I am trying to prune a dated species tree with >10,000 taxa down to ~700. I want to keep the dates as they are in the full tree, however, when using the
drop.tip function in the
ape package in
R to prune the tree, my divergence times drastically change. E.g., the estimated divergence for bacteria changes from 3.8 to 3.2 gya and for archaea from 3.6 to 3.4 gya, which now moves the divergence of archaea before bacteria.
Due to computational limits, I am not able to perform my own molecular clock analysis with intensive software like BEAST and MCMCtree, what other solutions might there be? Is there a way to take the pruned species tree and assign new dates based on the original dates from the full tree?
Sorry, new field for me, so not sure what is and isn't appropriate here.
Thanks in advance, Morgan