Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?
暂无分享,去创建一个
Jeremy M. Brown | Robert C Thomson | R. C. Thomson | Rebecca A. Chong | Jeremy M Brown | E. Richards | A. J. Barley | Emilie J Richards | Anthony J Barley | Rebecca A Chong | R. A. Chong | A. Barley
[1] Jeremy M. Brown,et al. P3: Phylogenetic Posterior Prediction in RevBayes , 2018, Molecular biology and evolution.
[2] Chao Zhang,et al. ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches , 2017, RECOMB-CG.
[3] H. Shaffer,et al. Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines). , 2017, Molecular phylogenetics and evolution.
[4] Tandy Warnow,et al. To include or not to include: The impact of gene filtering on species tree estimation methods , 2017, bioRxiv.
[5] S. Ho,et al. New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity , 2017, Molecular biology and evolution.
[6] Anthony J. Geneva,et al. RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses. , 2017, Molecular biology and evolution.
[7] A. Rokas,et al. Contentious relationships in phylogenomic studies can be driven by a handful of genes , 2017, Nature Ecology &Evolution.
[8] Wen Huang,et al. Visualizing phylogenetic tree landscapes , 2017, BMC Bioinformatics.
[9] Jeremy M. Brown,et al. Bayes Factors Unmask Highly Variable Information Content, Bias, and Extreme Influence in Phylogenomic Analyses , 2016, Systematic biology.
[10] Jeremy M. Brown,et al. TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees. , 2016, Molecular biology and evolution.
[11] Nicolas Galtier,et al. Incomplete Lineage Sorting in Mammalian Phylogenomics , 2016, Systematic biology.
[12] Jeffrey P. Townsend,et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing , 2016, Nature.
[13] R. C. Thomson,et al. Assessing the performance of DNA barcoding using posterior predictive simulations , 2016, Molecular ecology.
[14] Tandy Warnow,et al. Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting. , 2016, Systematic biology.
[15] Matthew W. Hahn,et al. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation , 2016, PLoS biology.
[16] Bryan C. Carstens,et al. Posterior predictive checks of coalescent models: P2C2M, an R package , 2016, Molecular ecology resources.
[17] Jeremy M. Brown,et al. Can We Identify Genes with Increased Phylogenetic Reliability? , 2015, Systematic biology.
[18] Edward C Holmes,et al. Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations , 2015, Molecular biology and evolution.
[19] Tandy J. Warnow,et al. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes , 2015, Bioinform..
[20] L. Moroz,et al. Error, signal, and the placement of Ctenophora sister to all other animals , 2015, Proceedings of the National Academy of Sciences.
[21] Nicholas G. Crawford,et al. A phylogenomic analysis of turtles. , 2015, Molecular phylogenetics and evolution.
[22] B. Faircloth,et al. Incongruence among different mitochondrial regions: a case study using complete mitogenomes. , 2014, Molecular phylogenetics and evolution.
[23] Jeremy M. Brown,et al. Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit. , 2014, Systematic biology.
[24] Matthew W Pennell,et al. Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution. , 2014, Systematic Biology.
[25] Jeremy M. Brown,et al. Poor fit to the multispecies coalescent is widely detectable in empirical data. , 2014, Systematic biology.
[26] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[27] L. Nakhleh,et al. Computational approaches to species phylogeny inference and gene tree reconciliation. , 2013, Trends in ecology & evolution.
[28] É. Tannier,et al. The Inference of Gene Trees with Species Trees , 2013, Systematic biology.
[29] Zhen Yan,et al. Origin of land plants using the multispecies coalescent model. , 2013, Trends in plant science.
[30] Bret Larget,et al. The estimation of tree posterior probabilities using conditional clade probability distributions. , 2013, Systematic biology.
[31] B. Boussau,et al. Efficient Exploration of the Space of Reconciled Gene Trees , 2013, Systematic biology.
[32] Antonis Rokas,et al. Inferring ancient divergences requires genes with strong phylogenetic signals , 2013, Nature.
[33] M. Gouy,et al. Genome-scale coestimation of species and gene trees , 2013, Genome research.
[34] T. Townsend,et al. Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species , 2012, Biology Letters.
[35] Sen Song,et al. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model , 2012, Proceedings of the National Academy of Sciences.
[36] Ramón Doallo,et al. CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.
[37] Shane S. Sturrock,et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..
[38] Maxim Teslenko,et al. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.
[39] Sergei L. Kosakovsky Pond,et al. Statistics and truth in phylogenomics. , 2012, Molecular biology and evolution.
[40] A. Pyron,et al. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. , 2011, Molecular phylogenetics and evolution.
[41] J. Oaks. A TIME‐CALIBRATED SPECIES TREE OF CROCODYLIA REVEALS A RECENT RADIATION OF THE TRUE CROCODILES , 2011, Evolution; international journal of organic evolution.
[42] T. J. Robinson,et al. Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification , 2011, Science.
[43] H. Philippe,et al. Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough , 2011, PLoS biology.
[44] Jack Sullivan,et al. Assessment of substitution model adequacy using frequentist and Bayesian methods. , 2010, Molecular biology and evolution.
[45] Qixin He,et al. Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. , 2010, Systematic biology.
[46] Jeet Sukumaran,et al. DendroPy: a Python library for phylogenetic computing , 2010, Bioinform..
[47] H. Shaffer,et al. Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. , 2010, Molecular phylogenetics and evolution.
[48] Hadley Wickham,et al. ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .
[49] Nicolas Lartillot,et al. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating , 2009, Bioinform..
[50] Hervé Philippe,et al. Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons. , 2009, Molecular biology and evolution.
[51] Noah A Rosenberg,et al. Gene tree discordance, phylogenetic inference and the multispecies coalescent. , 2009, Trends in ecology & evolution.
[52] Corinne Da Silva,et al. Phylogenomics Revives Traditional Views on Deep Animal Relationships , 2009, Current Biology.
[53] Jeremy M. Brown,et al. PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy , 2009, Bioinform..
[54] B. Schierwater,et al. Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis , 2009, PLoS biology.
[55] S. Edwards. IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? , 2009, Evolution; international journal of organic evolution.
[56] Daniel J. White,et al. Revealing the hidden complexities of mtDNA inheritance , 2008, Molecular ecology.
[57] David Q. Matus,et al. Broad phylogenomic sampling improves resolution of the animal tree of life , 2008, Nature.
[58] M. Telford. Phylogenomics , 2007, Current Biology.
[59] Jeremy M. Brown,et al. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. , 2007, Systematic biology.
[60] F. Delsuc,et al. Phylogenomics: the beginning of incongruence? , 2006, Trends in genetics : TIG.
[61] S. Carroll,et al. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. , 2005, Molecular biology and evolution.
[62] F. Delsuc,et al. Phylogenomics and the reconstruction of the tree of life , 2005, Nature Reviews Genetics.
[63] B. Rannala,et al. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. , 2004, Systematic biology.
[64] Michael P. Cummings,et al. PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .
[65] D. Penny,et al. Genome-scale phylogeny and the detection of systematic biases. , 2004, Molecular biology and evolution.
[66] Peter G Foster,et al. Modeling compositional heterogeneity. , 2004, Systematic biology.
[67] Emily C. Moriarty,et al. The importance of proper model assumption in bayesian phylogenetics. , 2004, Systematic biology.
[68] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[69] S. Carroll,et al. Genome-scale approaches to resolving incongruence in molecular phylogenies , 2003, Nature.
[70] H. Gee. Evolution: Ending incongruence , 2003, Nature.
[71] R. Nielsen. Mapping mutations on phylogenies. , 2002, Systematic biology.
[72] Jonathan P. Bollback,et al. Bayesian model adequacy and choice in phylogenetics. , 2002, Molecular biology and evolution.
[73] Jonathan P. Bollback,et al. Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology , 2001, Science.
[74] J. S. Rogers,et al. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. , 2001, Systematic biology.
[75] Bin Ma,et al. From Gene Trees to Species Trees , 2000, SIAM J. Comput..
[76] Andrew Rambaut,et al. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees , 1997, Comput. Appl. Biosci..
[77] Ziheng Yang. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.
[78] J. Huelsenbeck,et al. SUCCESS OF PHYLOGENETIC METHODS IN THE FOUR-TAXON CASE , 1993 .
[79] Nick Goldman,et al. Statistical tests of models of DNA substitution , 1993, Journal of Molecular Evolution.
[80] D. Robinson,et al. Comparison of phylogenetic trees , 1981 .
[81] H. Akaike. A new look at the statistical model identification , 1974 .
[82] Scott V Edwards,et al. Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. , 2016, Molecular phylogenetics and evolution.
[83] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[84] Alexei J Drummond,et al. Guided tree topology proposals for Bayesian phylogenetic inference. , 2012, Systematic biology.
[85] Robert C Thomson,et al. Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. , 2010, Systematic biology.
[86] Jonathan P. Bollback,et al. Posterior Mapping and Posterior Predictive Distributions , 2005 .