DOI: 10.5061/dryad.7cs3g
title: Data from: Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens

description: The range of hosts that a parasite can infect in nature is a trait
 determined by its own evolutionary history and that of its potential
 hosts. However, knowledge on host range diversity and evolution at the
 family level is often lacking. Here, we investigate host range variation
 and diversification trends within the Sclerotiniaceae, a family of
 Ascomycete fungi. Using a phylogenetic framework, we associate
 diversification rates, the frequency of host jump events, and host range
 variation during the evolution of this family. Variations in
 diversification rate during the evolution of the Sclerotiniaceae define
 three major macro-evolutionary regimes with contrasted proportions of
 species infecting a broad range of hosts. Host-parasite co-phylogenetic
 analyses pointed towards parasite radiation on distant hosts long after
 host speciation (host jump or duplication events) as the dominant mode of
 association with plants in the Sclerotiniaceae. The intermediate
 macro-evolutionary regime showed a low diversification rate, high
 frequency of duplication events, and the highest proportion of broad host
 range species. Our findings suggest that the emergence of broad host range
 fungal pathogens results largely from host jumps, as previously reported
 for oomycete parasites, probably combined with low speciation rates. These
 results have important implications for our understanding of fungal
 parasites evolution and are of particular relevance for the durable
 management of disease epidemics.
description: Records of Host-pathogen
 associations used in the studyWe analyzed the 7101
 records from the fungus-host distribution database
 (https://nt.ars-grin.gov/fungaldatabases/fungushost/fungushost.cfm) that
 served as a basis for our study on the Sclerotiniaceae. Host species were
 classified as crops (crop) according to the USDA Natural Resources
 Conservation Service database (https://plants.usda.gov/npk/main), other
 cultivated plants (cult), ornamental plants (orn) and “others”, including
 largely wild plant species (wild). A total of 37% of the Fungus-Host
 database entries were from the USA (US), 17% from Europe (Eur), leaving a
 total of 46% of the entries that were neither from the USA or Europe (Afr,
 Africa; Asia; Can, Canada; Oce, Oceania; SA, South America; ?, others).
 These distributions do not reveal a strong bias towards crops or
 USA/Europe records in the records used for this
 analysis.entries_formatted.txtSupplementary File 1 (Host families tree)Phylogenetic tree of host plant families used for co-phylogenetic analyses in this work (newick format).Supplementary File 2 (ITS multiple sequence alignment)Curated multiple ITS sequence alignment for 200 Leotiomycete species, including 105 Sclerotiniaceae and 56 Rutstroemiaceae species. This alignment includes 797 informative sites and was used to generate the phylogenetic tree shown in Figure 1 and downstream analyses (fasta format).Supplementary File 3 (ML tree with SH-aLRT support)Phylogenetic tree of 200 Leotiomycete species including 161 Sclerotiniaceae and Rutstroemiaceae species used in Figure 1, obtained by maximum likelihood approach and featuring SH-aLRT branch support (newick format).Supplementary File 4 (ML tree with bootstrap support)Same phylogenetic tree as in supplementary file 3 including bootstrap from 100 replicates as branch support (newick format).Supplementary File 5 (Chronotree Sclerotiniaceae)Time calibrated phylogenetic tree of the 105 Sclerotiniaceae species used in Figure 2.Supplementary File 6 (Table host-fungus associations)List of host-parasite associations tested for co-phylogenetic analyses.Supplementary Table 1List of Sclerotiniaceae and Rutstroemiaceae species used for phylogenetic analysis and their corresponding host range. 1 refers to position in the tree shown in Figure 1; 2 refers to the code used in RASP analysis (Sup. Figure 5). NA, not applicable; Rutst., Rutstroemiaceae; Sclero. Sclerotiniaceae.