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All results obtained were supported by high Bayesian and Maximum likelihood support values.
The model where gains and losses were constrained to be equal produced an extremely tentative estimate of one transition (either gain or loss) every 500 MY, with 2 log likelihood support limits (equivalent to 95% confidence intervals) between once every 100 MY and 0 (never).
The "ripple" command was used to verify the log likelihood support for local order.
For Group 4 the likelihood support value was higher than the Bayesian value (91% versus 0.76).
For Groups 2, 3 and 5 maximum likelihood support values were similar to Bayesian support values.
Representatives of these two genera also clustered with the members of Neurospora and Sordaria in Sordariomycetes, with strong likelihood support.
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The phylogenetic analyses using parsimony and maximum likelihood supported the results from Bayesian inference on the combined five-locus dataset.
The first model is the null model without adaptive evolution and the second model is the alternative model with adaptive evolution, so a significant improvement in maximum likelihood supports positive selection.
The log-likelihood support for marker ordering was therefore variable in different map segments.
Maximum-likelihood support was calculated for the trees inferred from the three data supermatrices.
Maximum-likelihood support for the Bayesian maximum-clade-credibility trees was estimated using 1,000 bootstrap replicates.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com