jamm at nhm.ac.uk
Fri Oct 31 10:16:50 EST 1997
This is one of the most sensible questions to ask before begining a proje=
and unfortunately, not enough people bother to ask it. Rather, there is =
herd-instinct to follow whatever has gone before.
First of all, in order to compare your data with previously-published dat=
might be desirable to sequence one of the 'popular' genes. These are the=
ribosomal RNA genes small and large subunit (and also the mitochondrials)=
elongation factors, rubisco, ATPases, GroESL genes, RecA, Cytochrome B, a=
A huge number of genes are siutable for phylogenetic studies, but perhaps=
is sensible to sequence a gene for which there is a large database.
I would then suggest that you perform a preliminary study on a small
(judiciously chosen so that they are representative) number of taxa. Ali=
the sequences and see if:
They are easily and unambiguously alignable.
There is sufficient variation among the sequences.
The resulting trees make sense (duplications and lateral transfers can
It would also be nice if all the variation is not concentrated on a few
residues. This could lead to the situation where the variable sites are
saturated with substitutions.
It will be interesting to hear other peoples thoughts on this. I don't t=
that enough people spend enough time thinking about this issue.
My =A30.02 - worth.
Peter Schuchert wrote:
> How would you select the most suitable gene for investigating
> the molecular phylogeny of a particular clade?
James O. McInerney email: J.mcinerney at nhm.ac.uk
Department of Zoology, phone: +44 171 938 9247
The Natural History Museum, Fax: +44 171 938 9158
Cromwell Road, =
London SW7 5BD. =
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