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Prasanna AN, Gerber D, Kijpornyongpan T, Aime MC, Doyle VP, Nagy LG. Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships. Syst Biol 2020; 69:17-37. [PMID: 31062852 DOI: 10.1093/sysbio/syz029] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 11/12/2022] Open
Abstract
Resolving deep divergences in the tree of life is challenging even for analyses of genome-scale phylogenetic data sets. Relationships between Basidiomycota subphyla, the rusts and allies (Pucciniomycotina), smuts and allies (Ustilaginomycotina), and mushroom-forming fungi and allies (Agaricomycotina) were found particularly recalcitrant both to traditional multigene and genome-scale phylogenetics. Here, we address basal Basidiomycota relationships using concatenated and gene tree-based analyses of various phylogenomic data sets to examine the contribution of several potential sources of bias. We evaluate the contribution of biological causes (hard polytomy, incomplete lineage sorting) versus unmodeled evolutionary processes and factors that exacerbate their effects (e.g., fast-evolving sites and long-branch taxa) to inferences of basal Basidiomycota relationships. Bayesian Markov Chain Monte Carlo and likelihood mapping analyses reject the hard polytomy with confidence. In concatenated analyses, fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and coalescent analyses. On the contrary, the most conserved data subsets grouped rusts and allies with mushroom-forming fungi, although this relationship proved labile, sensitive to model choice, to different data subsets and to missing data. Excluding putative long-branch taxa, genes with high proportions of missing data and/or with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for any resolution of rusts, smuts, and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of tree space that is difficult to access using both concatenation and gene tree-based approaches. Inference-based assessments of absolute model fit strongly reject best-fit models for the vast majority of genes, indicating a poor fit of even the most commonly used models. While this is consistent with previous assessments of site-homogenous models of amino acid evolution, this does not appear to be the sole source of confounding signal. Our analyses suggest that topologies uniting smuts with mushroom-forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. We speculate that improved models of sequence evolution could shed more light on basal splits in the Basidiomycota, which, for now, remain unresolved despite the use of whole genome data.
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Affiliation(s)
- Arun N Prasanna
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary
| | - Daniel Gerber
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary.,Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | | | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70803, USA
| | - Laszlo G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary
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Swann EC, Frieders EM, McLaughlin DJ. Microbotryum, Kriegeria and the changing paradigm in basidiomycete classification. Mycologia 2019. [DOI: 10.1080/00275514.1999.12060993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Eric C. Swann
- Department of Plant Biology, 220 Biological Sciences Center, 1445 Gortner Ave., University of Minnesota, St. Paul, MN 55108-1095
| | - Elizabeth M. Frieders
- Department of Plant Biology, 220 Biological Sciences Center, 1445 Gortner Ave., University of Minnesota, St. Paul, MN 55108-1095
| | - David J. McLaughlin
- Department of Plant Biology, 220 Biological Sciences Center, 1445 Gortner Ave., University of Minnesota, St. Paul, MN 55108-1095
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Thorn RG, Moncalvo JM, Reddy CA, Vilgalys R. Phylogenetic analyses and the distribution of nematophagy support a monophyletic Pleurotaceae within the polyphyletic pleurotoid-lentinoid fungi. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- R. Greg Thorn
- Department of Botany, University of Wyoming, Laramie, Wyoming 82071
| | | | - C. A. Reddy
- Department of Microbiology, Michigan State University, East Lansing, Michigan 48824
| | - Rytas Vilgalys
- Department of Botany, Duke University, Durham, North Carolina 27708
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Hughey BD, Adams GC, Bruns TD, Hibbett DS. Phylogeny of Calostoma, the gelatinous-stalked puffball, based on nuclear and mitochondrial ribosomal DNA sequences. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Brandi D. Hughey
- Department of Botany & Plant Pathology, 166 Plant Biology Laboratory, Michigan State University, East Lansing, Michigan 48824-1312
| | - Gerard C. Adams
- Department of Botany & Plant Pathology, 166 Plant Biology Laboratory, Michigan State University, East Lansing, Michigan 48824-1312
| | - Tom D. Bruns
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, California 94720-3102
| | - David S. Hibbett
- Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts 02138
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Affiliation(s)
- Robert Bauer
- Universität Tübingen, Botanisches Institut, Lehrstuhl Spezielle Botanik und Mykologie, Auf der Morgenstelle 1, D-72076 Tübingen, Germany
| | - Kálmán Vánky
- Universität Tübingen, Botanisches Institut, Lehrstuhl Spezielle Botanik und Mykologie, Auf der Morgenstelle 1, D-72076 Tübingen, Germany
| | - Dominik Begerow
- Universität Tübingen, Botanisches Institut, Lehrstuhl Spezielle Botanik und Mykologie, Auf der Morgenstelle 1, D-72076 Tübingen, Germany
| | - Franz Oberwinkler
- Universität Tübingen, Botanisches Institut, Lehrstuhl Spezielle Botanik und Mykologie, Auf der Morgenstelle 1, D-72076 Tübingen, Germany
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Wubet T, Weiß M, Kottke I, Oberwinkler F. Morphology and molecular diversity of arbuscular mycorrhizal fungi in wild and cultivated yew (Taxus baccata). ACTA ACUST UNITED AC 2003. [DOI: 10.1139/b03-020] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Taxus baccata L. roots collected from two sites in southern Germany were heavily colonized by arbuscular mycorrhizal fungi (AMF). The colonization pattern was of the Paris type. The diversity of the colonizing AMF species was investigated using polymerase chain reaction based molecular techniques. The internal transcribed spacer (ITS) region of the DNA from AMF within the roots was amplified using Glomeromycota-specific primers and then cloned and sequenced. Phylogenetic analysis using a data set of 5.8S rDNA sequences from a wide range of glomeralean taxa as well as data sets of partial ITS2 sequences from glomeralean subgroups indicated root colonization by four sequence types of Glomus and one sequence type of Archaeospora. These sequence types are distinct from any previously published sequences and differed between the two study sites.Key words: arbuscular mycorrhiza, Paris-type AM, molecular diversity, ribosomal internal transcribed spacers, Taxus baccata.
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Maier W, Begerow D, Weiß M, Oberwinkler F. Phylogeny of the rust fungi: an approach using nuclear large subunit ribosomal DNA sequences. ACTA ACUST UNITED AC 2003. [DOI: 10.1139/b02-113] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sequence data from nuclear large subunit ribosomal DNA was used to infer phylogenetic relationships of selected genera of the Uredinales. We investigated 52 rust fungi representing nine families and three outgroup species. Neighbor joining analysis and a Bayesian method of phylogenetic inference using Monte Carlo Markov chains confirm the rust fungi as a natural group and indicate that Puccinia, Uromyces, Endophyllum, and Cumminsiella have a common origin. The autoecious Rosaceae-rusts Phragmidium, Kuehneola, Triphragmium, and Trachyspora are a monophyletic group. The gasteroid genus Ochropsora is closely related to Tranzschelia. While the Pucciniastreae sensu Dietel (1938) is recognized as a monophyletic group in neighbor joining analysis, the Pucciniaceae s.l. (Dietel 1928) is supported by Bayesian analysis. The following genera appear to be monophyletic: Chrysomyxa, Coleosporium, Cronartium, Gymnosporangium, Melampsora, Phragmidium, and Tranzschelia, whereas the genera Puccinia, Pucciniastrum, Thekopsora, and Uromyces are not.Key words: molecular phylogeny, systematics, nuclear large subunit rDNA, Basidiomycota, Urediniomycetes, Uredinales.
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Peterson SW, Sigler L. Molecular genetic variation in Emmonsia crescens and Emmonsia parva, etiologic agents of adiaspiromycosis, and their phylogenetic relationship to Blastomyces dermatitidis (Ajellomyces dermatitidis) and other systemic fungal pathogens. J Clin Microbiol 1998; 36:2918-25. [PMID: 9738044 PMCID: PMC105088 DOI: 10.1128/jcm.36.10.2918-2925.1998] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Emmonsia crescens, an agent of adiaspiromycosis, Blastomyces dermatitidis, the agent of blastomycosis, and Histoplasma capsulatum, the agent of histoplasmosis, are known to form meiotic (sexual) stages in the ascomycete genus Ajellomyces (Onygenaceae, Onygenales), but no sexual stage is known for E. parva, the type species of the genus Emmonsia. To evaluate relationships among members of the putative Ajellomyces clade, large-subunit ribosomal and internal transcribed spacer region DNA sequences were determined from PCR-amplified DNA fragments. Sequences were analyzed phylogenetically to evaluate the genetic variation within the genus Emmonsia and evolutionary relationships to other taxa. E. crescens and E. parva are distinct species. E. crescens isolates are placed into two groups that correlate with their continents of origin. Considerable variation occurred among isolates previously classified as E. parva. Most isolates are placed into two closely related groups, but the remaining isolates, including some from human sources, are phylogenetically distinct and represent undescribed species. Strains of B. dermatitidis are a sister species of E. parva. Paracoccidioides brasiliensis and Histoplasma capsulatum are ancestral to most Emmonsia isolates, and P. brasiliensis, which has no known teleomorph, falls within the Ajellomyces clade.
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Affiliation(s)
- S W Peterson
- Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604-3999, USA.
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Begerow D, Bauer R, Oberwinkler F. Phylogenetic studies on nuclear large subunit ribosomal DNA sequences of smut fungi and related taxa. ACTA ACUST UNITED AC 1997. [DOI: 10.1139/b97-916] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To show phylogenetic relationships among the smut fungi and their relatives, we sequenced a part of the nuclear LSU rDNA from 43 different species of smut fungi and related taxa. Our data were combined with the existing sequences of seven further smut fungi and 17 other basidiomycetes. Two sets of sequences were analyzed. The first set with a representative number of simple septate basidiomycetes, complex septate basidiomycetes, and smut fungi was analyzed with the neighbor-joining method to estimate the general topology of the basidiomycetes phylogeny and the positions of the smut fungi. The tripartite subclassification of the basidiomycetes into the Urediniomycetes, Ustilaginomycetes, and Hymenomycetes was confirmed and two groups of smut fungi appeared. The smut genera Aurantiosporium, Microbotryum, Fulvisporium, and Ustilentyloma are members of the Urediniomycetes, whereas the other smut species tested are members of the Ustilaginomycetes with Entorrhiza as a basal taxon. The second set of 46 Ustilaginomycetes was analyzed using the neighbor-joining and the maximum parsimony methods to show the inner topology of the Ustilaginomycetes. The results indicated three major lineages among Ustilaginomycetes corresponding to the Entorrhizomycetidae, Exobasidiomycetidae, and Ustilaginomycetidae. The Entorrhizomycetidae are represented by Entorrhiza species. The Ustilaginomycetidae contain at least two groups, the Urocystales and Ustilaginales. The Exobasidiomycetidae include five orders, i.e., Doassansiales, Entylomatales, Exobasidiales, Georgefischeriales, and Tilletiales, and Graphiola phoenicis and Microstroma juglandis. Our results support a classification mainly based on ultrastructure. The description of the Glomosporiaceae is emended. The Doassansiopsaceae, Melanotaeniaceae, and Urocystaceae are proposed as new taxa. Key words: basidiomycete systematics, LSU rDNA, Microbotryales, molecular phylogeny, smut fungi, Ustilaginomycetes.
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