Re: Kerberosaurus manakini

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

Mickey Mortimer (Mickey_Mortimer111@msn.com) wrote:

  <In Bolotsky and Godefroit's, characters 1-5 were all designed to group
hadrosaurids together to the exclusion of the outgroup. Characters 6-8 are
designed to group hadrosaurines together.  9-12 and 13(1) are just
lambeosaurine apomorphies (so 9 out of 21 characters were useless, how
about that?). Characters 13(2), 14 and 15 are designed to group
brachylophosaurins together, while character 16 groups the rest of the
hadrosaurines together to the exclusion of brachylophosaurins. 13(3) and
17 group saurolophins and edmontosaurins together. 21 is meant to group
saurolophins together, 18 and 19 to group Prosaurolophus with Saurolophus,
and 20 to group edmontosaurins together. Only two codings disagree with
this. Maiasaura lacks the hadrosaurine character 7, and lambeosaurines
also have saurolophin character 21.>

  I think a slight misunderstanding here is occuring. The nature of the
arrangement of characters may only represent the intuitive neccessity of
placing characters that diagnose clades one is aware of in a series. I
certainly have done this for my oviraptorosaurian analysis, in which
characters are arranged in a hierarchy. I represent possible characters
diagnosing alternate clades or other possible taxon arrangements below the
clade that I assume to be more correct by previous analyses. Below all
this are other characters I treat as being variable among all taxa, or
general characters. Characters including in the subsets, as in Sereno's
"sorted" character lists, are supported by the "intuitive" knowledge they
should be there to help "support" a grouping, even though I add states or
split characters that I am aware can diagnose other clades, or seek to
reduce the effective use of that character. Characters 1-24 in my analysis
are used to diagnose Oviraptorosauria alone. I also separate stem and node
characters for other reasons. This sorting does not make the analysis
intuitively predetermining. PAUP* does not care how binary or supra-binary
characters are arranged, only genetic codings. I understand this can lead
to assuming a "loaded" analysis, but the data should only have to speak
for itself. Now imagine the lack of consistent placement for half the taxa
in one's analysis, and how that is determined. The prevalence of uncodable
states or high percentage of uncodable taxa below 50% doesn't help,
either.

  As Mickey has shown, however, removing taxa with low percentage of coded
characters DOES alter the matrix, so there is an effect. However, less
tested in these analyses is the effect of removing those characters which
have less than 50% coded positions among all taxa. One can get a lower CI
also by enforcing a topology. There are many ways to adversely affect a
matrix _a priori_ to the set run, but Mickey's complaint seems to be with
Bolotsky/Godefroit's so-called "loaded" analysis and a predetermination he
has no awareness of. Sereno's process, unlike that of Godefroit, is
slightly different, as characters are culled _a posteriori_ (pers. comm.)
as has occured with most people who run analyses. The particular mindset
that "every possible character able to be put into the matrix" has another
adverse problem: inclusion of characters that are considered
"size-related," while having a likely phylogenetic component (say, within
tyrannosaurids) does not help the analysis when it could lump the classic
"Carnosauria" together, despite their exclusion showing tyrannosaurids lie
closer to birds. Large titanosaurids versus smaller ones? Maybe, maybe
not. Dromaeosaurids appear to have a trend towards large, terrestrial
forms evolving from smaller, arboreal/scansorial/aerial forms, so there is
definately a phylogenetic component to a size increase. Relation of
humeral and femoral circumference to length of the bone, or position and
ratio of lengths of moment arms and their bony equivalents, may also
signal a phylogenetic component, as in hadrosaurids, but these can also be
size-related. These are culled _a priori_ from most recent analyses and
are usually discussed as such, but I don't see anyone complaining. If one
includes ALL possible characters, one may be lumping a large series of
convergent conditions found throughout the skeleton relating to
proportions and robusticity indeces that can influence the other,
non-size-related features and skew results. A "perfect" scenario is FAR
from reality, and neither _a priori_ inclusion or exclusion may be the
answer. There is always a bias in selecting characters for inclusion, and
at least we are given the exact reasons in Bolotsky and Godefroit's
continuing Kundur/Jaiyin Amurese papers of hadrosaurs. This gives us a
more capable means of assessing the data that in some phylogenies that
have been casually posted HERE.

  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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