[Taxacom] nuclear vs chloroplast or mt trees

[Richard Zander]

Gene trees are incongruent with other gene trees of the same taxon because they can be of different histories, as was just noted by another taxacomer. Trees of the same taxon can be incongruent because the same taxon can have different molecular races. 

Molecular races can be radically different from morphological races because odd morphology may be negatively selected, while odd combinations of DNA tracking traits are (mostly) not and the probability distribution of mutational combinations is much wider.

Phylogenetic trees of terminal taxa are not congruent with evolutionary trees of stem taxa because continuity in phylogenetic trees is between nodes of a minimum spanning tree or a Markov chain, which are artifacts of the optimization method and cladograms therefore do not model evolutionary transformations.

It is, thus, difficult to squeeze worthwhile information from a molecular cladistic tree. Now IF we had a molecular evolutionary tree showing serial transformations between TAXA, more information would be available. However, no one has created software to do this. (I don't think so, anyway, somebody let me know if so.)


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Richard H. Zander
Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri – 63110 – USA
richard.zander at mobot.org 
Web sites: http://www.mobot.org/plantscience/bfna/bfnamenu.htm and http://www.mobot.org/plantscience/resbot/ 

-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
Sent: Wednesday, February 24, 2016 11:28 PM
To: taxacom
Subject: [Taxacom] nuclear vs chloroplast or mt trees

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
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