I am trying to run Beast 1.8.4 using two fossil calibrations of clouded leopard and Lion-Jaguar with tiger subspecies sequences. Under strict clock model with Yule process, my priors for clouded leopard and Lion-Jaguar are in normal distribution with specified divergence times and tmrca (tiger subspecies) under "Using tree prior". Kappa also in normal distribution. Unfortunately I am getting good convergence for all ESS but not for tmrca and branchRate. Can anyone suggest what is wrong with this?
Dear Abdul Aziz, this is a a very open question, I would try to relax the clock model (uncorrelated lognormal distribution), reduce the number of hypotheses (priors), revise the calibration, use a log normal distribution for tmrca priors if needed, and launch the analysis again... (assuming that chain size and sampling rate are ok given other ESS values) with the correct substitution model selected for your dataset. Hope you will solve your problem!
Dear Abdul Aziz, this is a a very open question, I would try to relax the clock model (uncorrelated lognormal distribution), reduce the number of hypotheses (priors), revise the calibration, use a log normal distribution for tmrca priors if needed, and launch the analysis again... (assuming that chain size and sampling rate are ok given other ESS values) with the correct substitution model selected for your dataset. Hope you will solve your problem!
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