How can I increase my effective sampling size apart from increasing the number of generations/chain length in BEAST?

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Daniel Zinder

You can join multiple chains together, running multiple instances of BEAST.

There's a built-in tool for merging the results.

If you have less taxa and parameters beast will run faster.

Jan Tünnermann

I don't know BEAST, but to obtain a higher ESS you should try to remove the auto-correlation in the chain. You can try to reparametrize your model, there is a technique called parameter expansion which may help. I'm no expert, but if you google along these lines, you may find some good explanations. E.g., this seems to discuss techniques to increase the ESS by reducing auto-correlation: http://seis.bris.ac.uk/~frwjb/materials/birdMMNL1.pdf

Jan

Bruno C. Perez

Increasing thinning intervals could help to reduce autocorrelation, although some authors discourage thinning technique.

Inclusion of parameter extensions is probabbly what you`re looking for. Some packages, as MCMCglmm (in R), already include easy ways to implement parameter extensions in the variance structure.