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The Bucket New Papers

Hi All! -

    Yes, another long drought without any posts, but I'm glad others are
picking up my slack!  Before we get to the new papers, here's some old ones:
all the issues (1983-2004; I'm uncertain if there are newer issues) of the
Spanish journal _Zubia_ are now available on-line, and there is a veritable
wealth of rarely-cited, rarely-seen dinosaur papers in them (mostly, but not
entirely, on footprints).  I've added the link to my Journal Links page, but
here it is anyway:
a=1493.  Also available via Dialnet are all the papers from a 2005 volume
entitled "Dinosaurios y Otros Reptiles Mesozoicas en Espana" -- again,
mostly tracks, but some other stuff, too:
http://dialnet.unirioja.es/servlet/libro?codigo=3953.  (Thanks to Jay Nair
for these discoveries!  There may well be more up at Dialnet now, but I
haven't had time to explore...)

    OK, so now a few new things:

Hwang, K.-G., Lockley, M.G., Huh, M., and Paik, S. 2008. A reinterpretation
of dinosaur footprints with internal ridges from the Upper Cretaceous
Uhangri Formation, Korea. Palaeogeography, Palaeoclimatology, Palaeoecology
258(1-2):59-70. doi: 10.1016/j.palaeo.2007.10.029.

ABSTRACT: Very unusual dinosaur footprints with radial internal ridges from
the Late Cretaceous of southern Korea have been the subject of much
controversy. All footprints are in black laminated mudstone/shale, and have
gently curved cross-sections that show deformation of a flexible substrate
by dinosaur footprint registration. These peculiar patterns have not been
recorded at any other site in the world, although natural casts of such
features have been reported from a few localities. Each footprint consists
of several sectors or pockets partitioned by conspicuous radial ridges.
These tracks were first interpreted as sauropod manus-only tracks,
supporting Roland Bird's swimming sauropod hypothesis. However, our study
casts serious doubt on this theory for two reasons. First, the footprints
sometimes exhibit characteristic features such as ungual, digit or heel
impressions, suggesting that the mysterious traces are those of a tridactyl,
bipedal dinosaur. Second, the unusual tracks are underprints, and the
internal ridges are molds of radial cracks on the underside of a sand bed on
which large bipeds were walking.

Mayr, G. 2008. The fossil record of galliform birds: comments on Crowe et
al. (2006). Cladistics 24(1):74-76. doi: 10.1111/j.1096-0031.2007.00170.x.

ABSTRACT: In a recent article, Crowe et al. (2006) analyzed the
interrelationships of galliform birds, combining molecular sequence data
with morphological characters from a study by Dyke et al. (2003). They
calibrated the resulting phylogeny with fossil galliforms and concluded that
"basal lineages" of galliforms diverged prior to the Cretaceous . Tertiary
(K-T) Event and that the subsequent cladogenesis was influenced by the
break-up of Gondwana" (Crowe et al., 2006, p. 495; note that this statement
refers to putatively "basal" crown group Galliformes, not to the existence
of early Cretaceous stem lineage representatives). Unfortunately, however,
several of the statements concerning fossil Galliformes are erroneous and
the calibration of the molecular data is based on incorrectly assigned
fossil taxa.

Dyke, G.J., and Crowe, T.M. 2008. Avian paleontology: opinions and
quasi-phenetics versus characters and cladistics. Cladistics 24(1):77-81.
doi: 10.1111/j.1096-0031.2007.00188.x.

ABSTRACT: Gerald Mayr's (2007) recent critique of the Crowe et al. (2006)
analysis of the phylogenetic relationships of, and inferred ages of
divergences between, major clades of galliform (=''chicken-like'') birds
raises a number of questions concerning the theory and practice of avian
paleontology.While we take issue both with the tone and content of this
critique, we nevertheless feel that rebutting it is a useful exercise in
that it highlights the epistemological differences between us with regard to
inferring the phylogenetic placement(s) of fossil taxa and then using them
to help calibrate molecular evolutionary ''clocks''. More specifically, Mayr
(2007) maintains: (1) that ''several of the statements concerning fossil
Galliformes [cited by Crowe et al., 2006] are erroneous''; (2) that ''the
morphological character matrix underlying their analysis contains severe
miscodings''; and (3) ''calibration of the[ir] molecular data is based on
incorrectly assigned fossil taxa'', i.e., Gallinuloides wyomingensis and
Amitabha urbsinterdictensis.

     OK, those aren't really the abstracts, but the first paragraphs from
each.  This and the preceding are responses to a slightly older paper:

Crowe, T.M., Bowie, R.C.K., Bloomer, P., Mandiwana, T.G., Hedderson, T.A.J.,
Randi, E., Pereira, S.L., and Wakeling, J. 2006. Phylogenetics, biogeography
and classification of, and character evolution in, gamebirds (Aves:
Galliformes): effects of character exclusion, data partitioning and missing
data. Cladistics 22(6):495-532. doi: 10.1111/j.1096-0031.2006.00120.x.

ABSTRACT: The phylogenetic relationships, biogeography and classification
of, and morpho-behavioral (M/B) evolution in, gamebirds (Aves: Galliformes)
are investigated. In-group taxa (rooted on representatives of the
Anseriformes) include 158 species representing all suprageneric galliform
taxa and 65 genera. The characters include 102 M/B attributes and 4452
nucleic acid base pairs from mitochondrial cytochrome b (CYT B), NADH
dehydrogenase subunit 2 (ND2), 12S ribosomal DNA (12S) and control region
(CR), and nuclear ovomucoid intron G (OVO-G). Analysis of the combined
character data set yielded a single, completely resolved cladogram that had
the highest levels of jackknife support, which suggests a need for a revised
classification for the phasianine galliforms. Adding 102 M/B characters to
the combined CYT B and ND2 partitions (2184 characters) decisively overturns
the topology suggested by analysis of the two mtDNA partitions alone,
refuting the view that M/B characters should be excluded from phylogenetic
analyses because of their relatively small number and putative character
state ambiguity. Exclusion of the OVO-G partition (with > 70% missing data)
from the combined data set had no effect on cladistic structure, but
slightly lowered jackknife support at several nodes. Exclusion of third
positions of codons in an analysis of a CYT B + ND2 partition resulted in a
massive loss of resolution and support, and even failed to recover the
monophyly of the Galliformes with jackknife support. A combined analysis of
putatively less informative, "non-coding" characters (CYT B/ND2 third
position sites + CR +12S + OVO-G sequences) yielded a highly resolved
consensus cladogram congruent with the combined-evidence cladogram.
Traditionally recognized suprageneric galliform taxa emerging in the
combined cladogram are: the families Megapodiidae (megapodes), Cracidae
(cracids), Numididae (guineafowls), Odontophoridae (New World quails) and
Phasianidae (pheasants, pavonines, partridges, quails, francolins, spurfowls
and grouse) and the subfamilies Cracinae (curassows, chachalacas and the
horned guan), Penelopinae (remaining guans), Pavoninae sensu lato (peafowls,
peacock pheasants and argus pheasants), Tetraoninae (grouse) and Phasianinae
(pheasants minus Gallus). The monophyly of some traditional groupings (e.g.,
the perdicinae: partridges/quails/francolins) is rejected decisively,
contrasted by the emergence of other unexpected groupings. The most
remarkable phylogenetic results are the placement of endemic African
galliforms as sisters to geographically far-distant taxa in Asia and the
Americas. Biogeographically, the combined-data cladogram supports the
hypothesis that basal lineages of galliforms diverged prior to the
Cretaceous/Tertiary (K-T) Event and that the subsequent cladogenesis was
influenced by the break-up of Gondwana. The evolution of gamebirds in
Africa, Asia and the Americas has a far more complicated historical
biogeography than suggested to date. With regard to character evolution:
spurs appear to have evolved at least twice within the Galliformes; a
relatively large number of tail feathers (= 14) at least three times;
polygyny at least twice; and sexual dimorphism many times.

Brown, J.W., Rest, J.S., Garcia-Moreno, J., Sorenson, M.D., and Mindell,
D.P. 2008. Strong mitochondrial DNA support for a Cretaceous origin of
modern avian lineages. BMC Biology 6. doi: 10.1186/1741-7007-6-6.

ABSTRACT: Background
Determining an absolute timescale for avian evolutionary history has proven
contentious. The two sources of information available, paleontological data
and inference from extant molecular genetic sequences (colloquially, 'rocks'
and 'clocks'), have appeared irreconcilable; the fossil record supports a
Cenozoic origin for most modern lineages, whereas molecular genetic
estimates suggest that these same lineages originated deep within the
Cretaceous and survived the K-Pg (Cretaceous-Paleogene; formerly
Cretaceous-Tertiary or K-T) mass-extinction event. These two sources of data
therefore appear to support fundamentally different models of avian
evolution. The paradox has been speculated to reflect deficiencies in the
fossil record, unrecognized biases in the treatment of genetic data, or
both. Here we attempt to explore uncertainty and limit bias entering into
molecular divergence time estimates through i) improved taxon (n = 135) and
character (n = 4594 bp mtDNA) sampling; ii) inclusion of multiple
cladistically-tested internal fossil calibration points (n = 18); iii)
correction for lineage-specific rate heterogeneity using a variety of
methods (n = 5); iv) accommodation of uncertainty in tree topology; and v)
testing for possible effects of episodic evolution.

The various 'relaxed clock' methods all indicate that the major (basal)
lineages of modern birds originated deep within the Cretaceous, although
temporal intraordinal diversification patterns differ across methods. We
find that topological uncertainty had a systematic but minor influence on
date estimates for the origins of major clades, and Bayesian analyses
assuming fixed topologies deliver similar results to analyses with
unconstrained topologies. We also find that, contrary to expectation, rates
of substitution are not autocorrelated across the tree in an
ancestor-descendent fashion. Finally, we find no signature of episodic
molecular evolution related to either speciation events or the K-Pg boundary
that could systematically mislead inferences from genetic data.

The 'rock-clock' gap has been interpreted by some to be a result of the
vagaries of molecular genetic divergence time estimates. However, despite
measures to explore different forms of uncertainty in several key
parameters, we fail to reconcile molecular genetic divergence time estimates
with dates taken from the fossil record; instead, we find strong support for
an ancient origin of modern bird lineages, with many extant orders and
families arising in the mid-Cretaceous, consistent with previous molecular
estimates. Although there is ample room for improvement on both sides of the
'rock-clock' divide (e.g. accounting for 'ghost' lineages in the fossil
record, and developing more realistic models of rate evolution for molecular
genetic sequences), the consistent and conspicuous disagreement between
these two sources of data more likely reflects a genuine difference between
estimated ages of i) stem-group origins and ii) crown-group morphological
diversifications, respectively. Further progress on this problem will
benefit from greater communication between paleontologists and molecular
phylogeneticists in accounting for error in avian lineage age estimates.

     ...OK, that one's not _really_ available yet (even that abstract is
called "preliminary"), but it's making the blog/list server rounds, so
thought I'd mention it in case no one else has, yet.  Anyway, there should
be floggings for people that format abstracts this way...!

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