In article <52g4lu$sh7 at mserv1.dl.ac.uk>,
James O. McInerney PhD <j.mcinerney at nhm.ac.uk> wrote:
>Jonathan Badger wrote:
>>>> 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.
>>This point is true. One of the main reasons the rRNA have been used for
>phylogeny reconstruction (apart from ease of isolation, firstly using
>RNA-directed technology and later using the PCR) is the idea that they
>are directly vertically transmitted and not subject to lateral gene
>transfer.....
One of the main reasons that gene X has been used for phylogeny reconstruction
is the idea that it is vertically transmitted and not subject to lateral
gene transfer.
You can plug anything you want into "gene X". All such statements have about
the same scientific legitimacy. Why do some people feel that rRNA genes
are special in this sense? This is an argument that seems to be widely
disseminated but rarely questioned. Can anyone supply a reference to an
article makes the case that rRNA genes cannot be horizontally transferred
but others can?
>As far as we know, "ribosomal RNA....minimises many of the
>problems...[associated with constructing organismal phylogenies from
>other genes]", but lets be careful.
Well it certainly doesn't minimize the problem of having to deal with
nucleic acid sequences and it certainly doesn't minimize the problem
of obtaining a reliable unambiguous alignment. There's also this
embarassing little fact that the LSU and SSU dendrograms don't always
agree. (-:
Larry Moran
