Re: Kerberosaurus manakini

["Jaime A. Headden" <qilongia@yahoo.com>]

Mickey Mortimer (Mickey_Mortimer111@msn.com) wrote:

<Sereno's (2000) pachcephalosaur analysis has a ton of missing data, but
is still "loaded" as you put it, with a whole 2 discordant characters out
of 574!  Missing data has no affect on CI, which is an astounding 0.97 for
that analysis.>

  Very amazing, in fact, that so much "complete" data doesn't result in a
high CI, as dictated previously, but a low value of completeness does the
same. Indicating that completeness and CI lack as secure a relationship as
was implied. Hence the misunderstanding that appears to be occuring. A
misrepresentation of the _ordering_ of the characters was implied due to
the statement that Bolotsky and Godefroit were "loading" their tree with
only support, somehow validated by thew arrangement of their characters;
this is indicated (last post) as being incorrect.

<No, that was tested by Wiens (2003) as well.  He concluded this generally
has a negative effect on the accuracy.>

  I have read the paper, as well as use and lack of use of wild-card taxa
(other papers, including Norell, Wroblewsky, and Wheeler, etc.). The
implication, oddly enough requiring a contradictory statement from Mickey,
was that Mickey had pointed out Wiens work. Hence, "As Mickey has shown."
But I guess we need to be objectionable even when a criticism was never
offered.

<By enforcing a less parsimonious topology, given your data set, yes.>

  By enforcing ANY topology, trees with varying positions for the key
taxa, such as enforcing an (Allosaurus (Ornithomimus (Tyrannosaurus
(Deinonychus + bird)))) are not considered part of the data set; they are
ignored. The topology will result in a lower consistency index of provided
characters since some characters will in essence be given negative weight
(or rather, some will be given positive weight, rather than null values in
the matrix). I have never ran a data set with an enforced topology except
to assess variation of values and bootrap support and arrangement of "hot"
taxa (taxa that appear to "bounce" around the tree). To get the relatively
high CI and shorter run, in fact some researchers, including our dear
Holtz, have enforced topologies to test matrices. This is good for looking
at testing the quality of the analysis, but not to find a "good"
phylogeny.

<Really?  Why would you cull a character a posteriori?  If your matrix
finds a topology despite "bad characters", why erase them from your
published matrix?  It only ends up misrepresenting your analysis.  And why
wouldn't you report this action in your Methods section?>

  I don't use this option. However, the logic is as follows:

  A) If your matrix affords that a given character provides change in the
phylogeny with or without it, it is a "spandrel," lacking any informative
use. In fact, such a character only increases the CI and lowers the HI
indeces, which may lead to false appraisal of the "better" analysis. The
use of the higher CI problem faced by some versus a lower CI is felt as
beneficial. Note: Kearney and Clark (2003) regard this issue in much
better detail than does Wiens (2003).

  Kearney, M. & Clark, J.M. 2003. Problems due to missing data in
  phylogenetic analyses including fossil: A critical review. _Journal of
  Vertebrate Paleontology_ 23 (2): 263-274.

  Including of excessive characters that provide no additional data do
nothing BUT higher the CI. At which point do they become important to the
production of a phylogeny? They can be listed under "supportive
information" without ever being a part of the analysis. 

  B) If the character is scorable only for a single taxon (apomorphy), it
also lacks any value to the matrix, and does nothing but increase branch
length of a taxon from it's neighbors.

  These reasons would give you criteria for excluding a character
post-analysis. Kearney and Clark (2003) and Wilkinson (2003) both discuss
wildcard problems and how one can cull TAXA from the analysis due to lack
of any effective change. Again, these can be applied outside the analysis.
This would usually be effective in noting polytomies where effective
beneficial information is absent.

  Wilkinson, M. 2003. Missing entries and multiple trees: Instability,
  relationships, and support in parsimony analysis. _Journal of Vertebrate
  Paleontology_ 23 (2): 311-323.

  From page 316: "My approach has been to assume that we wish to infer
    relationships on the basis of all the available evidence unless we
have
    good (and explicit!) reasons for ignoring some subset of the data. In
    this view, that we achieve a more resolved consensus by excluding taxa
    is not itself a sufficient justification for excluding the taxa (and
    their character data) from the analysis because in excluding data we
    have not necessarily found the relationships that are strictly
    supported by the full data, which is our main objective. We should be
    happier about excluding taxa if their inclusion or exclusion makes no
    difference to the inferred relationships of the other remaining taxa.
    Deleting such taxa a priori would be analytically equivalent to
pruning
    them from the MPTs for the full data (and discarding duplicate trees),
    i.e., to deleting them a posteriori. It would reduce the number of
MPTs
    but not alter relationships among the remaining taxa. This is the
    central idea behind safe taxonomic reduction (STR) (Wilkinson, 1992,
    1995a). Elimination of taxa is safe precisely when it has no effect
    upon the inferred relationships among the remaining taxa."

  Wilkinson, M. Ph.D. thesis (1992). Consensus, compatibility and missing
  data in phylogenetic inference. (Department of Geology, Faculty of
  Science, University of Bristol, U.K.) 367 pp.

  Wilkinson, M. 1995a. Coping with missing entries in phylogenetic
  inference using parsimony. _Systematic Biology_ 44: 501?514.

  One can therefore safely prune without missing or loosing resolution or
information both _a priori_ and _a posteriori_. It seems ridiculous, but
it _is_ effective and no loss of information occurs at deleting taxa or
characters that have NO benefit but to raise ot decrease the indeces,
increase number of MPT's (most parsimonious trees for those who don't
know) and, decrease bootstrap or jackknife values.

<Because there are valid reasons to think such characters are correlated,
as you know.>

  We _assume_ correlation, and we assume it is negligible. This is still
_a priori_ exclusion of information that can have a phylogenetic
importance. For instance, there are no tyrannosaurids under 20 feet in
length at adulthood. Dwarfism does not occur. Large size is enforced.
Thus, there is a phylogenetic signal. The circumference of long bones,
robusticity indeces, and so-called "size-related" and even
"gender-related" differences (variable morphology of the femur and pelvis
in *Coelophysis* spp. and *Platosaurus* spp. into two "morph" classes have
been documented, as have the ischia and maxillae of *Tyrannosaurus* [refs
from Colbert, 1990; Raath, 1990; and Galton, 1990 for starters and mroe
lit.]) show taxonomic variation in some groups that would be of benefit to
research. If the pelvis and ankle fuse in older maturity in some
non-tetanurans, then this too is a phylogenetic signal. There is otherwise
little reason to exclude them other than the "correllation" problem of two
characters sharing states or "being" the same thing; aka, "splitting" of
characters and over-weighting of a condition. It is still phylogenetically
informative. We cull these _a priori_ because we think, as do some others
for other characters or taxa, they are detrimental to the analysis or
would enforce topologies we "know" are wrong (aka, tyrannosaurs as
"carnosaurs").

<Sereno is obviously not just culling correlated characters from his
matrix, because these would not affect the CI in most cases.>

  Loss of a character that shows an effective change in the matrix or
phylogeny or length of branches _will_ cause a change in CI.

<So the "extraneous" correlated character will have a similar CI to its
partner, and the resultant CI of the matrix will be similar to a matrix
without the extraneous character.>

  See points above, as this agrees with Wilkinson (2003) -- however, it
does so only for the "extraneous" character, except that support values do
change. Notably, relation of two characters with effectively 3 states
between then can have a variable expression, as in the relationship of
tooth loss and extent coded in separate characters:

                 12
Hesperornis      01
Incisivosaurus   01
Caudipteryx      11

1. Maxilla: teeth present anteriorly (0); absent (1).
2. Maxilla: teeth present caudally (0); absent (1).

  Limited to this, the run finds a topology of (Caudi (Hesper +
Incisivo)). Ignoring the other characters that would show convergence or
latency, this can be treated as one character in which the matrix then
represents a series of polymorphies that attempt to show the same form of
data -- the "machine" attempts to treat it as a set of two characters:

                 1
Hesperornis      (12)
Incisivosaurus   (01)
Caudipteryx      (22)

1. Maxilla: teeth present anteriorly (0); teeth present caudally (1);
teeth absent anteriorly (2); teeth absent caudally (3). "unordered"

  The result places (Incisivo (Caudi + Hesper)) due to convergent loss of
a portion of the maxillary dentition -- or maybe its synapomorphic loss?

  Thus the use of "correllated" characters DOES alter the field. I fail to
see very many correllated characters that are noted ONLY for the ingroup
that possess equal distribution. If such were there, I would suspect
"weighting" or "loading" the data set. Some features that crop up with
regards to size-related features include the presence of rugose scarring
or processes not otherwise present in smaller forms. However, both
tyrannosaurids and *Caudipteryx* show rugosities and "laminae" of the ilia
that appear to be absent in most of the rest of Coelurosauria (I note a
few other taxa also possess these, many of which are small, as well as
large hadrosaurs and sauropods) -- a function of age? Such inclusion thus
has a phylogenetic signal, as it would tie two taxa together outside of
mutual size ranges.

<I can see this happening in some matrices.  I _cannot_ see this happening
in _every single_ matrix Sereno makes, regardless of the number of
characters, taxa or which group he is examining.  So Sereno's culling is
not due to character correlation, which leaves the question of his reason
for culling characters open.>

  Ask him why, then. He is, to my knowledge, in the country. Do this
instead of making assumptions of about why he did it and mocking him or
his work or similar works for things that one has no knowledge of, only
assumptions.

<As for your oh-so-ambiguous reference to my coelurosaur analysis posts,
you hit the nail on the head with your use of the term "casually". In the
publication of my phylogeny, discussion will be included. Right now
though, my posts just serve as updates to those interested.>

  Why? I do not see people ask. The two people who seemed most eager for
updates were Ken Kinman and Stephan Pickering who, to my knowledge, only
considered the content of the phylogeny, rather than the support for them.
Perhaps a separate message board where data will actually be presented and
responded to. This is not meant to be mocking or insulting, but when data
results are presented, usually one should cite their derivation or
supporting data. This would be equivalent to making statements of
relationship as in "I find this to be more likely," and run with the ball,
in papers by Holtz or Sereno or Brochu, who always presented their data in
full. This provides the analytical utility of such, whereas before they
lack it.

  Cheers,

=====
Jaime A. Headden

  Little steps are often the hardest to take.  We are too used to making leaps 
in the face of adversity, that a simple skip is so hard to do.  We should all 
learn to walk soft, walk small, see the world around us rather than zoom by it.

"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)


                
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