises
• Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise
• Inverse Ising inference with correlated samples
• Phylogenetic studies of Mammillaria (Cactaceae)—insights from chloroplast sequence variation and hypothesis testing using the parametric bootstrap
• Phylogenetic analysis of the Monogenea and their relationships with Digenea and Eucestoda inferred from 28S rDNA sequences1Note: Nucleotide sequence data reported in this paper are available in the EMBL, GenBank™ and DDJB data bases under the accession numbers AF026103–AF026119.1
• EVOLUTION OF LONG-DISTANCE MIGRATION IN AND HISTORICAL BIOGEOGRAPHY OF CATHARUS THRUSHES: A MOLECULAR PHYLOGENETIC APPROACH
• Evolutionary differentiation of bimaculatus group anoles based on analyses of mtDNA and microsatellite data
• Evolutionary Relationships of the Anolis bimaculatus Group from the Northern Lesser Antilles
• piBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios
• Taxonomy was the foundation of Darwin's evolution
• New Chinese turtles: endangered or invalid? A reassessment of two species using mitochondrial DNA, allozyme electrophoresis and known-locality specimens
• Mitogenomic phylogeny of Nassariidae (Neogastropoda: Buccinoidea)
• Phylogenetic Tree Inference with Tropical Axial Attention
• Metagenomics-guided cloning, expression, and characterization of thermotolerant multifunctional cellulase from Rehai Hot Spring
• Molecular clock-like evolution of human immunodeficiency virus type 1
• Seeing the wood for the trees: philosophical aspects of classical, Bayesian and likelihood approaches in statistical inference and some implications for phylogenetic analysis
• High-precision binary trait association on phylogenetic trees
• A model capturing novel strand symmetries in bacterial DNA
• Molecular dating of the ‘Gondwanan’ plant family Proteaceae is only partially congruent with the timing of the break‐up of Gondwana
• Higher level phylogenetic relationships of euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data
• Phylogenetics [wikipedia]
• SIMMAP: stochastic character mapping of discrete traits on phylogenies. [europepmc]
• Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. [europepmc]
• MultiSeq: unifying sequence and structure data for evolutionary analysis. [europepmc]
• Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. [europepmc]
• Classification and nomenclature of all human homeobox genes. [europepmc]
• Bayesian inference of population size history from multiple loci. [europepmc]
• African swine fever virus isolate, Georgia, 2007. [europepmc]
• Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. [europepmc]
• Architecture and secondary structure of an entire HIV-1 RNA genome. [europepmc]
• BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. [europepmc]
• Bayesian random local clocks, or one rate to rule them all. [europepmc]
• A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. [europepmc]
• pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. [europepmc]
• MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity. [europepmc]
• B-cell-lineage immunogen design in vaccine development with HIV-1 as a case study. [europepmc]
• The fossilized birth-death process for coherent calibration of divergence-time estimates. [europepmc]
• IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. [europepmc]
• Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. [europepmc]
• Phylogenomics and systematics in Pseudomonas. [europepmc]
• bModelTest: Bayesian phylogenetic site model averaging and model comparison. [europepmc]
• Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. [europepmc]
• Contentious relationships in phylogenomic studies can be driven by a handful of genes. [europepmc]
• UFBoot2: Improving the Ultrafast Bootstrap Approximation. [europepmc]
• IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. [europepmc]
• Eleven grand challenges in single-cell data science. [europepmc]