In article <49ld73$1qv at onramp.arc.nasa.gov>,
Dr. David Faguy <David.Faguy at qmgate.arc.nasa.gov> wrote:
>lamoran at medisun.med.utoronto.ca (Laurence Moran) wrote:
>>>There are several genes that appear to be more phylogenetically useful than
>>16S RNA. One of these is the glutamine synthetase gene and dendrograms
>>constructed using these sequences tend to show that Thermotoga maritima
> Although I don't want to start an ideological war, what makes GS 'more
> phylogenetically useful' than 16S?
> In my (extremely humble) opinion 16S RNA phylogeny - while certainly not
> perfect - is the best single predictor of phylogenetic
> ationships that is available.
There are several reasons why GS can be a better marker than 16S RNA.
1. You can use amino acid seqeunces in the alignment and analysis.
This avoids the compositional bias of nucleotide sequences.
2. The entire sequence can be aligned - you don't have to discard
some ambiguous sequences as you do with 16S RNA.
3. The GS gene is more highly conserved than 16S RNA.
4. There are parologous GS genes and that allows the universal
tree to be rooted.
Of course, depending on one's biases, there may be a more important reason.
The GS dendrogram may be correct while the 16S RNA dendrogram may be wrong!
Now, can you give me the reasons for stating so catagorically that the
16S RNA phylogeny "...is the best single predictor of phylogenetic
relationships that is available"? I assume that you have studied the
alternatives so you should have no trouble understanding the significance
of the points that I made above.