Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference

1996/09/01 by Bruce Rannala, Ziheng Yang · 100 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Genomics and Phylogenetic Studies #Evolution and Paleontology Studies #Genetic diversity and population structure

paper · doi:10.1007/bf02338839

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

• The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model
• A New Species of River Dolphin from Brazil or: How Little Do We Know Our Biodiversity
• The conditioned reconstructed process
• Impact of Pleistocene geoclimatic events on the genetic structure in mid-latitude South American plants: insights from the phylogeography of Turnera sidoides complex (Passifloraceae, Turneroideae)
• Relationships of the haematophagous marine snailColubraria(Rachiglossa: Colubrariidae), within the neogastropod phylogenetic framework
• Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species
• Plectosphaerella species associated with root and collar rots of horticultural crops in southern Italy
• Culturable mycobiota from Karst caves in China, with descriptions of 20 new species
• Caulicolous Botryosphaeriales from Thailand
• The evolutionary relationships and age of Homo naledi: An assessment using dated Bayesian phylogenetic methods
• PHYLOGENETIC ANALYSIS IN MOLECULAR EVOLUTIONARY GENETICS
• A General Substitution Matrix for Structural Phylogenetics
• The Meaning and Measure of Concordance Factors in Phylogenomics
• The Complete Mitochondrial Genome of an 11,450-year-old Aurochsen (Bos primigenius) from Central Italy
• Species diversity of edible mushrooms IV: Morphology and phylogenetic analysis reveal two new species of Lyophyllum (Lyophyllaceae, Basidiomycota) from Yunnan Province, Southwestern China
• Elsinoë citricola is prevalent in rangpur lime scab in Brazil and also occurs on Tahiti lime
• Melomastia (Dothideomycetes, Ascomycota) species associated with Chinese Aquilaria spp.
• Three new species of Cudonia (Rhytismatales) from the Qinghai-Xizang Plateau, China
• Stochastic Mapping of Morphological Characters
• Cryptic biodiversity in the commercial diamondback squid Thysanoteuthis rhombus Troschel 1857
• Calibrated birth-death phylogenetic time-tree priors for Bayesian inference
• Morpho-phylogenetic evidence uncovers new taxa of lignicolous freshwater Sordariomycetes from Yunnan and Guizhou provinces, China
• Toward a genomic understanding of the tree of life
• Two new species of Phaeoclavulina (Gomphaceae, Gomphales) from North China based on morphological and phylogenetic analysis
• Sampling through time and phylodynamic inference with coalescent and\n birth-death models
• Integrative taxonomy of Tetraplosphaeriaceae from the Nujiang River Basin, China, reveals two new species and a new record
• Taxonomic and phylogenetic analyses reveal two new Comoclathris taxa (Dothideomycetes, Pleosporaceae) from Inner Mongolia, China
• Phylogenetic Accuracy Under Non-stationary and Non-homogeneous Conditions: A Simulation Study
• Psychrophilic fungi from the world’s roof, II: Species delimitation within an integrative taxonomic framework
• Morpho-phylogenetic evidence reveals Pseudolomaantha thailandica gen. et sp. nov. and Submultiguttulispora multiseptata gen. et sp. nov. in Chaetosphaeriaceae
• Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
• Molecular evidence for hybridization and introgression in the neotropical coastal desert-endemic Palaua (Malveae, Malvaceae)
• Fungal Biodiversity Profiles 11–20
• Morphological and Molecular Characterization of a Novel Species ofSimplicilliumfrom China
• Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning
• Microbotryozyma lacustris sp. nov. (Basidiomycota, Ustilentylomataceae) and Cyberlindnera basumtsoensis sp. nov. (Ascomycota, Phaffomycetaceae), two novel yeasts isolated from freshwater Lake Basom Tso, China
• PAML 4: Phylogenetic Analysis by Maximum Likelihood
• The polyphasic approach reveals ten novel and one known Ascomycota taxa from terrestrial agarwood‐producing trees
• A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
• RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
• Bayesian Estimation of Ancestral Character States on Phylogenies
• Inhomogeneous branching trees with symmetric and asymmetric offspring and their genealogies
• Pleopunctum xizangense sp. nov. (Pleosporales, Phaeoseptaceae) and Pseudolophiostoma yunnanense sp. nov. (Pleosporales, Lophiostomataceae), and a new record of Pleopunctum pseudoellipsoideum on Fagales
• Morphological and phylogenetic analyses reveal three new species of Chaetosphaeriaceae from China
• Two new soil-inhabiting fungi, Malbranchea cavernicola (Onygenales, Malbrancheaceae) and Talaromyces pangmaphaensis (Eurotiales, Trichocomaceae), from a cave in northern Thailand
• Closing the Evidence Gap: reddemcee, a Fast Adaptive Parallel Tempering Sampler
• Morpho-phylogenetic evidence reveals new species and records of Beltraniaceae (Amphisphaeriales, Sordariomycetes) from southern China
• Morphological and molecular identification of new species and records of Daldinia (Hypoxylaceae, Xylariales) from Guizhou Province, China
• Three new species of Sanguinoderma (Ganodermataceae, Basidiomycota) from Southwest China revealed by morphology and phylogenetic analysis
• Phylogenetic Inference from Atomized 3D Morphometric Data: A Case Study using Kangaroos
• Two new Periconia species (Pleosporales, Ascomycota) in China
• Biogeography and species diversity of freshwater Savoryellomycetidae ( Sordariomycetes ) fungi
• Morpho-phylogenetic evidence reveals novel hyphomycetous fungi on medicinal plants in Southwestern China
• Morpho-molecular analyses reveal two novel species and two new records of Dictyosporiaceae (Pleosporales) from Dulongjiang River in northwestern Yunnan Province, China
• Morpho-phylogenetic evidence reveals four novel species of Coniella (Diaporthales, Schizoparmaceae) from southern China
• Somnuekia flaviflora (Malvaceae, Brownlowioideae), a new genus and species from Thailand
• Two novel hyphomycetes associated with ferns from China
• Morpho-molecular characterization of Discosia ravennica sp. nov. and a new host record for Sporocadus rosigena
• Marginal likelihoods in phylogenetics: a review of methods and applications
• Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology)
• Pratylenchus brasiliensis sp. nov. (Nematoda: Pratylenchidae): An Emerging Threat to Soybean in an Important New Agricultural Frontier in Brazil
• Mitochondrial genome and phylogenetic placement of the enigmatic mole beetle, Hypocephalus armatus Desmarest, 1832 (Coleoptera: Chrysomeloidea)
• A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data
• Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes
• Systematics of the southern Patagonian-Fueguian endemic Abrothrix lanosus (Rodentia: Sigmodontinae): Phylogenetic position, karyotypic and morphological data
• Investigating the origin of transoceanic distributions: Mtdna showsMabuyalizards (Reptilia, Scincidae) crossed the Atlantic twice
• Maximum Likelihood Estimation for Single Linkage Hierarchical Clustering
• Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection
• Diversity of culturable fungi in six Tibetan Plateau lakes, with descriptions of eight new taxa
• Phylogenetic automata, pruning, and multiple alignment
• The conditioned reconstructed process
• Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds
• The inference of gene trees with species trees
• Finding the right path: statistical mechanics of connected solutions in constraint satisfaction problems
• Phylogenetics [wikipedia]
• Predicting evolutionary potential: in vitro evolution accurately reproduces natural evolution of the tem beta-lactamase. [europepmc]
• Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales. [europepmc]
• European species of Hypocrea Part I. The green-spored species. [europepmc]
• Highly specialized microbial diversity in hyper-arid polar desert. [europepmc]
• Phylogenetic relationships and biogeographical patterns in Circum-Mediterranean subfamily Leuciscinae (Teleostei, Cyprinidae) inferred from both mitochondrial and nuclear data. [europepmc]
• Genomes-based phylogeny of the genus Xanthomonas. [europepmc]
• Plectosphaerella species associated with root and collar rots of horticultural crops in southern Italy. [europepmc]
• Phylogenetic analysis reveals a high prevalence of Sporothrix brasiliensis in feline sporotrichosis outbreaks. [europepmc]
• A new species of river dolphin from Brazil or: how little do we know our biodiversity. [europepmc]
• Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen. [europepmc]
• The fossilized birth-death process for coherent calibration of divergence-time estimates. [europepmc]
• Sampling through time and phylodynamic inference with coalescent and birth-death models. [europepmc]
• Naming and outline of Dothideomycetes -2014 including proposals for the protection or suppression of generic names. [europepmc]
• A biologist's guide to Bayesian phylogenetic analysis. [europepmc]
• Culturable mycobiota from Karst caves in China, with descriptions of 20 new species. [europepmc]
• Modeling Hybridization Under the Network Multispecies Coalescent. [europepmc]
• The Spectre of Too Many Species. [europepmc]
• High diversity of Diaporthe species associated with dieback diseases in China, with twelve new species described. [europepmc]
• Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning. [europepmc]
• Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China. [europepmc]
• An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola). [europepmc]
• Fungi vs. Fungi in Biocontrol: An Overview of Fungal Antagonists Applied Against Fungal Plant Pathogens. [europepmc]
• Cytospora ( Diaporthales ) in China. [europepmc]
• The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages. [europepmc]
• Fungal diversity notes 1512-1610: taxonomic and phylogenetic contributions on genera and species of fungal taxa. [europepmc]