Human and ape phylogeny

[David Orlovich]

I think you're mixing two meanings for the term "phenetic".  On the one
hand, "phenetic" could be used to mean "of the phenotype" or something
like that - in which case measuring a phenetic character would simply
mean measuring something of an organism's phenotype - basically any
character you measure, for whatever purpose, is phenetic.  I think even
DNA sequence data is phenetic in the sense that it is something
specific to the organism that you measure.

On the other hand, "phenetic" is used to mean certain methods of
analysis based on overall similarity, some of which I think were
largely discredited as a set of non-phylogenetic methods - isn't this
partly what the "cladistics wars" were about?

It means that using the word "phenetic" is politically incorrrect and
associated with a non-cladistic way of thinking, but in reality (well,
my reality!) all characters are phenetic - it's that way they are
analysed that makes the difference.

You imply that one can do a cladistic analysis in two ways - either
with polarised characters (i.e. only chosing synapomorphies) or with
phenetic data (i.e. without any pre-selection for only 'good'
characters).  I don't think many people explicitly do cladistic
analyses the first way any more.  To me, it is circular reasoning to
polarise characters before doing a phylogenetic analysis.  Constructing
a most parsimonious tree, and rooting it, defines the direction of
evolution and sorts out the synapomorphies from the plesiomorphies and
parallelisms - it is an inherent and intrinsic part of the tree
construction.  Thus, in doing a cladistic analysis, one is testing the
homology of the characters that were measured and defining which ones
are synapomorphies and which ones are homoplasy  - we make an
hypothesis of homology by measuring a character in different taxa and
we test this hypothesis by doing a cladistic analysis.  The more
non-homologous characters I put into a cladistic analysis the worse the
tree will be - reflected in a lower consistency index (i.e. more
homoplasy (noise)) in the tree.  It could be seen as subjective to
select characters that will not be homoplasious to get a more workable
phylogenetic hypothesis, but some people even embrace this idea and use
techniques like successive weighting (not without critics) to weight
characters with high consistency indices (from prior cladistic
analyses) in subsequent analyses - thus generating a tree that is
better supported by the data.  Another way to get around the problem of
only 'wanting' non-homoplasious characters is to choose a LOT of
characters in the hope that the homoplasies will be swamped by the
synapomorphies and result in a robust tree.  It's funny that this is
exactly the same way to make a phenetic 'tree' (say a UPGMA dendrogram)
approach a phylogeny - and the UPGMA dendrogram has the advantage that
it is rooted!

The apparent circularity of the above scenario can be avoided in
another way - by generating the phylogeny from a data set that is not
the same as the morphological data in which you wish to test homology.
I see this as the main scientific reason for doing phylogenetics on DNA
sequence data.  One can generate an hypothesis of phylogeny (either by
cladistics or other phylogenetic methods like maximum likelihood) and
then test the homology of the morphological characters by mapping them
on to the molecular phylogeny.  It breaks the link of the characters
being used to generate the phylogeny being the same characters on which
to test homology.

DNA sequence data is in the same boat as morphological data when it
comes to generating an hypothesis of homology to test by a phylogenetic
analysis.  The advantage is that is can often be less subjective - the
hypothesis of homology is generated by an alignment algorithm (I think
usually simply a pairwise cluster analysis) where there are only 4 or 5
possible character states - and ever character is more or less the
same.  Taking into account codon positions, secondary structure and
transition/transversion ratio where possible makes for an even better
hypothesis of homology.

So ... where does this leave your problem:

> "No a priori
> judgements were made as to the primitive or derived condition of
> characters". My reading of that statement is that the characters were
> not
> 'cladistic' in the sense of each standing as proposed synapomorphies.
> Instead they were phenetic.

I think it's not an issue - in doing their phylogenetic analysis, they
are hypothesising that the characters they measured will be
synapomorphies for particular clades in the tree, and they are testing
the hypothesis by doing the cladistic analysis.  Rooting the tree will
polarise the characters and indicate which character state changes are
synapomorphies and which are plesiomorphy or convergence.  In saying
that the authors made "No a priori [judgments] ... as to the primitive
or derived condition of characters" I take this to mean that they allow
the cladistic analysis and rooting to determine the direction of
evolution.  As far as cladistic vs phenetic is concerned, all
characters are phenetic - it all in the analysis.

You also asked:

> Am I correct to view this paper as a 'cladistic' analysis of phenetic
> characters with an arbitrary rooting of one of the taxa being
> analyzed[?]

Arbitrary?  The ingroup is assumed to be monophyletic with respect to
the outgroup.  Did the authors meet this criterion?  An issue could
arise where the outgroup taxa/taxon are/is on a long branch (i.e. not
much in common with the ingroup) then many of the character state
changes could be autapomorphic for the outgroup, thus creating
uncertainty in the position of attachment to the rest of the tree (the
same problem applies to ingroup taxa of course).  Where there are lots
of ingroup taxa, this might only affect the relative position of a few
of the more 'basal' ingroup taxa, whereas the clades more distant from
the outgroup will be relatively unaffected by the position of the
outgroup (I think this is why midpoint rooting is considered to be a
valid alternative - could be wrong though).

Cheers,

David Orlovich.

On Saturday, April 5, 2003, at 02:55 AM, John Grehan wrote:

> Here's a question for all the cladistic experts on this list. I admit
> to
> having a relatively superficial expertise with cladistics so I want to
> measure my current perceptions against any responses on this list. My
> question concerns the 'cladistic' quality of an article cited on this
> list
> as increasing the support for a human-chimp/african ape clade vs human
> orangutan by S. Gibbs, M. Collard, and B. Wood (2002) Soft-tissue
> anatomy
> of the extant hominids: a review and phylogenetic analysis. Journal of
> Anatomy 200: 3-49.
>
> At first glance the paper seemed very impressive. The authors utilized
> 171
> characters and a cladistic analysis. The number of taxa was limited to
> humans and extant apes only which did make me wonder if some of their
> characters might not qualify as synapomorphies with further comparison
> including at least the old world monkeys. Then I read that "No a priori
> judgements were made as to the primitive or derived condition of
> characters". My reading of that statement is that the characters were
> not
> 'cladistic' in the sense of each standing as proposed synapomorphies.
> Instead they were phenetic.
>
> The authors then state that "Hylobates was assumed to be the basal
> hominoid
> genus and the cladograms were rooted accordingly". Since the characters
> were not defined as synapomorphies with respect to an outgroup, making
> one
> of the taxa the basal lineage seems to be an externally imposed
> criterion
> rather than being generated from the characters themselves. With this
> root
> the characters were subject to 'cladistic' analysis.
>
> Am I correct to view this paper as a 'cladistic' analysis of phenetic
> characters with an arbitrary rooting of one of the taxa being
> analyzed. If
> I am then this paper hardly seems to me to stand up as a reliable
> support
> for the human-chimp clade. I am getting old and perhaps my
> understanding of
> cladistics based on what I read by Hennig, Nelson where cladistics was
> all
> about the analysis of proposed synaomorphies is now out of date and I
> missed the boat where cladistics is now all about the analysis of
> phenetic
> characters.
>
> John
>
> Dr. John Grehan
> Director of Science and Collections
> Buffalo Museum of Science
> 1020 Humboldt Parkway
> Buffalo, New York 14211-1293
> Voice 716-896-5200 x372
> Fax 716-897-6723
> jgrehan at sciencebuff.org