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Master and Commander: The Far Side of the New Papers

Nod to Michael Barton for that title!  Only a couple of things; first,
another dissertation:

Moreno Fuentealba, K. 2006. Jurassic-Cretaceous Dinosaur Footprints from
South America and Pedal Biomechanics in Ornithopod Dinosaurs. Ph.D.
dissertation thesis/dissertation, University of Bristol, Bristol, 162 pp.

...available on-line at http://www.geocities.com/dinohuella/research.htm.


Clarke, J.A., and Middleton, K.M. 2008. Mosaicism, modules, and the
evolution of birds: results from a Bayesian approach to the study of
morphological evolution using discrete character data. Systematic Biology
57(2):185-201. doi: 10.1080/10635150802022231.

ABSTRACT: The study of morphological evolution after the inferred origin of
active flight homologous with that in Aves has historically been
characterized by an emphasis on anatomically disjunct, mosaic patterns of
change. Relatively few prior studies have used discrete morphological
character data in a phylogenetic context to quantitatively investigate
morphological evolution or mosaic evolution in particular. One such
previously employed method, which used summed unambiguously optimized
synapomorphies, has been the basis for proposing disassociated and
sequential "modernizing" or "fine-tuning" of pectoral and then pelvic
locomotor systems after the origin of flight ("pectoral early-pelvic late"
hypothesis). We use one of the most inclusive phylogenetic data sets of
basal birds to investigate properties of this method and to consider the
application of a Bayesian phylogenetic approach. Bayes factor and
statistical comparisons of branch length estimates were used to evaluate
support for a mosaic pattern of character change and the specific pectoral
early-pelvic late hypothesis. Partitions were defined a priori based on
anatomical subregion (e.g., pelvic, pectoral) and were based on those
hypothesized using the summed synapomorphy approach. We compare 80 models
all implementing the Mk model for morphological data but varying in the
number of anatomical subregion partitions, the models for among-partition
rate variation and among-character rate variation, as well as the branch
length prior. Statistical analysis reveals that partitioning data by
anatomical subregion, independently estimating branch lengths for
partitioned data, and use of shared or per partition gamma-shaped
among-character rate distribution significantly increases estimated model
likelihoods. Simulation studies reveal that partitioned models where
characters are randomly assigned perform significantly worse than both the
observed model and the single-partition equal-rate model, suggesting that
only partitioning by anatomical subregion increases model performance. The
preference for models with partitions defined a priori by anatomical
subregion is consistent with a disjunctive pattern of character change for
the data set investigated and may have implications for parameterization of
Bayesian analyses of morphological data more generally. Statistical tests of
differences in estimated branch lengths from the pectoral and pelvic
partitions do not support the specific pectoral early-pelvic late hypothesis
proposed from the summed synapomorphy approach; however, results suggest
limited support for some pectoral branch lengths being significantly longer
only early at/after the origin of flight.

Jerry D. Harris
Director of Paleontology
Dixie State College
Science Building
225 South 700 East
St. George, UT  84770   USA
Phone: (435) 652-7758
Fax: (435) 656-4022
E-mail: jharris@dixie.edu
 and     dinogami@gmail.com

"There's a saying that goes 'people who live in glass houses shouldn't throw
stones'... OK. How about...NOBODY should throw stones. That's crappy
behavior! My policy is 'no stone-throwing regardless of housing situation.'
There's an exception, though. If you're TRAPPED in a glass house...and you
have a stone, then throw it! What are you, an idiot? It's really 'ONLY
people in glass houses should throw stones'... provided they're trapped, in
a house... with a stone. It's a little longer, but you know..."
                                 --- Demetri Martin