randomize the location assignments at the tips? - phylogeography

[dhao...@gmail.com]

Hi all wondering if i can get some help on this?

I have my dataset which uses fragmented samples from a species all around Australia, so the sampling geographic location is biased to what i can get access to and whats on Genbank. I can try to investigate the unsampled geographic locations  by what is suggested by Edwards et al., 2011 Polar bear paper... however my question is how do i investigate the influence of tip location frequencies on Ancestral state reconstruction. The same paper suggests to perform an additional analysis to randomize the tips by implementing a new MCMC transition kernel ('operator' in BEAST nomenclature) that swaps the location states between two randomly selected taxa......

Who do i implement this? 

if this randomization changes the state of my data what can you suggest i try, to test the validity of the dispersion of this species??

Regards,

Dalal

[Philippe Lemey]

Dear Dalal,

You can add this operator to your operators in your xml:

<tipStateSwapOperator weight="10">

<ancestralTreeLikelihood idref="location.treeLikelihood"/>

</tipStateSwapOperator>

replacing "location.treeLikelihood" with the id of your ancestralTreeLikelihood.

It indeed randomizes the states and was used to see if the number of samples impacts the root state location probabilities (independent of how they cluster)

Best,

Philippe

 

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