molecular phylogeny

James McInerney jamm at nhm.ac.uk
Fri Oct 31 10:16:50 EST 1997


Peter,

This is one of the most sensible questions to ask before begining a proje=
ct
and unfortunately, not enough people bother to ask it.  Rather, there is =
a
herd-instinct to follow whatever has gone before.

First of all, in order to compare your data with previously-published dat=
a, it
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=
nd more.

A huge number of genes are siutable for phylogenetic studies, but perhaps=
 it
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=
gn
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
confound =

	phylogeny reconstruction).


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=
hink
that enough people spend enough time thinking about this issue.


My =A30.02 - worth.

James

Peter Schuchert wrote:
> =

> How would you select the most suitable gene for investigating
> the molecular phylogeny of a particular clade?
> =

> Peter

-- =

=3D=3D=3D=3D=3D=3D=3D=3D=3D
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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