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. 2023 Jun 16;9(6):680. doi: 10.3390/jof9060680

Figure 3.

Figure 3

Figure 3

The phylogram based on a Maximum Likelihood analysis of combined LSU, tef1-α, rpb2 and ITS sequence datasets. The analyzed gene contains 154 fungal strains and 3832 total characters including gaps (LSU: 1–853 bp, tef1-α: 854–1769 bp, rpb2: 1770–3228 bp, ITS: 2819–3438 bp). The tree topology of the ML resembles BI. The matrix had distinct alignment patterns, with the final ML optimization likelihood value of −59,582.416081 (ln). All free model parameters were estimated by RAxML model, with 1781 distinct alignment patterns and 21.90% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.242692, C = 0.256407, G = 0.261351 and T = 0.239550, with substitution rates AC = 1.186006, AG = 5.169063, AT = 2.123954, CG = 0.808118, CT = 10.262422 and GT = 1.000000. The gamma distribution shape parameter alpha = 0.705889, and the Tree-Length = 10.099715. The final average standard deviation of split frequencies at the end of total MCMC generations was calculated as 0.009897 in BI analysis. The type strains are denoted in bold with the symbol “✱” at the ends, and newly introduced species in this study are denoted in red. The nodes provide bootstrap values of at least 60% (ML, left) and Bayesian posterior probabilities of at least 0.95 (BI, right); hyphens (-) signify values that are less than 60% in ML and less than 0.95 in BI. The bluish and pale brown backgrounds were used to distinguish different genera in Tubeufiaceae, while the yellow background indicates the genus Excipulariopsis.