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RFTRA



My favorite New Mexican, Jerry D. Harris, wrote:
>        Never having done any formal morphometric analysis of anything
>(that is, using a program such as RFTRA -- I've been forced to just eyeball
        I understand that this may be an unpopular attitude amongst dinosaur
workers, but I don't like RFTRA. It is an interesting way of showing you the
difference between reconstructions. However, it does not explicitly address
allometry, the "RFTRA coefficients" generated are by no means objective
measures of difference (note the clustering of points in Chapman and
Brett-Surman's and study,  and, as Chapman points out (in _Dinosaur
Systematics_), it is highly sensitive to the reconstruction used. This adds
a level of uncertainty to the uncertainty already present when dealing with
fossil material. Here is an excerpt from a review I wrote on the Chapman and
Brett-Surman paper for a class:

Chapman, R. E., and M. K. Brett-Surman. 1990 Morphometric observations on
hadrosaurid ornithopods. pp. 163-177 in K. Carpenter and P. J. Currie
(eds.), Dinosaur Systematics: Approaches and Perspectives. Cambridge
University Press, Cambridge, New York, Melbourne

        "This study provides an interesting case-study in the use of
morphometric (phenetic) date to evaluate evolutionary difference and support
phylogenetic inferences. The study provides characterizations of
morphological variation in advanced ornithopods, and indicates some
interesting correlations between shape analysis and phylogenetic analysis,
but fails to present either set of results in an effective, cogent,
applicable manner. Part of the reason for this inefficacy is an inability on
the part of the authors to draw an explicit philosophical and functional
separation between phenetic and phylogenetic evidence.
        "This is further complicated by a lack of clarity in outlining the
goals of the study. The exploratory aspect of the study is coupled with an
implicit confirmatory aspect. The same methodology is used for both
functions, and both purposes are served by a highly interpretive approach to
the handling of the results. No criteria for confirmation are established,
and exploration is largely limited to conscious or unconscious attempts to
support a priori observations. For example, it is noted that the landmarks
showing the greatest change in lambeosaurines are those associated with the
snout and crest, while other landmark positions remained conservative in
their location. However, landmarks were specifically concentrated in areas
which were expected to show the most change, and fewer landmarks were placed
in other parts of the skull (see below).
        "Any study which attempts to use morphometric (and therefore
phenetic) similarity to evaluate phylogeny treads on unsteady ground. In
this case, the authors do not establish a reasonable criterion by which
phenetic assessments are to be used to evaluate a phylogenetic hypothesis.
The authors state that since it is more parsimonious to explain
morphological similarity in the context of homology (i.e. it is inherited
from a common ancestor), if morphological similarity among phylogenetically
disparate taxa cannot be "recognized" as convergence, then the phylogenetic
hypothesis must be re-evaluated. How convergence is to be "recognized", and
what weight this is to be given with respect to phylogenetic analysis is not
addressed. For example, they evaluate the cranial similarities between
Ouranosaurus and Anatotitan as convergent, presumably within the context of
another phylogenetic study. They do not explain how this convergence is
"recognized", except to point out that both taxa posses an elongate snout
with an unexpanded narial opening.
        "The explanation of the overall greater similarity among
non-lambeosaurines within the context of hadrosaurid monophyly is restricted
to a vague assertion that this indicates a high degree of morphological
evolution among the lambeosaurines. Given their earlier statements the
authors should be required to explain [how they] "recognize" this apparent
convergence among the non-lambeosaurines. Obviously, this is a case of
symplesiomorphy, with the less derived members of the group exhibiting a
greater phenetic affiliation for each other, and hardly warrants
"recognition". Direct reference to this concept would both keep the reader
aware of the implications of the study and assure the reader that the
authors are aware of those implications. However, throughout the discussion
of their results, the authors make no explicit attempt to relate the
findings of this study to phylogenetic concepts, nor do they recognize the
implications of their results in such a context, beyond very general
statements such as the one above.
        "As a means of summarizing data the UPGMA dendrograms may be useful,
however conclusions drawn from them are phenetic, and are therefore not
necessarily useful in elucidating phylogeny. The authors do not explicitly
interpret the meaning of the dendrograms, and references to them are usually
in the context of a confirmation of previous observations, or noting where
the dendrograms produce unexpected clusters. In the analysis of pubes, it is
noted that the clustering of Camptosaurus and specimens of Iguanodon reflect
"family-level similarities." This reflects the use of the dendrograms to
confirm previous non-phylogenetic classificatory hypotheses rather than
elucidate phylogenetic relationships. Among the lambeosaurine crania, the
nearest neighbor among non-lambeosaurines is always Saurolophus, yet this
taxon is in a completely separate cluster on the UPGMA dendrogram.
Additionally, juvenile "Procheneosaurus" was the nearest neighbor for all
non-lambeosaurines. Little interpretation of these phenomena is given,
despite their importance for phylogeny and ontogeny respectively. How these
various phenetic techniques relate to phylogenetic patterns is left unclear.
        "Further, the authors use paraphyletic groups (iguanodonts and
possibly hadrosaurines) in their analyses. Paraphyletic groups are less
useful than monophyletic groups in elucidating phylogeny. The use of
paraphyletic groups demands a series of conceptual considerations which the
authors do not appear to have made. Instead, the authors consistently treat
these groups as if they were real evolutionary entities, potentially
undermining the utility of their results. 
        "The authors do make broad attempts at relating the overall results
with respect to a particular phylogeny. They suggest that conventional
phylogenetic hypotheses are supported by the fact that lambeosaurines show
greatest overall similarity with hadrosaurines among non-lambeosaurines,
followed by iguanodonts and the Camptosaurus. While this statement makes
intuitive sense, it lacks a theoretical basis. It is not difficult to
construct an hypothetical example where such a correspondence would not be
observed. While such a case would require "recognition" of some other
phenomenon (as the authors state above), such a recognition will come
directly from the analysis of derived similarity which produced the original
phylogenetic hypothesis. The phylogenetic analysis, being based on derived
similarity, would carry more weight than a phenetic one. Unless the phenetic
analysis develops new characters not considered in the previous phylogenetic
analysis, then that analysis sufficiently "recognized" the convergence
before the phenetic analysis began. Correspondence between morphometric and
phylogenetic studies is a welcome occurrence, but it is by no means a
requirement. It is unclear what theoretical basis the authors have for
testing phylogenetic inferences using phenetic methods. 
        "While RFTRA seems to be a powerful tool for describing shape
changes, it may not be the best one for the purposes of this study. By
isolating size and concentrating on shape variations, size-related variation
and extreme allometric effects may have been eliminated which might
adversely affect any measure of distance as applied to a phylogenetic study.
RFTRA may thus confound evolutionary or developmental interpretations of
shape differences, and may exaggerate differences among taxa. For example,
RFTRA output suggests that the difference between the prepubic processes of
Edmontosaurus and Parasaurolophus (representative hadrosaurine and
lambeosaurine taxa, respectively) are manifested in increased depth in the
latter taxon. However, in the text it is explained that the prepubic process
of Edmontosaurus is absolutely longer than that of Parasaurolophus. A visual
evaluation of the outline drawings provided will show that if the two pubes
were scaled to the same acetabular dimensions, shape differences in most
parts of the bones would resolve themselves neatly. The primary difference
between the pubes of the two taxa would then be expressed as an increase in
the length of the prepubic process. The RFTRA analysis might be useful in
determining the likely taxonomic affinity isolated bones of the same size as
those used in the study, but it is unclear whether this will extend to bones
of different sizes. A similar situation is apparent in their analysis of the
ischium, where the primary difference again appears to involve a lengthening
(and possibly thickening, see below)of the shaft coupled with distal
expansion. As before, the RFTRA analysis redistributes these effects over
all landmarks, resulting in comparison which appears less biologically
useful. While RFTRA is touted as being capable of analyzing localized
differences among landmarks, it seems unable to isolate localized variation.
In the process of finding a best fit, better fits in one part of the
landmark configuration must be sacrificed for the overall fit. Distance
coefficients from such analyses may thus exaggerate overall differences if
static allometries among groups vary significantly from isometry, as is
likely the case in most phylogenetic contexts.
        "There are also inadequacies in the landmark configurations used in
the study. The authors make repeated statements concerning the utility of
their cranial study for phylogenetic purposes, as opposed to the study of
the pelvic bones, due to the use of homologous landmarks. However, casual
scrutiny reveals that 11 of 20 cranial landmarks (numbers 1-4, 6, 10-13, 16,
20) are in actuality pseudolandmarks, and two (7, 8) are defined as a
pseudolandmarks although they may represent true homologous points as they
are applied within the study. Further, these landmarks are arrayed about the
lateral profile of the cranium to characterize expected differences in
morphology among hadrosaurids rather than quantify overall shape. The
resulting geometric coverage of the form is good. It is unclear, however,
whether the distance measurements arrived at truly reflect overall
similarity among the hadrosaurids included in the study.
        "The authors employ non-hadrosaurid taxa apparently as in parallel
to the outgroup method of polarizing characters in phylogenetic studies.
However the landmark configuration is designed to quantify variation among
hadrosaurids, not among ornithopods in general, and may not be optimal for
characterizing difference among all ornithopods. That hadrosaurines appear
more similar to iguanodonts than lambeosaurines may be due to the use of
distance measurements derived from such a landmark configuration. Further,
landmarks are clustered around areas of interest, and the combined effect of
their changes among lambeosaurines and hadrosaurines may serve to overweight
the differences between these two groups relative to the differences between
hadrosaurines and other non-lambeosaurines.
        "In their interpretations of the results of the cranial analyses,
the authors must repeatedly caution that similarities among
non-lambeosaurines are partially due to the derived nature of the skull of
lambeosaurines. This is manifested as very high RFTRA distances between
lambeosaurines and non-lambeosaurines, due to the tremendous differences in
positions of landmarks associated with the premaxillary-nasal crest. In a
modern approach to discovering phylogeny (i.e. phylogenetic systematics),
autapomorphic character states are not useful in elucidating phylogeny. In a
morphometric study aimed at elucidating the phylogenetic relationships among
these groups, and specifically addressing the supposed diphyletic nature of
the Hadrosauridae, it might be appropriate to select a landmark
configuration which ignores the very derived nature of premaxillae and
nasals of lambeosaurines. This might reduce the very high RFTRA distances
between lambeosaurine and non-lambeosaurine, and increase the low
differences among the lambeosaurines, allowing a more balanced evaluation of
overall similarity. However, this would affect the utility of the point
configuration in assessing overall differences among the taxa studied. The
effectiveness of a particular point configuration is dependent on the
purpose of the study. Since this study had the twofold purpose of
characterizing variation and evaluating phylogenetic hypotheses, the
conclusions suffer from using a landmark configuration used to address both
goals.
        "The authors bemoan the lack of homologous points for comparison of
the pelvic bones. They manage to identify several useful pseudolandmarks on
the pubis and ilium. Here, as opposed to the cranial study, their use of
pseudolandmarks is more understandable. The landmark configuration on the
ischium fails to capture at least one important difference among taxa,
namely the thicker shaft. The lack of landmarks along the shaft of the
ischium may also account for the peculiar configuration of the outline
drawings which resulted from the analysis, and, as with the pubis, may have
unduly affected RFTRA distance coefficients (see above). It seems unlikely
that, with such a bewildering array of pseudolandmarks in the other bones
studied, that some pseudolandmarks could not have been produced to more
adequately model the ischium.
        "Although the analyses in this study demonstrate that RFTRA is
capable of isolating size to allow a pure shape comparison, this comparison
is only useful insofar as the point configurations reflect the actual shape
of the element. It is unclear whether isolating size produces biologically
meaningful information. Such an analysis might be useful for broadly
comparing shapes of bones and groups of bones for classification, but may
not be useful in evaluating a phylogenetic hypothesis. Further, given a
phylogenetic hypothesis, it is unclear whether RFTRA will be useful in
characterizing derived difference in morphology. RFTRA, and the use of RFTRA
distance in dendrograms, is not an "assumption-free" analysis. RFTRA
distance is only useful insofar as the landmark configuration reflects the
requirements for solving the problem at hand. Various size-dependent and
landmark-dependent phenomena might obscure whatever relevant information is
contained in the forms. RFTRA distance can be useful in providing some
measure of evolutionary change among organisms. Utilizing this distance as a
test of a phylogenetic hypothesis requires a theoretical foundation which is
lacking in this study. Without both a theoretical basis and a practical
basis for using RFTRA to test a phylogenetic hypothesis, it might be best to
restrict its role in phylogenetic analysis to developing characters, and
characterizing changes among taxa.
        "The results of any such analysis must still be evaluated in a
broader context, as they may not accurately reflect variation among
specimens. It is clear from the above discussion that RFTRA should not be
the only method used for the purpose of analyzing variation among taxa. Some
form of orthogonal decomposition technique, for example principle component
analysis, coupled with a landmark method to orient distances and allow
reconstruction of forms for comparison, may prove more capable of isolating
localized variation and analyzing similarity and difference within a more
biologically informative size-shape decomposition. Using any morphometric
technique to evaluate phylogenetic relationships requires a more solid
foundation than that which is provided here, and no further suggestions can
be made with regards to an appropriate technique until such a theoretical
basis is established."

        I suspect I spent a little too much time on this assignment...

        Wagner


--------------------------------------------------------------------------------
     Jonathan R. Wagner, Dept. of Geosciences, TTU, Lubbock, TX 79409-1053
 "Only those whose life is short can truly believe that love is forever"-Lorien