Xylariales Nannf., Nova Acta R. Soc. Scient. upsal., Ser. 4 8(no. 2): 66 (1932)
MycoBank number: MB 90505; Index Fungorum number: IF 90505; Facesoffungi number: FoF 12988;
Maharachchikumbura et al. (2016b) accepted Xylariales as the only order in the subclass Xylariomycetidae, which comprised 22 families. However, Samarakoon et al. (2016) and Hongsanan et al. (2017) provided phylogenetic and divergence time estimations for the subclass Xylariomycetidae and accepted Amphispheriales and Xylariales. Wijayawardene et al. (2018a) accepted 12 families in Xylariales, including Myelospermataceae, which lacks molecular data. However, the phylogenetic placements of the families Oxydothidaceae and Polystigmataceae are uncertain in two different analyses (Figs 1, 4). However, following the previous phylogenetic treatments (Konta et al. 2016, Dayarathne et al. 2017) we accept Oxydothidaceae and Polystigmataceae as families of Xylariales. We accept 15 families in Xylariales, including Barrmaeliaceae, Cainiaceae, Clypeosphaeriaceae, Coniocessiaceae, Diatrypaceae, Graphostromataceae, Hansfordiaceae, Hypoxylaceae, Induratiaceae, Lopadostomataceae, Microdochiaceae, Polystigmataceae, Requienellaceae, Xylariaceae and Zygosporiaceae, while Myelospermataceae is placed in the Xylariomycetidae families, incertae sedis. The divergence time for Xylariales is estimated as 147 MYA (Fig. 2). Here we accept 160 genera in Xylariales.
Figure 1 – Maximum likelihood (ML) majority rule combined LSU, SSU, tef1 and rpb2 consensus tree for the analyzed Sordariomycetes isolates. Families are indicated in yellow and green coloured blocks and orders are indicated in dark and light grey coloured blocks. RAxML bootstrap support values (MLB above 50 %) are given at the nodes. The scale bar represents the expected number of changes per site. The tree is rooted with Botryotinia fuckeliana (AFTOL ID-59), Dothidea sambuci (DAOM 231303), and Pyxidiophora arvernensis (AFTOL-ID 2197).
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 4 – Phylogram generated from maximum likelihood analysis based on combined ITS, LSU, rpb2 and tub2 sequence data for Xylariomycetidae. Two hundred and seventy-two strains are included in the combined analyses which comprised 4211 characters (1168 characters for ITS, 937 characters for LSU, 1128 characters for rpb2, 978 characters for tub2) after alignment. Achaetomium macrosporum (CBS 532.94), Chaetomium elatum (CBS 374.66) and Sordaria fimicola (CBS 723.96) are outgroup taxa. Single gene analyses were carried out and the topology of each tree had clade stability. The best RaxML tree with a final likelihood value of – 132297.706952 is presented. Estimated base frequencies were as follows: A = 0.241914, C = 0.251908, G = 0.265558, T = 0.240620; substitution rates AC = 1.281946, AG = 3.512297, AT = 1.499895, CG = 1.121065, CT = 6.472834, GT = 1.000000; gamma distribution shape parameter a = 0.678614. Bootstrap support values for ML greater than 75% are given near the nodes. Ex-type strains are in bold. The newly generated sequences are indicated in blue.