general question about utility of brownie

[pbj]

Hello,
I would be interested to hear any comments about the utility of
brownie in investigating different rates of character evolution for
three floral traits related to selfing among two sister species where
there is dense sampling within each subspecies (i.e., ~70 individuals
from each species with phylogenetic inference based on 8 nDNA loci and
3 cpDNA loci). One taxon is predominantly selfing, the other
outcrossing, and we are interested in mating system evolution where it
would be interesting to make statements about different rates of
phenotypic evolution. The selfing taxa is monophyletic and the
outcrossing taxa is paraphyletic. Preliminary results from brownie
show strong differences between the subspecies but I am a bit cautious
about how to interpret such results given that the set up is not
really in line with how brownie has been used in the literature (e.g.,
to investigate character evolution among more evolutionary divergent
groups with little sampling of multiple conspecifics).

Any insight would be greatly appreciated and thanks for your time.

Sincerely,
James