19 research outputs found
Fungi Classification Update 2014
No full text<p>These are working files that correspond to a project towards updating the fungal taxonomy. The tree has been built in mesquite by hand, and depecit our current knowledge in fungal systematics. This tree needs revision by the authors, so relationships might change before publication. For the taxa described after Hibbett et al. 2007, a list of references is attached. - See more at: http://figshare.com/preview/_preview/915435#sthash.24V3frT4.dpuf</p
Supplement_data2
No full textCommunity matrix with fungal species as rows and host plant species as columns
Additional file 1: of Evolutionary dynamics of host specialization in wood-decay fungi
No full textrusda: an R interface to the United States Department of Agriculture’s Fungus-Host Distribution Database. Figure S1. Genomic phylogenetic tree compiled from Floudas et al. 2012; Kohler et al. 2015; Nagy et al. 2015 used as the backbone for the comprehensive guide tree for the RAxML tree inference. Figure S2. Maximum Likelihood phylogeny of the Agaricomycetes with color coding for 14 orders. Figure S3. Phylogeny with SH support values. Figure S4. Transition rates between the states in 6 × 6 Q-matrices with six states: (1) white rot/angiosperm specialist, (2) brown rot/angiosperm specialist, (3) white rot/gymnosperm specialist, (4) brown rot/ gymnosperm specialist, (5) white rot/generalist, and (6) brown rot/generalist. Figure S5. Transition rates among six character states based on a maximum likelihood (ML) phylogeny, 100 alternative trees and the one-genus-subset (100 times bootstrapped). Figure S6. Dynamics of host specialization in wood decay fungi within the Agaricomycetes based on the 100–0 exclusivity coding. Figure S7. Branching times for backbone of time-dated Agaricomycetes phylogeny. Figure S8 Overview of query results using R package “rusda” based on the Fungus-Host Distribution Database (FHDD) using 29,591 Dikarya and 105,350 Spermatophyta species as input. Table S1. Best partition scheme found by IQ-Tree [11, 12]. Table S2. Tip state frequencies of white and brown rot specialization based on different thresholds of host association [%]. Table S3. Re-classification of taxonomic orders based on Binder et al., 2005; Hibbett et al., 2014; Larsson, Larsson, & Kõljalg, 2004. Table S4. Table of reference species and association numbers from NCBI. Table S5 Phylogenetic and normal linear regression on the number of angio- and gymnosperm hosts between white and brown rot species. Table S6. The fit of three alternative models of host association evolution in white and brown rot lineages of Agaricomycetes based on the exclusivity coding (100–0). (DOCX 22788 kb
Additional file 3: of Evolutionary dynamics of host specialization in wood-decay fungi
No full textNewick file for the maximum likelihood phylogeny of the decay fungi of this study. (TRE 56.6 kb
Additional file 7: of Evolutionary dynamics of host specialization in wood-decay fungi
No full textGUIDANCE column reliability score for the maximum likelihood phylogeny. (TXT 88.5 kb
Additional file 2: of Evolutionary dynamics of host specialization in wood-decay fungi
No full textThe alignment used in maximum likelihood analyses. (FAS 43500 kb
Additional file 6: of Evolutionary dynamics of host specialization in wood-decay fungi
No full textNexus file for the 100 alternative phylogenetic trees of the decay fungi of this study. (NEXUS 36100 kb
Additional file 4: of Evolutionary dynamics of host specialization in wood-decay fungi
No full textNewick file for the comprehensive guide tree used for the maximum likelihood phylogeny. (TRE 27.5 kb
