I have a couple of questions regarding the reporting of ML/Bayesian values on a phylogenetic tree. Firstly, is there a general consensus as to what the threshold value for reporting is for each output? I have read suggestions of over 50 for the ML values but I'm not sure for the Bayesian. Something I read suggested 0.33-1 had weak support for the null hypothesis, but I haven't seen values as low as 0.33 in publications.
I'm also wondering if it is possible to report both outputs on one phylogenetic tree if branching further up the tree is not the same. Some clades (including the clade I am interested in) are the same but earlier branching is not identical. Is it therefore best to report both trees separately?
Many thanks for any advice given!
Thank you both for taking the time to reply. Your responses are very helpful.
Recent Versions of MrBayes now put out trees containing SDs on each node, which may give you a hint about a tendency. Generally, check if your runs converged via tracer, it is possible that your runs should be running a bit longer or you should exclude more burnin.
Hillis & Bulls 1993 considered everything above 70% reliable in context of a simulation study but that is really weak. I'd go for > 0.95 posterior probability or 95% Bootstrap support as a significant value. No discussion on lower values, as these nodes are likely to change in topology if you change taxon sampling, partitioning schemes etc.
http://www.jstor.org/stable/2992540%5Cnhttp://about.jstor.org/terms
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