Additional file 1: of Evolutionary dynamics of host specialization in wood-decay fungi

rusda: 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