Torpedosporales E.B.G. Jones, Abdel-Wahab & K.L. Pang, Fungal Divers. 73(1): 42 (2015)
The families Etheirophoraceae, Juncigenaceae and Torpedosporaceae form well-separated (99% ML, 1.00 PP, 99% ML, 1.00 PP and 100% ML, 1.00 PP) clades within Torpedosporales in the phylogram generated from combined LSU, SSU and rpb2 sequence data (Fig. 24). This observation is supported by previous studies of Jones et al. (2015) and Maharachchkumbura et al. (2016b). The divergence time for Torpedosporales is estimated as 185 MYA (Fig. 2). Currently there are three families and ten 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 24 – Phylogram generated from maximum likelihood analysis based on combined LSU, SSU and rpb2 sequence data of selected taxa from Falcocladiales and Torpedosporales. Twenty-six strains are included in the combined gene analyses comprising 3557 characters after alignment (1142 characters for LSU, 1440 characters for SSU and 967 characters for rpb2). Nectria haematococca (GJS89-70) is used as the outgroup taxon. Analyses of each single gene were performed and the topology of each tree had clade stability. The tree topology in maximum likelihood analysis was similar to the Bayesian and maximum parsimony analyses. Maximum likelihood analysis with 1000 bootstrap replicates yielded a best tree with the likelihood value of – 14936.746257. The matrix had 1096 distinct alignment patterns, with 25.55% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.247642, C = 0.231060, G = 0.304405, T = 0.216894; substitution rates AC = 1.746605, AG = 3.110551, AT = 1.540183, CG = 1.746965, CT = 7.476678, GT = 1.000000; gamma distribution shape parameter α = 0.291342. Maximum parsimony (black) and maximum likelihood (black) bootstrap values >65% and Bayesian posterior probabilities (blue) >0.90 (ML/BYPP) are given above the nodes. Ex-type strains are in bold.