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Open Access Highly Accessed Research article

Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support

Yu Liu13, Emma T Steenkamp2, Henner Brinkmann1, Lise Forget1, Hervé Philippe1 and B Franz Lang1*

Author Affiliations

1 Robert Cedergren Centre, Département de biochimie, Université de Montréal, Montréal, Québec, Canada

2 Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa

3 Present address: Donnelly Centre for Cellular and Bio-molecular Research, Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada

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BMC Evolutionary Biology 2009, 9:272  doi:10.1186/1471-2148-9-272

Published: 25 November 2009

Additional files

Additional file 1:

Tree of eukaryotes with the Eukaryotic Dataset and ML inference. The analyses using RAxML (WAG+Gamma; four categories) support the grouping of Malawimonadozoa and JEH with a BS of 77%. Other differences with the tree using BI method (Figure 1) include Plantae relationships, and the placement of Haptophyceae, which receive no support for both BI and ML analyses with this dataset. For more details see legend of Figure 1.

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Additional file 2:

Phylogeny with Eukaryotic Dataset after removing fast-evolving species. The tree was inferred with ML (RAxML) using the WAG+Gamma model with four categories. Numbers at branches represent support values obtained with 100 bootstrap replicates.

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Additional file 3:

Phylogeny with Eukaryotic Dataset after recoding amino acids into six groups. The amino acids of the Eukaryotic Dataset were recoded into six groups as follows: (1) ASTGP, (2) DNEQ, (3) RKH, (4) MVIL, (5) FYW and, (6) C. This allowed the use of a 6 × 6 general time-reversible rate matrix with free parameters rather than a fixed empirical matrix. Sequence composition and among-site rate variation parameters were also free in the BI analysis, as implemented in P4 (Foster PG: Modeling compositional heterogeneity. Syst Biol 2004, 53(3):485-495); 50 000 generations, first 10 000 removed as burn-in). Numbers at branches represent PP values.

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Additional file 4:

Complete mitochondrial DNA (mtDNA) of Nuclearia simplex strain 1552/2. The circular-mapping mtDNA (74,120 bp) is displayed starting with the rnl gene (coding for the large subunit rRNA), clockwise in direction of transcription. Black bars, genes or exons; grey bars, introns and intronic ORFs; tRNA genes are named by the one-letter amino acid code.

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Additional file 5:

Phylogenetic relationship of the 29 species used for VLB analyses. The phylogeny was inferred using nuclear data and RAxML with the WAG + Gamma model. In order to minimize missing data in the mitochondrial dataset, we exchanged Saccharomyces and Schizosaccharomyces that both lost the six mitochondrion-encoded nad genes with Candida albicans and Taphrina.

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Additional file 6:

Proteins included in phylogenetic datasets. List of proteins included in the Eukaryotic and Fungal Datasets.

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