More on the 'cladistics' of sequences

[David Orlovich]

>>> Of course, changing the outgroup can have significant effect on
>>> relationships in the tree, but that's another story.
>> Are you certain of this?
> Yes.

I'm sure too. Since an outgroup can have as many autapomorphies as it
likes, there is no guarantee that an outgroup taxon will be easily
alignable.  I find it much easier to include a suite of outgroup taxa
that have differing degrees of closeness to the ingroup. It can make it
easier to feel confident about the attachment of the branch leading to
the outgroup taxa, even if some of the more distantly related outgroup
taxa are hard to align with the ingroup. This sometimes works,
sometimes doesn't - depends on what outgroup sequences you have at your
disposal.

This idea that one would try to work out in advance of the analysis
which characters are derived by outgroup comparison seems too biased to
me. It might seem OK if one 'knows' (or thinks they know) a group very
very well - but in this case I suspect you probably don't need to do a
phylogenetic analysis anyway - if you know the polarity of the
characters then you must know the underlying tree that gives the
characters that polarity - what else is there to know?  For some groups
I'm working on, I couldn't (wouldn't) begin to suppose that having
hairy lemmas, or long awns, or unequal glumes could be either primitive
or derived. It just seems impossible to make such a decision without
basing my assumptions of existing (implicit taxonomic) phylogenies. If
I was to do this by comparing with outgroup taxa, then there is no way
of knowing whether those characters in the outgroups are derived or
not, so it doesn't get me anywhere.

Cheers, David

Dr David Orlovich,
Senior Lecturer in Botany.

Department of Botany,
University of Otago,
P.O. Box 56,
(Courier: 464 Great King Street)
Dunedin,
New Zealand.

Phone: (03) 479 9060
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