Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Philosophical Transactions of the Royal Society B: Biological Sciences

• Publication date

  2008-12-27

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1098/rstb.2008.0178PMID 18852097PMCID PMC2607421
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Bayesian data analysis.

  2010cited by this paper
• Phylogenetic mixture models can reduce node-density artifacts.

  2008cited by this paper
• A mixed branch length model of heterotachy improves phylogenetic accuracy.

  2008cited by this paper
• Changing Selective Pressure during Antigenic Changes in Human Influenza H3

  2008cited by this paper
• Mathematics of Evolution and Phylogeny

  2008cited by this paper
• A Phylogenetic Mixture Model for Heterotachy

  2008cited by this paper
• Testing for covarion-like evolution in protein sequences.

  2007cited by this paper
• Mixture models in phylogenetic inference

  2007cited by this paper
• Evaluation of the models handling heterotachy in phylogenetic inference

  2007cited by this paper
• Systematics and Evolution of the Tropical Monocot Family Costaceae (Zingiberales): A Multiple Dataset Approach

  2006cited by this paper
• Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible‐Jump Markov Chain Monte Carlo

  2006cited by this paper
• Likelihood, parsimony, and heterogeneous evolution.

  2005cited by this paper
• Covarion structure in plastid genome evolution: a new statistical test.

  2005cited by this paper
• Heterotachy and long-branch attraction in phylogenetics

  2005cited by this paper
• Rate of change of concomitantly variable codons

  2005cited by this paper
• Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss

  2004cited by this paper
• A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data.

  2004cited by this paper
• A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process.

  2004cited by this paper
• Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.

  2004cited by this paper
• Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous

  2004cited by this paper
• Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes.

  2004cited by this paper
• Testing a covariotide model of DNA substitution.

  2002cited by this paper
• Seed Plant Relationships and the Systematic Position of Gnetales Based on Nuclear and Chloroplast DNA: Conflicting Data, Rooting Problems, and the Monophyly of Conifers

  2002cited by this paper
• Heterotachy, an important process of protein evolution.

  2002cited by this paper
• PHYLOGENY OF THE CHLOROPHYCEAE WITH SPECIAL REFERENCE TO THE SPHAEROPLEALES: A STUDY OF 18S AND 26S rDNA DATA

  2001cited by this paper
• Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution

  2001cited by this paper
• Bayesian selection of continuous-time Markov chain evolutionary models.

  2001cited by this paper
• A comparison of reversible jump MCMC algorithms for DNA sequence segmentation using hidden Markov models

  2001cited by this paper
• Maximum-likelihood phylogenetic analysis under a covarion-like model.

  2001cited by this paper
• Variation in the Pattern of Nucleotide Substitution Across Sites

  1999cited by this paper
• Inferring the historical patterns of biological evolution

  1999cited by this paper
• Models of natural mutations including site heterogeneity

  1998cited by this paper
• Modeling the covarion hypothesis of nucleotide substitution.

  1998cited by this paper
• PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees

  1997cited by this paper
• Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

  1997cited by this paper
• Reversible jump Markov chain Monte Carlo computation and Bayesian model determination

  1995cited by this paper
• Introducing Markov chain Monte Carlo

  1995cited by this paper
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

  1994cited by this paper
• Bayesian Mixture Modeling

  1992cited by this paper
• Estimating the Dimension of a Model

  1978cited by this paper
• A new look at the statistical model identification

  1974cited by this paper
• An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution

  1970cited by this paper
• Monte Carlo Sampling Methods Using Markov Chains and Their Applications

  1970cited by this paper

• A covarion model for phylogenetic estimation using discrete morphological datasets

  2026cites this paper
• Practical Guide and Review of Fossil Tip-Dating in Phylogenetics

  2025cites this paper
• Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock

  2024cites this paper
• Genomic Signature in Evolutionary Biology: A Review

  2023cites this paper
• Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling

  2022cites this paper
• Lineage and role in integrative taxonomy of a heterotrophic orchid complex

  2022cites this paper
• A New Species of Lepidochitona (Polyplacophora: Mopalioidea) from the Panamic Province

  2022influential citation
• Phylogenetic relationships, origin and historical biogeography of the genus Sprattus (Clupeiformes: Clupeidae)

  2021cites this paper
• PERSPECTIVES AND HYPOTHESIS in uncovered

  2021cites this paper
• Phylogenetic position and morphological descriptions of Chiton species from the south-eastern Pacific

  2020cites this paper
• Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection

  2020cites this paper
• Big Data Scalability of BayesPhylogenies on Harvard's Ozone 12k Cores

  2019cites this paper
• Phylogeny, divergence times and species delimitation of Tonicia (Polyplacophora: Chitonidae) from the eastern Pacific Ocean

  2019cites this paper
• mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria

  2019cites this paper
• Molecular evidence for conspecificity of two desert Liolaemus lizards (Iguania: Liolaemidae).

  2018cites this paper
• Comprehensive phylogeny of acariform mites (Acariformes) provides insights on the origin of the four-legged mites (Eriophyoidea), a long branch.

  2018cites this paper
• The prevalence of terraced treescapes in analyses of phylogenetic data sets

  2018cites this paper
• Coevolution of landesque capital intensive agriculture and sociopolitical hierarchy

  2018cites this paper
• The identification of sympatric cryptic free-living nematode species in the Antarctic intertidal

  2017cites this paper
• The evolutionary relationships and age of Homo naledi: An assessment using dated Bayesian phylogenetic methods.

  2016cites this paper
• Disentangling Incomplete Lineage Sorting and Introgression to Refine Species‐Tree Estimates for Lake Tanganyika Cichlid Fishes

  2016cites this paper
• Consequences of the last glacial maximum on Nyctelia confusa (Coleoptera: Tenebrionidae) in Patagonia

  2016cites this paper
• The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)

  2016cites this paper
• Adelinia and Andersonglossum (Boraginaceae), Two New Genera from New World Species of Cynoglossum

  2015influential citation
• Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships

  2015cites this paper
• Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation

  2015cites this paper
• Capturing heterotachy through multi-gamma site models

  2015cites this paper
• The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages.

  2015cites this paper
• Les cténophores : de leur position dans l'arbre des métazoaires (approche phylogénomique) à leur diversité taxonomique (phylogénie moléculaire et anatomie comparée)

  2014cites this paper
• Impacts of Terraces on Phylogenetic Inference.

  2014cites this paper
• Seven-locus molecular phylogeny of Myctophiformes (Teleostei; Scopelomorpha) highlights the utility of the order for studies of deep-sea evolution.

  2014cites this paper
• Inclusive taxon sampling suggests a single, stepwise origin of ectolecithality in Platyhelminthes

  2014cites this paper
• Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes.

  2014cites this paper
• Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae.

  2014influential citation
• Diversidad de nematodos marinos de Chile continental y antártico: una evaluación morfológica y molecular

  2014cites this paper
• Evolution of sexual size dimorphism and its relationship with sex ratio in carabid beetles of Genus Ceroglossus Solier

  2013influential citation
• Using phylogenetics and model selection to investigate the evolution of RNA genes in genomic alignments.

  2013cites this paper
• High-Throughput Genomic Data in Systematics and Phylogenetics

  2013cites this paper
• The South American radiation of Lepechinia (Lamiaceae): phylogenetics, divergence times and evolution of dioecy

  2013cites this paper
• Interchanging Functionality Among Homologous Elongation Factors Using Signatures of Heterotachy

  2013cites this paper
• Historical biogeography of Eastern Asian-Eastern North American disjunct Melaphidina aphids (Hemiptera: Aphididae: Eriosomatinae) on Rhus hosts (Anacardiaceae).

  2013cites this paper
• Phylogenetics, biogeography, and staminal evolution in the tribe Mentheae (Lamiaceae).

  2012cites this paper
• Colony Size Evolution and the Origin of Eusociality in Corbiculate Bees (Hymenoptera: Apinae)

  2012cites this paper
• Genetic divergence of the Siberian chipmunk Tamias sibiricusbarberi (Rodentia: Mammalia) in Korea using three conserved genes ( IRBP , 12S rRNA and 16S rRNA)

  2012cites this paper
• Primate socioecology at the crossroads: Past, present, and future

  2012cites this paper
• Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: insights from an eight-locus plastid phylogeny.

  2011cites this paper
• The devil in the details: interactions between the branch-length prior and likelihood model affect node support and branch lengths in the phylogeny of the Psoraceae.

  2011cites this paper
• Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics

  2011cites this paper
• ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods

  2011cites this paper
• Classification of molecular sequence data using Bayesian phylogenetic mixture models

  2011cites this paper
• Recent trends in molecular phylogenetic analysis: where to next?

  2011cites this paper
• Phylogenetic structure and species boundaries in the mountain pitviper Ovophis monticola (Serpentes: Viperidae: Crotalinae) in Asia.

  2011cites this paper
• A NOVEL COMPARATIVE METHOD FOR IDENTIFYING SHIFTS IN THE RATE OF CHARACTER EVOLUTION ON TREES

  2011cites this paper
• Evolving Perceptions on the Antiquity of the Modern Avian Tree

  2011cites this paper
• Fast statistical tests for detecting heterotachy in protein evolution.

  2011cites this paper
• Phylogeny, phylogeography and conservation genetics of the brachyotis group of rock-wallabies.

  2011cites this paper
• Evolution of Antifreeze Protein Genes in the Diatom Genus Fragilariopsis: Evidence for Horizontal Gene Transfer, Gene Duplication and Episodic Diversifying Selection

  2011cites this paper
• What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny

  2011cites this paper
• Molecular Clock: Testing

  2011cites this paper
• Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited

  2011cites this paper
• Detecting Phylogenetic Breakpoints and Discordance from Genome-Wide Alignments for Species Tree Reconstruction

  2011cites this paper
• Classification of molecular sequence data using a Bayesian phylogenetic mixture and related MCMC methods

  2010cites this paper
• Time--the emerging dimension of plant virus studies.

  2010cites this paper
• A Molecular Genetic Timescale for the Diversification of Autotrophic Stramenopiles (Ochrophyta): Substantive Underestimation of Putative Fossil Ages

  2010influential citation
• Rates of Molecular Evolution and Phylogenomic Inference

  2010cites this paper
• Vahliellaceae, a new family of cyanobacterial lichens (Peltigerales, Ascomycetes)

  2010influential citation
• Classification of phylogenetic data via Bayesian mixture modelling

  2010influential citation
• Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree

  2010cites this paper
• A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests.

  2010cites this paper
• A lightweight supercomputing Web portal for inferring phylogenetic trees

  2009cites this paper
• PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

  2009cites this paper
• Phylogénie, éléments transposables et évolution de la taille des génomes chez les lupins

  2009cites this paper
• Genotype–phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate

  2009cites this paper
• Introduction. Statistical and computational challenges in molecular phylogenetics and evolution

  2008cites this paper
• Recent Trends in Molecular Phylogenetic Analysis: Where to Next? Gap Coding Direct Optimization Phylogenetic Inference

  year unknowncites this paper
• Phylogeny, Adaptive Radiation, and Historical Biogeography in Phylogeny, Adaptive Radiation, and Historical Biogeography in Bromeliaceae: Insights from an Eight-Locus Plastid Phylogeny Bromeliaceae: Insights from an Eight-Locus Plastid Phylogeny

  year unknowncites this paper