chloroplast and other genes (was Lucy in Newsweek)

[Ken Kinman]

Rob Smissen wrote:
     Personally, for my own group, I'm quite strident in rejecting chloroplast DNA trees as representative of overall species relationships because I can advance realistic explanations, based on the biology of the organisms, for why they might be misleading.
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Rob,
     I have come to a similar conclusion.  Chloroplast genes are probably generally less reliable than nuclear genes for phylogeny reconstruction (although there are probably exceptions).  With respect to angiosperms in particular, I think phylogenies based on chloroplast genes may have been stretched beyond their reliability in some cases.

     As for ape phylogeny, I still don't know enough to hazard a guess whether nuclear genes are generally more reliable than mitochondrial genes.  I can only say that individual bases changes are generally the least reliable, and I am more comfortable relying on strings of bases that are inserted, deleted, or modified in other less probable ways (than single base changes).  There is also the higher order arrangement of whole genes that genome sequencing will uncover.  Those who reject ALL molecular data as phenetic and unreliable are failing to appreciate the potential of this broader genetic "morphology", although morphologists are right to question phylogenies based only on the less reliable patterns of individual base substitutions.   None of this is cut and dry, and certainly not simple.  We definitely have alot to learn about weighting characters, both molecular and morphological, and neither approach has all the answers.
          ------- Cheers,
                         Ken Kinman