Phyllachorales M.E. Barr, Mycologia 75(1): 11 (1983)

MycoBank number: MB 90495; Index Fungorum number: IF 90495; Facesoffungi number: FoF 06410;

Phyllachorales comprises three families viz. Phaeochoraceae, Phyllachoraceae and Telimenaceae (Dayarathne et al. 2017, Mardones et al. 2017). In our phylogenetic analyses with concatenated ITS, LSU and SSU sequence data, the Phaeochoraceae formed a monophyletic clade with high statistical support (98% ML) (Fig. 21). Phaeochoraceae comprises Cocoicola, Phaeochora, Phaeochoropsis and Serenomyces and sequence data are available only for two Cocoicola strains and one Serenomyces species. However, the type genus Phaeochora lacks sequence data. Phyllachoraceae formed a less stable clade within Phyllachorales. Out of 54 genera in Phyllachoraceae, sequence data are available for only five genera. A few Polystigma strains grouped within Phyllachorales in two different places, which is similar to the study of Dayarathne et al. (2017). However, Polystigma was excluded and placed within the reinstated Polystigmataceae by Jones et al. (2019) and Bundhun et al. (2019). Telimenaceae species also formed a monophyletic clade in our phylogram but with low statistical support. The divergence time for Phyllachorales is estimated as 168 MYA (Fig. 2). Currently, there are three families and 60 genera in this order (this paper).

Figure 2 – The maximum clade credibility (MCC) tree, using the same dataset from Fig. 1. This analysis was performed in BEAST v1.10.2. The crown age of Sordariomycetes was set with Normal distribution, mean = 250, SD = 30, with 97.5% of CI = 308.8 MYA, and crown age of Dothideomycetes with Normal distribution mean = 360, SD = 20, with 97.5% of CI = 399 MYA. The substitution models were selected based on jModeltest2.1.1; GTR+I+G for LSU, rpb2 and SSU, and TrN+I+G for tef1 (the model TrN is not available in BEAUti 1.10.2, thus we used TN93). Lognormal distribution of rates was used during the analyses with uncorrelated relaxed clock model. The Yule process tree prior was used to model the speciation of nodes in the topology with a randomly generated starting tree. The analyses were performed for 100 million generations, with sampling parameters every 10000 generations. The effective sample sizes were checked in Tracer v.1.6 and the acceptable values are higher than 200. The first 20% representing the burn-in phase were discarded and the remaining trees were combined in LogCombiner 1.10.2., summarized data and estimated in TreeAnnotator 1.10.2. Bars correspond to the 95% highest posterior density (HPD) intervals. The scale axis shows divergence times as millions of years ago (MYA).

Figure 2 – Continued.

Figure 2 – Continued.

Figure 21 – Phylogram generated from maximum likelihood analysis based on combined LSU, SSU and ITS sequence data of selected taxa from Phyllachorales. Related sequences are taken from Dayarathne et al. (2017). One hundred and sixteen strains are included in the combined gene analyses comprising 1326 characters after alignment (610 characters for LSU, 972 characters for SSU and 657 characters for ITS). Gelasinospora tetrasperma (CBS 178.33), Neurospora crassa (MUCL 19026) and Sordaria fimicola (CBS 508.50) are used as outgroup taxa. Analyses of each single gene were performed and the topology of each tree had clade stability. Maximum likelihood analysis with 1000 bootstrap replicates yielded a best tree with the likelihood value of – 27773.000538. The matrix had 1583 distinct alignment patterns, with 57.76% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.250314, C = 0.239655, G = 0.269539, T = 0.240492; substitution rates AC = 1.057397, AG = 2.260386, AT = 1.375589, CG = 0.834187, CT = 4.235196, GT = 1.000000; gamma distribution shape parameter α = 0.534795. Maximum likelihood bootstrap (ML, black) values > 60%) are given above the nodes. Ex-type strains are in bold.

Figure 21 – Continued.