Beast - Divergence Time Estimation For Recombinant / Positively Selected Genes

Question

[Kartik Sunagar]

Dear all,

Are there any special models in BEAST which enable the estimation of divergence times for positively selected or recombinant genes? (I have tried the BEAST forum but haven't found any solution yet). What other packages do you guys suggest for estimating divergence times.

Thank you very much,

Cheers, Kartik

[Kartik Sunagar]

Thanks Casey for the correction. I posted the question in a hurry, so... :D

Answer 1

[David W]

Hi Katrik,

Sorry, I'm pretty sure that neutrality and a lack of recombination within loci are built into the way BEAST works - especially the *BEAST methods which use the coalescent.

I don't know of any methods that are built for positive selection (after all, you'd have to be co-estimating the tree and the way selection changed the substitution rate in branch which sounds like a nightmare :) ) or recombination. The results might be relatively robust to these matters - you could compare estimates from the "full" dataset to those you get when you remove those genes you think have been under selection / have internal recombination to get a feel for it?

[Kartik Sunagar]

Hi there David :)

Thank you for the informative reply again. I was thinking the same but was hoping the authors had considered this situation as well and had made a model or two coping up with the recombination / selection pressures acting on the genes.

The thing is, I want to date the divergence-time of the positively selected gene I am working on. So most of the sequences are under positive selection.

Thank you very much, Kartik