lamoran at gpu.utcc.utoronto.ca (L.A. Moran) writes:
Andrew Roger wrote:
>>All 7 of Gupta and Goldings proteins showing the above topology are
>>complicated by one or several of the following problems:
>>-multiple phylogenetically distinct homologs in single organisms
>>(GS, proC, GDH)
>>-group polyphyly (all)
>>-probable cases of lateral transfer (GS, GDH, aat, hsp70)
>>-comparisons of NON-HOMOLOGOUS proteins (ferredoxins of 2FE-2S and
> 4Fe-4S types)
>You raise a number of interesting problems but don't forget that many of
>them also apply to those genes that seem to support Woese's Three Domain
>Hypothesis. We should be skeptical of *all* current hypotheses concerning
>the tree of life.
Yes, it is always worthwhile to be skeptical of all scientific
theories. However, it is it also worthwhile to recognize that all data
are not of equal significance. The fact that one can make gene trees
showing any desired relationship is not particularly surprising nor
informative in regard to organism trees. One of the reasons ribosomal
RNA is a popular molecule for estimating phylogeny is that it
minimizes many of the problems given above. This is not to suggest
that *only* ribosomal RNA is good for phylogeny, but genes should be
chosen with some amount of care to minimize these problems.
