[Taxacom] nuclear vs chloroplast or mt trees

[John Grehan]

I have a curiosity question arising from examination of a fair number of
molecular phylogenies where the nuclear DNA tree is incongruent with the
chloroplast tree to some greater or lesser degree. Authors generally
address this incongruence by generating a consensus tree. In some cases one
is just presented with the two trees. If molecules are so good at
recovering phylogeny the prevalence of such incongruence would seem a bit
incongruous (at least to me). For biogeographic analysis its not so much a
critical problem as sometimes both trees are quite interesting for what
they may tell. But I am curious to know whether anyone has published a
general assessment of to what extent incongruence is present between
nuclear and chloroplast trees, or nuclear and mt trees and whether that has
any bearing on the veracity of molecular results. I presume the question
has been addressed and perhaps if I looked further I could find the answer.
But since it is not a critical question for my studies I am availing myself
of the expertise that may be present on this list just in case someone is
familiar with this issue and can provide a summary comment.

Many thanks,

John Grehan