Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

[1]  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.

[2]  Jeffrey P. Townsend,et al.  A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing , 2016, Nature.

[3]  David Posada,et al.  Phylogenomics for Systematic Biology. , 2016, Systematic biology.

[4]  Daniel B. Sloan,et al.  The effects of subsampling gene trees on coalescent methods applied to ancient divergences. , 2016, Molecular phylogenetics and evolution.

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

[6]  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.

[7]  Katsumi Tsukamoto,et al.  Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling , 2015, Proceedings of the National Academy of Sciences.

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

[9]  Correction for Song et al., Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model , 2015, Proceedings of the National Academy of Sciences.

[10]  S. Edwards,et al.  Comment on “Statistical binning enables an accurate coalescent-based estimation of the avian tree” , 2015, Science.

[11]  Md. Shamsuzzoha Bayzid,et al.  Response to Comment on “Statistical binning enables an accurate coalescent-based estimation of the avian tree” , 2015, Science.

[12]  H. Ellegren,et al.  The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds , 2015, PLoS biology.

[13]  Michael G. Nute,et al.  A comparative study of SVDquartets and other coalescent-based species tree estimation methods , 2015, BMC Genomics.

[14]  Tandy Warnow,et al.  On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods. , 2015, Systematic biology.

[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]  M. Steel,et al.  Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent. , 2015, Theoretical population biology.

[17]  Md. Shamsuzzoha Bayzid,et al.  Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses , 2014, PloS one.

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

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

[20]  Laura Salter Kubatko,et al.  Quartet Inference from SNP Data Under the Coalescent Model , 2014, Bioinform..

[21]  G. Giribet,et al.  Animal Phylogeny and Its Evolutionary Implications , 2014 .

[22]  John Gatesy,et al.  Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. , 2014, Molecular phylogenetics and evolution.

[23]  Alexandros Stamatakis,et al.  ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era , 2014, Molecular biology and evolution.

[24]  W. Wheeler,et al.  Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal. , 2014, Molecular biology and evolution.

[25]  G. Ortí,et al.  Conserved genes, sampling error, and phylogenomic inference. , 2014, Systematic biology.

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

[27]  Kevin Murray,et al.  Revisiting fitting monotone polynomials to data , 2013, Comput. Stat..

[28]  Frédéric Delsuc,et al.  Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. , 2013, Molecular biology and evolution.

[29]  G. Ortí,et al.  Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). , 2013, Systematic biology.

[30]  Wei‐Jen Chen,et al.  EVOLUTIONARY ORIGIN AND EARLY BIOGEOGRAPHY OF OTOPHYSAN FISHES (OSTARIOPHYSI: TELEOSTEI) , 2013, Evolution; international journal of organic evolution.

[31]  M. Hofreiter,et al.  Capturing protein-coding genes across highly divergent species. , 2013, BioTechniques.

[32]  Liang Liu,et al.  STRAW: Species TRee Analysis Web server , 2013, Nucleic Acids Res..

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

[34]  Thaine W. Rowley,et al.  The Tree of Life and a New Classification of Bony Fishes , 2013, PLoS currents.

[35]  J. Degnan.  Anomalous unrooted gene trees. , 2013, Systematic biology.

[36]  Manolis Kellis,et al.  TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees , 2012, Systematic biology.

[37]  Sudhir Kumar,et al.  MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis , 2012, Bioinform..

[38]  Chenhong Li,et al.  EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies , 2012, Molecular ecology resources.

[39]  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.

[40]  Peter C. Wainwright,et al.  Resolution of ray-finned fish phylogeny and timing of diversification , 2012, Proceedings of the National Academy of Sciences.

[41]  Liang Liu,et al.  Estimating species trees from unrooted gene trees. , 2011, Systematic biology.

[42]  M. Miya,et al.  Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation , 2011, BMC Evolutionary Biology.

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

[44]  Emily H Turner,et al.  Target-enrichment strategies for next-generation sequencing , 2010, Nature Methods.

[45]  Federico Abascal,et al.  TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations , 2010, Nucleic Acids Res..

[46]  John A Rhodes,et al.  Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent , 2009, Journal of mathematical biology.

[47]  A. Drummond,et al.  Bayesian Inference of Species Trees from Multilocus Data , 2009, Molecular biology and evolution.

[48]  D. Pearl,et al.  Estimating species phylogenies using coalescence times among sequences. , 2009, Systematic biology.

[49]  Chad D. Brock,et al.  Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates , 2009, Proceedings of the National Academy of Sciences.

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

[51]  Adam P. Arkin,et al.  FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix , 2009, Molecular biology and evolution.

[52]  Pablo A. Goloboff,et al.  TNT, a free program for phylogenetic analysis , 2008 .

[53]  G. Lecointre,et al.  New insights into the organization and evolution of vertebrate IRBP genes and utility of IRBP gene sequences for the phylogenetic study of the Acanthomorpha (Actinopterygii: Teleostei). , 2008, Molecular phylogenetics and evolution.

[54]  D. Pearl,et al.  High-resolution species trees without concatenation , 2007, Proceedings of the National Academy of Sciences.

[55]  Guoqing Lu,et al.  A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study , 2007, BMC Evolutionary Biology.

[56]  L. Kubatko,et al.  Inconsistency of phylogenetic estimates from concatenated data under coalescence. , 2007, Systematic biology.

[57]  F. Delsuc,et al.  Phylogenomics: the beginning of incongruence? , 2006, Trends in genetics : TIG.

[58]  Kenji Saitoh,et al.  Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala. , 2005, Molecular phylogenetics and evolution.

[59]  D. Hillis,et al.  Analysis and visualization of tree space. , 2005, Systematic biology.

[60]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

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

[62]  J. Inoue,et al.  Mitochondrial Genomics of Ostariophysan Fishes: Perspectives on Phylogeny and Biogeography , 2003, Journal of Molecular Evolution.

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

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

[65]  Bin Ma,et al.  From Gene Trees to Species Trees , 2000, SIAM J. Comput..

[66]  W. W. Dimmick,et al.  A molecular and morphological perspective on the phylogenetic relationships of the otophysan fishes. , 1996, Molecular phylogenetics and evolution.

[67]  W. Fink,et al.  Interrelationships of the ostariophysan fishes (Teleostei) , 1981 .

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

[69]  Scott V Edwards,et al.  Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. , 2016, Molecular phylogenetics and evolution.

[70]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[71]  J. Alves-Gomes.  The Mitochondrial Phylogeny of the South American Electric Fish (Gymnotiformes) and an Alternative Hypothesis for the Otophysan Historical Biogeography , 2010 .

[72]  D. Maddison,et al.  Mesquite: a modular system for evolutionary analysis. Version 2.6 , 2009 .