Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta)

Lumbsch, H. Thorsten; Schmitt, Imke; Lindemuth, Ralf; Miller, Andrew N.; Mangold, Armin; Fernandez, Fernando A. S.; Huhndorf, Sabine M.

doi:10.1016/j.ympev.2004.11.007

Cited by 88 publications

(76 citation statements)

References 57 publications

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“…2) largely agree with other recent large analyses where the Dothideomycetes is resolved as monophyletic but with low statistical support (Lumbsch et al 2005). A possible sister relationship of Dothideomycete/Arthoniomycetes has been proposed (Barr 1987, Tehler 1990) and there is some phylogenetic support for this (Lumbsch et al 2005.…”

Section: Resultssupporting

confidence: 87%

“…2) contains representatives of the major classes in the Ascomycota, as defined previously (Eriksson 2001). The supraclass relationships in our analysis indicated no support for a close relationship between the Dothideomycetes and Sordariomycetes, alluded to in an earlier study and the sister relationships of the Sordariomycetes and Leotiomycetes are supported in agreement with recent data (Lumbsch et al 2005). A few taxon pairs containing isolates used in previous works have remarkably high similarity to each other over all four loci.…”

Section: Resultssupporting

confidence: 64%

“…Initial analyses using DNA sequence data from the small subunit ribosomal RNA gene did not support the monophyly of the Loculoascomycetes (Spatafora et al 1995, Berbee 1996. A more recent phylogeny produced from protein gene coding data (Liu and Hall 2004) was inferred as supporting the taxonomic concepts for a monophyletic lineage for ascostromatic taxa, but the ontogenetic designations were considered oversimplified by some (Lumbsch et al 2005). Other studies combining data from protein-coding genes and the ribosomal operon have shown the paraphyly of ascostromatic, bitunicate lineages , Reeb et al 2004.…”

Section: Introductionmentioning

confidence: 98%

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A multigene phylogeny of the Dothideomycetes using four nuclear loci

Schoch

Shoemaker²,

Seifert³

et al. 2006

Mycologia

252

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We present an expanded multigene phylogeny of the Dothideomycetes. The final data matrix consisted of four loci (nuc SSU rDNA, nuc LSU rDNA, TEF1, RPB2) for 96 taxa, representing five of the seven orders in the current classification of Dothideomycetes and several outgroup taxa representative of the major clades in the Pezizomycotina. The resulting phylogeny differentiated two main dothideomycete lineages comprising the pseudoparaphysate Pleosporales and aparaphysate Dothideales. We propose the subclasses Pleosporomycetidae (order Pleosporales) and Dothideomycetidae (orders Dothideales, Capnodiales and Myriangiales). Furthermore we provide strong molecular support for the placement of Mycosphaerellaceae and Piedraiaceae within the Capnodiales and introduce Davidiellaceae as a new family to accommodate species of Davidiella with Cladosporium anamorphs. Some taxa could not be placed with certainty (e.g. Hysteriales), but there was strong support for new groupings. The clade containing members of the genera Botryosphaeria and Guignardia resolved well but without support for any relationship to any other described orders and we hereby propose the new order Botryosphaeriales. These data also are consistent with the removal of Chaetothyriales and Coryneliales from the Dothideomycetes and strongly support their placement in the Eurotiomycetes.

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Section: Resultssupporting

confidence: 87%

Section: Resultssupporting

confidence: 64%

Section: Introductionmentioning

confidence: 98%

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A multigene phylogeny of the Dothideomycetes using four nuclear loci

Schoch

Shoemaker²,

Seifert³

et al. 2006

Mycologia

252

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“…All our phylogenies infer a sister group relationship between the Sordariomycetes and Leotiomycetes species (Figs. 1, 2, 3, and 4), this sister group relationship is supported by previous analyses (Fitzpatrick et al 2006;James et al 2006a;Kuramae et al 2006;Lumbsch et al 2005;Schoch et al 2009). Our SG supertree fails to infer sister group relationships between the Sordariomycetes/Leotiomycetes, Dothideomycetes and Eurotiomycetes clades and instead infers a trichotomy at the base of the Pezizomycotina clade (Fig.…”

Section: Phylogenetic Relationships Among the Pezizomycotinasupporting

confidence: 85%

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

2011

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We have used three independent phylogenomic approaches (concatenated alignments, single-, and multigene supertrees) to reconstruct the fungal tree of life (FTOL) using publicly available fungal genomes. This is the first time multi-gene families have been used in fungal supertree reconstruction and permits us to use up to 66% of the 1,001,217 genes in our fungal database. Our analyses show that different phylogenomic datasets derived from varying clustering criteria and alignment orientation do not have a major effect on phylogenomic supertree reconstruction. Overall the resultant phylogenomic trees are relatively congruent with one another and successfully recover the major fungal phyla, subphyla and classes. We find that where incongruences do occur, the inferences are usually poorly supported. Within the Ascomycota phylum, our phylogenies reconstruct monophyletic Saccharomycotina and Pezizomycotina subphyla clades and infer a sister group relationship between these to the exclusion of the Taphrinomycotina. Within the Pezizomycotina subphylum, all three phylogenies infer a sister group relationship between the Leotiomycetes and Sordariomycetes classes. However, there is conflict regarding the relationships with the Dothideomycetes and Eurotiomycetes classes. Within the Basidiomycota phylum, supertrees derived from singleand multi-gene families infer a sister group relationship between the Pucciniomycotina and Agaricomycotina subphyla while the concatenated phylogeny infers a poorly supported relationship between the Agaricomycotina and Ustilagomycotina. The reconstruction of a robust FTOL is important for future fungal comparative analyses. We illustrate this point by performing a preliminary investigation into the phyletic distribution of yeast prion-like proteins in the fungal kingdom.

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“…1) SSU 13 BPP ¼ 0.99 Del Prado et al (2006, fig. 1) LSU, mt-SSU 15 BPP ¼ 1 Lumbsch et al (2005, fig. 1 fig.…”

Section: Typus: Zoopage Drechsler 1935mentioning

confidence: 99%

A higher-level phylogenetic classification of the Fungi

Hibbett¹,

Binder²,

Bischoff³

et al. 2007

Mycological Research

Self Cite

2,001

1,178

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The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella.

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Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta)

Cited by 88 publications

References 57 publications

A multigene phylogeny of the Dothideomycetes using four nuclear loci

A multigene phylogeny of the Dothideomycetes using four nuclear loci

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

A higher-level phylogenetic classification of the Fungi

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