More on the 'cladistics' of sequences

[John Grehan]

At 03:15 PM 6/4/04 -0500, rjensen at SAINTMARYS.EDU wrote:
>John,
>
>Characters, in an of them themselves, are not phenetic or cladistic
>(although one might argue that continuous characters are phenetic).  The
>point you seem to be missing is this: historically, it was common practice
>to evaluate each character individually and arrange the states in an
>ancestral-descendant sequence prior to conducting a cladistic analysis;
>i.e., a character state tree was prepared for each character.  How was
>this done?  By examining the states of each character in other groups (the
>outgroups)  that were considered to be related to, but distinct from the
>ingroup.
>
>Well, constructing a most parsimonious network and then rooting it by
>noting the point where the outgroup(s) attach accomplishes the same thing,

I can see that rooting the tree after constructing a most parsimonious
network may give the appearance of the same thing, but if the characters
are not limited to derived states through prior analysis of each character
then my current conclusion is garbage in garbage out.

>but probably with less bias (i.e., the investigator is not making
>arbitrary decisions about what constitute the ancestral states).

If the decisions for what constitutes the ancestral states are verifiable
then they are not arbitrary in the sense that the choices are not
defensible. By selecting only those characters that can be defended at the
outset as being derived with respect to a chosen outgroup, one is making a
case for evaluating the level of confidence one may have for which proposed
synapomorphies have the greatest support by other proposed synapomorphies.
I content that if systematists know their group so poorly that they cannot
make a documented argument to support the identification of potential
synapomorphies before the analysis then I don't see how I could have any
confidence in the result.

>Of course, changing the outgroup can have significant effect on
>relationships in the tree, but that's another story.

True enough. I have seen this in the human-ape problem where morphologists
have limited comparisons to humans and great apes for example. There is an
example whereby there is a drop from the entrance to the nasal cavity to
the floor of the nasal cavity. This is found in African apes and
australpoithecines - thus australopithecines were said to have an 'african
ape' morphology. This contention ignored the fact that the same condition
is found in gibbons and monkeys and thus the comparison was one of
plesiomorphy for all that it was included in a cladistics analysis.

By the way, I still have not had ANYONE come up with synapomorphies for
just chimps, australopithecines, and humans. And that's not for the lack of
trying (Ken - in your system what characters did you use?).

John Grehna


>Dick
>
>
>
>----- Original Message -----
>From: John Grehan <jgrehan at SCIENCEBUFF.ORG>
>Date: Friday, June 4, 2004 2:30 pm
>Subject: More on the 'cladistics' of sequences
>
> > As I indicated earlier, I want to look into what is presented to
> > substantiate the claim that the a posteriori imposition of an outgroup
> > is sufficient to produce a 'cladistic' result using phenetic
> > characters(characters that are not limited to hypothesized
> > apomorphies before the
> > analysis).
> >
> >
> >
> > I took a quick look at Page and Holmes (1998) book "Molecular
> > evolution:a phylogenetic approach. All I have read so far is the
> > statement (p. 21)
> > that "Given a tree, we can distinguish between ancestral and derived
> > character states". There is no discussion of this approach (or
> > citation)in relation to that of Rosa or Hennig to show
> > substantiate the use of
> > cladistics as the appropriate label.
> >
> >
> >
> > So what I have read in this book so far is the claim, but not the
> > substance to counter my contention that approaches rooting
> > phenetic data
> > results in a phylogeny that is non-cladistic for all that it is
> > rooted.If I am not totally misguided, it would seem that the
> > pheneticists/evolutionary systematists a la Mayr won the cladistic
> > wardsafter all.
> >
> >
> >
> > I've asked Curtis Clark for a citation of the authority he goes by
> > and I
> > look forward to that in due course.
> >
> >
> >
> > John Grehan
> >