More on the 'cladistics' of sequences

[John Grehan]

My reference to 'latter' was to the cladistic analysis - not to the
algorithm, although even though the same data matric can be analysed by
a cladistic or phenetic algorithm I do think it makes a difference
whether the data are phenetic (combination of unrecognized plesiomorphic
and apomorphic characters) or cladistic (restricted to apomorphic
states). Apologies for the lack of clarifity here

I do not see how a cladistic algorithm can sort out primitive and
derived characters if they are not identified in the first place. For
example, a character may be said to be shared between tax a and b
because it is not in the outgroup, but if the feature actually happens
to be represented in the outgroup in some way, the algorithm cannot know
this without being told and if it is not told then it cannot come to
that conclusion.

John Grehan

-----Original Message-----
From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
Behalf Of Richard Jensen
Sent: Monday, June 14, 2004 9:33 AM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: [TAXACOM] More on the 'cladistics' of sequences

John Grehan wrote:

> At 01:24 PM 6/11/04 -0500, Richard Jensen wrote:
>
> >That's my point - the character could be used in either a phenetic or
a
> >cladistic analysis.  The same data matrix can be analysed by a
cladistic
> >algorithm or a phenetic algorithm.
>
> Well I can agree with this although I would say that the latter would
not
> be cladistics if the characters were not already limited to predicted
> synapomorphies.

By latter, I assume you mean my reference to a phenetic algorithm.
These
generally are not intended to provide cladistic interpretations in the
first
place (except for some methods, e.g., neighbor-joining) , so I'm not
sure what
the intent of your comment is.  As I noted several months ago, and
others have
more recently noted, there are corcumstances under which a phenetic
analysis
may yield results hat are a good reflection of phylogeny.  However, a
fundamental difference between phenetic (here is use the term
exclusively for
algorithms based on overall similarity) and cladistic (here I use the
erm
exclusively for methods such as that developed by Hennig) analyses is
that the
former does not treat characters as discrete entities with respect to
determining relationships while the latter does.  One can map discrete
characters on a tree derived from a phenetic analysis, but it is likely
to
illustrate more homoplasy than a cladistic tree derived for the same
data
matrix (as suggested by Sokal and others; real counter examples do
exist).  You
may create a data matrix limited "to predicted synapomorphies;" that
matrix may
be analyzed by any tree building protocol; the results will almost
certainly be
different as a function of the different ways the relationsghips among
the taxa
are evaluated and the tree is constructed.

>
>
> >The results will most likely be
> >different, as will the interpretation, but that's a function of how
the
> >characters are analyzed, not how they are are coded.
>
> I agree that the results may be different depending on what algorithm
is
> used, but I also assert that the results can be different depending on
what
> kind of characters are used. Using characters that are an undetermined
mix
> of primitive and derived characters is, to me, just a phenetic
analysis
> whether or not a cladistic algorithm is used on the data.

This is a point Pierre and I have been trying to make - if the matrix
consists
of a mix of "primitive and derived characters," the cladistic algorithm
will
sort them out for you and you'll have a cladistic result.  A cladistic
algorithm will not yield a phenetic result.

> So the lack of
> correspondence between the huaman-orangutan morphology and DNA
sequences
> could be due (with respect to the DNA sequences) that:
>
> 1. The DNA sequence data only represents an overall similarity of DNA
> sequences and is therefore not a necessary match for phylogeny;
> 2. And DNA sequences may not necessarily match the genetics connected
with
> speciation events that is represented in the morphological
synapomorphies.
>
> John Grehan
>

The morphological data could also be reflecting long-branch attraction
because
there are parallelisms between the orang-human lineages and these
(apparent)
parallelisms may not be reflected in the DNA data (and the reverse could
happen
as well).

Dick

--
Richard J. Jensen              | tel: 574-284-4674
Department of Biology      | fax: 574-284-4716
Saint Mary's College         | e-mail: rjensen at saintmarys.edu
Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen