A genome-scale phylogeny of the kingdom Fungi

[1]  A. Rokas,et al.  An investigation of irreproducibility in maximum likelihood phylogenetic inference , 2020, Nature Communications.

[2]  D. Moreira,et al.  Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota , 2020, Nature Communications.

[3]  A. Rokas,et al.  Rooting the Animal Tree of Life , 2020, bioRxiv.

[4]  A. Salamov,et al.  Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi , 2020, Scientific Reports.

[5]  J. Stajich,et al.  Toward a Fully Resolved Fungal Tree of Life. , 2020, Annual review of microbiology.

[6]  Yuanning Li,et al.  Feature frequency profile-based phylogenies are inaccurate , 2020, Proceedings of the National Academy of Sciences.

[7]  Jacob L. Steenwyk,et al.  Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota , 2020, Science Advances.

[8]  Javier F. Tabima,et al.  Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus , 2020, bioRxiv.

[9]  Donovan H. Parks,et al.  Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy , 2020, bioRxiv.

[10]  A. Salamov,et al.  101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens , 2020, Studies in mycology.

[11]  Olga Chernomor,et al.  IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era , 2019, bioRxiv.

[12]  Stephen A. Smith,et al.  PHYLOGENETIC CONFLICTS, COMBINABILITY, AND DEEP PHYLOGENOMICS IN PLANTS. , 2019, Systematic biology.

[13]  P. Kirk,et al.  Notes, outline and divergence times of Basidiomycota , 2019, Fungal Diversity.

[14]  M. C. Aime,et al.  Model Choice, Missing Data and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships. , 2019, Systematic biology.

[15]  J. Stajich,et al.  Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi). , 2019, Molecular phylogenetics and evolution.

[16]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v4: recent updates and new developments , 2019, Nucleic Acids Res..

[17]  J. Ruiz-Herrera,et al.  Cell wall glucans of fungi. A review , 2019, Cell surface.

[18]  L. Nagy,et al.  Comparative genomics reveals the origin of fungal hyphae and multicellularity , 2019, Nature Communications.

[19]  Anna Lipzen,et al.  Megaphylogeny resolves global patterns of mushroom evolution , 2019, Nature Ecology & Evolution.

[20]  D. Hibbett,et al.  Contemporaneous radiations of fungi and plants linked to symbiosis , 2018, Nature Communications.

[21]  D. Moreira,et al.  Global transcriptome analysis of the aphelid Paraphelidium tribonemae supports the phagotrophic origin of fungi , 2018, Communications Biology.

[22]  Moriya Ohkuma,et al.  Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum , 2018, Cell.

[23]  Donovan H. Parks,et al.  A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life , 2018, Nature Biotechnology.

[24]  Emmanuel Paradis,et al.  ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R , 2018, Bioinform..

[25]  Jacob L. Steenwyk,et al.  A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium , 2018, mBio.

[26]  Kessy Abarenkov,et al.  High-level classification of the Fungi and a tool for evolutionary ecological analyses , 2018, Fungal Diversity.

[27]  Chao Zhang,et al.  ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees , 2018, BMC Bioinformatics.

[28]  G. Torruella,et al.  Clarifying the Relationships between Microsporidia and Cryptomycota , 2018, The Journal of eukaryotic microbiology.

[29]  A. Salamov,et al.  Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species , 2018, Proceedings of the National Academy of Sciences.

[30]  T. James,et al.  The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism , 2017, eLife.

[31]  Joseph Heitman,et al.  The Fungal Kingdom , 2017 .

[32]  T. James,et al.  Early Diverging Fungi: Diversity and Impact at the Dawn of Terrestrial Life. , 2017, Annual review of microbiology.

[33]  J. Stajich,et al.  The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies. , 2017, Microbiology spectrum.

[34]  Siavash Mirarab,et al.  Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies , 2017, Genes.

[35]  Robert M. Waterhouse,et al.  BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics , 2017, bioRxiv.

[36]  Sung-Hou Kim,et al.  A genome Tree of Life for the Fungi kingdom , 2017, Proceedings of the National Academy of Sciences.

[37]  Robert Lücking,et al.  Fungal Diversity Revisited: 2.2 to 3.8 Million Species , 2017, Microbiology spectrum.

[38]  A. von Haeseler,et al.  UFBoot2: Improving the Ultrafast Bootstrap Approximation , 2017, bioRxiv.

[39]  Antonis Rokas,et al.  Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets , 2017, bioRxiv.

[40]  K. Hyde,et al.  A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective , 2017, Fungal Diversity.

[41]  Thomas K. F. Wong,et al.  ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.

[42]  A. Rokas,et al.  Contentious relationships in phylogenomic studies can be driven by a handful of genes , 2017, Nature Ecology &Evolution.

[43]  Evgeny M. Zdobnov,et al.  OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs , 2016, Nucleic Acids Res..

[44]  D. Weese,et al.  Phylogenomics of Lophotrochozoa with Consideration of Systematic Error , 2016, Systematic biology.

[45]  J. Stajich,et al.  A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data , 2016, Mycologia.

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

[47]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[48]  T. Jeffries,et al.  Genomics and the making of yeast biodiversity. , 2015, Current opinion in genetics & development.

[49]  A. Roger,et al.  Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi , 2015, Current Biology.

[50]  M. Berbee,et al.  Cytology and molecular phylogenetics of Monoblepharidomycetes provide evidence for multiple independent origins of the hyphal habit in the Fungi , 2015, Mycologia.

[51]  A. Salamov,et al.  Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants , 2015, Genome biology and evolution.

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

[53]  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.

[54]  Tandy J. Warnow,et al.  ASTRAL: genome-scale coalescent-based species tree estimation , 2014, Bioinform..

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

[56]  D. Forsdyke Evolutionary Bioinformatics , 2006, Springer International Publishing.

[57]  Inna Dubchak,et al.  MycoCosm portal: gearing up for 1000 fungal genomes , 2013, Nucleic Acids Res..

[58]  C. Gostinčar,et al.  Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent , 2013, BMC Genomics.

[59]  J. Stajich,et al.  Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia , 2013, Current Biology.

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

[61]  R. Humber,et al.  Phylogenetic lineages in Entomophthoromycota , 2013, Persoonia.

[62]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[63]  Alexandros Stamatakis,et al.  Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice , 2012, Systematic biology.

[64]  T. Gabaldón,et al.  Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi , 2012, BMC Biology.

[65]  D. Hibbett,et al.  The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. , 2012, Fungal genetics and biology : FG & B.

[66]  B. Lang,et al.  Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. , 2012, Molecular biology and evolution.

[67]  A. von Haeseler,et al.  A Consistent Phylogenetic Backbone for the Fungi , 2011, Molecular biology and evolution.

[68]  M. Berbee,et al.  A multigene phylogeny of Olpidium and its implications for early fungal evolution , 2011, BMC Evolutionary Biology.

[69]  M. Blackwell The fungi: 1, 2, 3 ... 5.1 million species? , 2011, American journal of botany.

[70]  Matthew W. Brown,et al.  Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta. , 2009, Molecular biology and evolution.

[71]  B. Lang,et al.  Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support , 2009, BMC Evolutionary Biology.

[72]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[73]  O. Gascuel,et al.  Phylogenetic mixture models for proteins , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[74]  G. Purschke,et al.  Detecting possibly saturated positions in 18S and 28S sequences and their influence on phylogenetic reconstruction of Annelida (Lophotrochozoa). , 2008, Molecular phylogenetics and evolution.

[75]  Michael Weiss,et al.  A higher-level phylogenetic classification of the Fungi. , 2007, Mycological research.

[76]  R. Agarwala,et al.  Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST , 2006, BMC Biology.

[77]  Kenji Matsuura,et al.  Reconstructing the early evolution of Fungi using a six-gene phylogeny , 2006, Nature.

[78]  Burkhard Morgenstern,et al.  AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..

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

[80]  Zemin Zhang,et al.  A profile hidden Markov model for signal peptides generated by HMMER , 2003, Bioinform..

[81]  Daniel Schwarzott,et al.  A new fungal phylum, the Glomeromycota: phylogeny and evolution * * Dedicated to Manfred Kluge (Tech , 2001 .

[82]  G. C. Johns,et al.  Proposal for a standardized temporal scheme of biological classification for extant species. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[83]  J. Felsenstein Cases in which Parsimony or Compatibility Methods will be Positively Misleading , 1978 .

[84]  J. K. Liu,et al.  Outline of Fungi and fungus-like taxa , 2020 .

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