Hey all, I'm using MrBayes 3.2 with four fossil calibrations. My entire MrBayes block is in the attached screenshot.
My topology from the analysis is absolutely fine, as are the ESS values, but it seems like my fossil calibrations are being ignored. When I visualise any trees my scale bar isn't in millions of years (i.e. it's 0.09 instead of the expected ~20) despite MrBayes telling me the constraints have been enforced.
Can anyone suggest how to fix this issue? It seems my monophyletic constraints are working but not the calibrations themselves.
I think you are missing nodeagepr?
From the command reference:
"To actually use the calibrations to obtain dated trees, you also need to set a clock model using relevant 'brlenspr' and 'nodeagepr' options of the 'prset' command. You may also want to examine the 'clockvarpr' and 'clockratepr' options. Furthermore, you need to activate the relevant constraint(s) using 'topologypr', if you use any dated interior nodes in the tree"
Xuankun Li Yes, I've tried BEAST. Unfortunately I'm having issues with parameters not mixing well and so MrBayes is my back-up option.
I think you are missing nodeagepr?
From the command reference:
"To actually use the calibrations to obtain dated trees, you also need to set a clock model using relevant 'brlenspr' and 'nodeagepr' options of the 'prset' command. You may also want to examine the 'clockvarpr' and 'clockratepr' options. Furthermore, you need to activate the relevant constraint(s) using 'topologypr', if you use any dated interior nodes in the tree"
Fantastic, thank you Emma Wahlberg! That solved my problem completely.
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