Contentious relationships in phylogenomic studies can be driven by a handful of genes

[1]  Mark P. Simmons,et al.  Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia , 2017, Cladistics : the international journal of the Willi Hennig Society.

[2]  Jeremy M. Brown,et al.  Bayes Factors Unmask Highly Variable Information Content, Bias, and Extreme Influence in Phylogenomic Analyses , 2016, Systematic biology.

[3]  Antonis Rokas,et al.  Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data , 2016, G3: Genes, Genomes, Genetics.

[4]  Jan P. Meier-Kolthoff,et al.  Comparative genomics of biotechnologically important yeasts , 2016, Proceedings of the National Academy of Sciences.

[5]  A. Rokas,et al.  A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference , 2016, Genome biology and evolution.

[6]  N. Takezaki,et al.  Resolving the Phylogenetic Position of Coelacanth: The Closest Relative Is Not Always the Most Appropriate Outgroup , 2016, Genome biology and evolution.

[7]  Raymond J. Moran,et al.  The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference , 2016, Genome biology and evolution.

[8]  Matthew W. Hahn,et al.  Irrational exuberance for resolved species trees , 2016, Evolution; international journal of organic evolution.

[9]  A. Stamatakis,et al.  Computing the Internode Certainty and Related Measures from Partial Gene Trees , 2015, bioRxiv.

[10]  John Gatesy,et al.  The gene tree delusion. , 2016, Molecular phylogenetics and evolution.

[11]  H. Philippe,et al.  Genomic data do not support comb jellies as the sister group to all other animals , 2015, Proceedings of the National Academy of Sciences.

[12]  Ernest K. Lee,et al.  Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa , 2015, BMC Genomics.

[13]  Peng Zhang,et al.  Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny. , 2015, Systematic biology.

[14]  Tandy J. Warnow,et al.  ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes , 2015, Bioinform..

[15]  L. Moroz,et al.  Error, signal, and the placement of Ctenophora sister to all other animals , 2015, Proceedings of the National Academy of Sciences.

[16]  Richard A. Goldstein,et al.  Nonadaptive Amino Acid Convergence Rates Decrease over Time , 2015, Molecular biology and evolution.

[17]  Liang Liu,et al.  Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting. , 2015, Molecular biology and evolution.

[18]  Matthew W. Hahn,et al.  Convergent evolution of the genomes of marine mammals , 2015, Nature Genetics.

[19]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[20]  Md. Shamsuzzoha Bayzid,et al.  Whole-genome analyses resolve early branches in the tree of life of modern birds , 2014, Science.

[21]  Md. Shamsuzzoha Bayzid,et al.  Statistical binning enables an accurate coalescent-based estimation of the avian tree , 2014, Science.

[22]  Thomas K. F. Wong,et al.  Phylogenomics resolves the timing and pattern of insect evolution , 2014, Science.

[23]  Saravanaraj N. Ayyampalayam,et al.  Phylotranscriptomic analysis of the origin and early diversification of land plants , 2014, Proceedings of the National Academy of Sciences.

[24]  Victor V. Solovyev,et al.  The Ctenophore Genome and the Evolutionary Origins of Neural Systems , 2014, Nature.

[25]  Alexandros Stamatakis,et al.  Novel information theory-based measures for quantifying incongruence among phylogenetic trees. , 2014, Molecular biology and evolution.

[26]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[27]  Nicholas H. Putnam,et al.  The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution , 2013, Science.

[28]  L. Nakhleh,et al.  Computational approaches to species phylogeny inference and gene tree reconciliation. , 2013, Trends in ecology & evolution.

[29]  Ning Wang,et al.  Identifying localized biases in large datasets: a case study using the avian tree of life. , 2013, Molecular phylogenetics and evolution.

[30]  David L. Stern,et al.  The genetic causes of convergent evolution , 2013, Nature Reviews Genetics.

[31]  Antonis Rokas,et al.  Inferring ancient divergences requires genes with strong phylogenetic signals , 2013, Nature.

[32]  M. Maldonado,et al.  Deep metazoan phylogeny: when different genes tell different stories. , 2013, Molecular phylogenetics and evolution.

[33]  D. Penny,et al.  Missing Data and Influential Sites: Choice of Sites for Phylogenetic Analysis Can Be As Important As Taxon Sampling and Model Choice , 2013, Genome biology and evolution.

[34]  N. Goldman,et al.  Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited , 2011, PloS one.

[35]  H. Philippe,et al.  Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough , 2011, PLoS biology.

[36]  Mark A. Miller,et al.  Creating the CIPRES Science Gateway for inference of large phylogenetic trees , 2010, 2010 Gateway Computing Environments Workshop (GCE).

[37]  B. Morgenstern,et al.  Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships , 2010, Molecular biology and evolution.

[38]  Ying Li,et al.  The hearing gene Prestin unites echolocating bats and whales , 2010, Current Biology.

[39]  M. Martindale,et al.  Assessing the root of bilaterian animals with scalable phylogenomic methods , 2009, Proceedings of the Royal Society B: Biological Sciences.

[40]  Todd A. Castoe,et al.  Evidence for an ancient adaptive episode of convergent molecular evolution , 2009, Proceedings of the National Academy of Sciences.

[41]  Noah A Rosenberg,et al.  Gene tree discordance, phylogenetic inference and the multispecies coalescent. , 2009, Trends in ecology & evolution.

[42]  Corinne Da Silva,et al.  Phylogenomics Revives Traditional Views on Deep Animal Relationships , 2009, Current Biology.

[43]  S. Edwards.  IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? , 2009, Evolution; international journal of organic evolution.

[44]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.

[45]  M. Mariadassou,et al.  Influence function for robust phylogenetic reconstructions. , 2008, Molecular biology and evolution.

[46]  D. Hillis,et al.  Taxon sampling and the accuracy of phylogenetic analyses , 2008 .

[47]  David Q. Matus,et al.  Broad phylogenomic sampling improves resolution of the animal tree of life , 2008, Nature.

[48]  M. Telford.  Phylogenomics , 2007, Current Biology.

[49]  P. Lockhart,et al.  Deciphering ancient rapid radiations. , 2007, Trends in ecology & evolution.

[50]  S. Carroll,et al.  Bushes in the Tree of Life , 2006, PLoS biology.

[51]  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.

[52]  F. Delsuc,et al.  Phylogenomics and the reconstruction of the tree of life , 2005, Nature Reviews Genetics.

[53]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[54]  Olivier Gascuel,et al.  Mathematics of Evolution and Phylogeny , 2005 .

[55]  D. Penny,et al.  Genome-scale phylogeny and the detection of systematic biases. , 2004, Molecular biology and evolution.

[56]  S. Carroll,et al.  Genome-scale approaches to resolving incongruence in molecular phylogenies , 2003, Nature.

[57]  Ziheng Yang,et al.  Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. , 2003, Genetics.

[58]  Hidetoshi Shimodaira.  An approximately unbiased test of phylogenetic tree selection. , 2002, Systematic biology.

[59]  Masami Hasegawa,et al.  CONSEL: for assessing the confidence of phylogenetic tree selection , 2001, Bioinform..

[60]  Z. Yang,et al.  Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. , 1998, Molecular biology and evolution.

[61]  Andrew Rambaut,et al.  Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees , 1997, Comput. Appl. Biosci..

[62]  Ross Ihaka,et al.  Gentleman R: R: A language for data analysis and graphics , 1996 .