[Taxacom] RES: nuclear vs chloroplast or mt trees

[Vitor F. O. de Miranda]

Dear John,

The point is the cladograms based on DNA are always "gene trees".
Incongruences are usually by reason of different histories recovered from each gene (or intron, spacer, etc.).

In my opinion, a consensus cladogram could not be a good option. If you have a history "A"  based on a gene A, and a "B" based on a gene B, you'll have a high chance to get a history "C" from a consensus analysis. And the history "C" may not represent a "real"  evolutionary history.

Best wishes,
Vitor

_______________________________
Vitor Fernandes Oliveira de Miranda, Prof.Dr.  
Universidade Estadual Paulista, Unesp, câmpus Jaboticabal
Faculdade de Ciências Agrárias e Veterinárias – FCAV
Departamento de Biologia Aplicada à Agropecuária
Via de Acesso Prof. Paulo Donato Castellane s/n
CEP 14884-900     Jaboticabal – SP – Brasil
Fone: VoIP: +55 (16) 3209-7205
email: vmiranda at fcav.unesp.br   Skype: vmirandum
http://www.fcav.unesp.br/vmiranda 


-----Mensagem original-----
De: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] Em nome de John Grehan
Enviada em: quinta-feira, 25 de fevereiro de 2016 02:28
Para: taxacom
Assunto: [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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