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molecular DNA, phylogeny, and random notes



After reading Darren's synopsis of the BBC programmes,
I couldn't help but be depressed. I haven't seen Peter
Jackson's two films. I do have, of course, the
screenplay his wife Fran Walsh wrote for the
forthcoming remake of KING KONG...Mr Jackson is going
to parley his team into doing an extravagant film (the
script is far better, in some respects, than the
original efforts by Edgar Wallace, James Creelman, and
Ruth Rose)...there will be an official version, with
animatronics and CGI, and a private print for Mr
Jackson's private archive, with everything done in
stop-motion animation. We shall see.
During the past year, comments have been advanced re:
molecular dating (and thoughts re: using isolated bone
scraps to derive Lewis Carroll-like extrapolations).
Comparative molecular sequence analyses are important
tools (S.B. Hedges, S. Kumar, et al., have published
fascinating forays into the past). But, I would like
to advance a few speculations about what they are
revealing about dinosaur evolution.
It is probable that dinosaurs, from the Triassic to
this very moment, have never evolved in a stately
manner all at the same time. Rather, like other taxa,
dinosaur radiation is a hierarchical branching
pattern, with divergences and stasis variable within
clades, most of these, of course, occurring well
before the K/T events.
The problem with applicability of molecular sequencing
to phylogenetic systematics is that, so far, recovered
DNA from pre-Cenozoic material, while interesting, is
not useful in answering phylogenetic questions. DNA
and protein sequences, even from living dinosaurs, are
not amendable to morphological analyses either. And
this is a key point for me. Without knowing the
genetic foundations of the evolutionary processes
giving rise to certain morphologies, one cannot
quantify differences in morphogenesis. For example: we
have inklings of tyrannosaur evolution, but we do not
know the genomic "engines", their interrelationality
to other theropods (allosaurs, etc.). Moreover, even
with the numerous taxa of extant dinosaurs (however
numerous they are -- cf. Sibley/Ahlquist -- they are
remnants of the clades of the end-Cretaceous who,
somehow, survived), we have no models of analysis to
allow one to predict rates of morphological changes.
In fact, I argue, the fossil record of Mesozoic
dinosaurs is not, in a sense, "evidence" of
evolutionary processes. A tyrannosaur skeleton tells
one a magnificent organism once lived, but not much of
the evolutionary processes of tyrannosaurs, the
polarities of ancestor/descendent nodes of character
traits.
Let me give an imperfect illustration. I have been
enveloped for some years in sorting through the
characters of "megalosaurs", basal tetanurines, as it
were, who appear, often, to be transitional taxa,
difficult to pinpoint in theropod evolution. I know of
the hypodigms of these taxa -- Megalosaurus,
Eustreptospondylus, Metriacanthosaurus, in particular
-- but have yet to determine on the basis of their
morphologies when different taxa diverged...or why.
Where other clades have been remarkably well analysed
(I am thinking of Tom Holtz's pioneering efforts, and
those of Julia Clarke et al. on avians, or Jeff
Wilson's work on sauropods), the "megalosaurs" remain
elusive. Thus, one has a degree of phylogenetic
uncertainty.
A classic example of this are murine rodents. Using
molar cusp characters of numerous specimens, the
divergence of rats and mice is thought to be ca. < 17
myr ago, with "spiny" mice and "true" mice thought to
be more closely related than are "true" mice and rats.
Alas, the systematics is wrong. "Spiny" mice are more
closely related to gerbils than to more distantly
related "true" mice and rats. The evidence comes not
from sifting isolated rodent teeth at an excavation
site, but from rigorous molecular data, using
bea-blobin family of genes. 
In time, I do not doubt that Lebanon amber specimens
will be found with a baby dinosaur (or sizable chunks
of one) or pterosaur. We already have some data on
molecular evolution of avian theropods (from S.B.
Hedges et al.), mutational processes of divergences
and subsequent radiations. With an actual specimen of
a dinosaur body, answers (and even more questions)
will arise, because one will have to couple the
anatommical information with the known biogeography of
dinosaurs at the time of the animal being trapped in
amber (continental fission during the Mesozoic may
have seen isolated dinosaur populations decimated by
diseases from encroaching taxa). Nuclear DNA and
mitochondrial DNA obtained from the amber-trapped
dinosaur may, in all probability, give different
divergence times for various theropod radiations. We
have partially known mitochondrial genomes for some
extant dinosaurs, with discrepancies ariving from
estimated based on nuclear sequences.
My own "gut feeling" is that mitochondrial genome data
is unreliable, as it is this data set which often
"contradicts" the actual known fossil record
(mitochondrial genomes tend to act like a single
gene). Thus, our amber-trapped dinosaur, and the
emerging genomes of living dinosaurs, will have to be
analysed with a combination of mitochondrial and
nuclear DNA data sets.
For me (and here I am basing it on rumours shared with
me of those who believe there are small
dinosaurs-in-amber in Lebanon), the excitement is
growing. An isolated humerus, vertebra, or whatever,
may provide numerous papers on avian evolution (nomina
dubia remain domina dubia), with little or no real
contributions to knowledge of dinosaur evolution. But
what if one has a shoulder girdle of a small dinosaur
trapped in amber?

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