Estimating Fungal Divergence Times

The divergence times were estimated with the BEAST v2.6.5 software package (Bouckaert et al. 2019 (link)) with a dataset composed of ITS + nLSU + TEF1 + RPB1 + RPB2 sequences (Table 1). Sequences of the species are adopted partly from the topology established by Song and Cui (2017 (link)). An XML file was generated with BEAUti (version 2). The rates of evolutionary changes at nuclear acids were estimated using ModelTest (version 3.7) with the GTR substitution model (Posada and Crandall 1998 (link)). A log-normal distribution was employed for molecular clock analysis and the tree prior was set to Yule speciation. Three fossil calibrations, Archaeomarasmius leggettii (Hibbett et al. 1995 (link); 1997 (link)), Quatsinoporites cranhamii (Smith et al. 2004 (link); Berbee and Taylor 2010 (link)) and Paleopyrenomycites devonicus (Taylor et al. 1999 (link); 2005 (link)), representing the minimum divergence time of Agaricales (90 Mya), Hymenochaetaceae (125 Mya), and between Ascomycota and Basidiomycota (400 Mya), respectively, were used as calibrations. After 10,000,000 generations, the first 10% of the sampled trees were removed as burn-in. The log file was checked for convergence with Tracer (version 1.52), and the trees file was interpreted to a maximum clade credibility (MCC) tree with TreeAnnotator (version 2.6.5), annotating clades with more than 0.8 Bayesian posterior probability (BPP).