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Open Access Highly Accessed Research article

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

David A Fitzpatrick1*, Mary E Logue1, Jason E Stajich2 and Geraldine Butler1

Author Affiliations

1 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

2 Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27708, USA

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BMC Evolutionary Biology 2006, 6:99  doi:10.1186/1471-2148-6-99

Published: 22 November 2006

Additional files

Additional File 1:

MSSA supertree derived from 4,805 fungal gene families. Bootstrap scores for all nodes are displayed. Rhizopus oryzae has been selected as an outgroup. The Basidiomycota and Ascomycota phyla form distinct clades. Subphyla and class clades are highlighted.

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Additional File 2:

Descriptions of the 153 universally distributed genes.

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Additional File 3:

Average consensus supertrees for WGD specific clade. For each of the 1,368 underlying gene families, fast evolving sites were categorised into 8 classes. Different site classes were systematically removed and phylogenies were reconstructed based on reduced alignments. (A) Fastest evolving sites (class 8) were removed. (B) The two fastest evolving site classes (classes 7 and 8) were removed. (C) The three fastest evolving site classes (classes 6, 7 and 8) were removed. Supertrees A and B group S. castelli and C. glabrata together, supertree C places C. glabrata at the base of the WGD clade.

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Additional File 4:

Additional Methods and Results.

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Additional File 5:

Bootstrap scores for phylogenetic Network.

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Additional File 6:

Supertrees (AV (A), MRP (B) and MSSA (C)) derived from the strict gene family dataset that contains 809 genes. Bootstrap scores are shown at selected nodes. Overall there is agreement with supertrees derived from the larger (liberal) dataset.

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