"I tried Brownian rate parameter estimation by tranforming the branch
lengths according to the lambda values of trait in each group. It gives
me lower varaince for the group that has higher lambda value and that is
confusing. In fact with the same trait values, if I transform the branch
lengths of the tree with different lamda values it gives me higher
varaince for higher lambda value."
This is not at all unsurprising. In fact, as lambda->0 then then
estimated Brownian rate will go to the among-species variance (divided
by the total tree length for an ultrametric tree), which will nearly
always be smaller than the rate on the original tree.
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected]
blog: http://blog.phytools.org
On 5/5/2014 6:15 AM, imran khaliq wrote:
Dear All,
I am trying to understand the effects of incomplete phylogenies on the
phylogenetic signal. I am using different trees and I have at least 100 species
in each tree but still these are only 2 % of total species. So how can I be
sure that results are generalize enough to apply on the whole group? Secondly,
if I want to compare varaition in trait's rates in two groups e.g. tropical and
temperate, what methods are appropriate to estiamte the evolutionary rates. I
tried Brownian rate parameter estimation by tranforming the branch lengths
according to the lambda values of trait in each group. It gives me lower
varaince for the group that has higher lambda value and that is confusing. In
fact with the same trait values, if I transform the branch lengths of the tree
with different lamda values it gives me higher varaince for higher lambda value.
Can anyone help me?
Best regards,
Imran
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