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RE: Fear and New Papers in Las Vegas

> Peterson, K.J., Summons, R.E., and Donoghue, P.C.J.
> 2007. Molecular 
> palaeobiology. Palaeontology 50(4):775-809. doi: 
> 10.1111/j.1475-4983.2007.00692.x.
> ABSTRACT: For more than a generation, molecular
> biology has been used to 
> approach palaeontological problems, and yet only
> recently have attempts been 
> made to integrate research utilizing the geological
> and genomic records in 
> uncovering evolutionary history. We codify this
> approach as Molecular 
> Palaeobiology for which we provide a synthetic
> framework for studying the 
> interplay among genotype, phenotype and the
> environment, within the context 
> of deep time. We provide examples of existing
> studies where molecular and 
> morphological data have been integrated to provide
> novel insights within 
> each of these variables, and an account of a case
> study where each variable 
> has been tackled to understand better a single
> macroevolutionary event: the 
> diversification of metazoan phyla. We show that the
> promise of this approach 
> extends well beyond research into the evolutionary
> history of animals and, 
> in particular, we single out plant evolution as the
> single greatest 
> opportunity waiting to be exploited by molecular
> palaeobiology. Although 
> most of our examples consider how novel molecular
> data and techniques have 
> breathed new life into long-standing
> palaeontological controversies, we 
> argue that this asymmetry in the balance of
> molecular and morphological 
> evidence is an artefact of the relative 'newness' of
> molecular data. In 
> particular, palaeontological data provide unique and
> crucial roles in 
> unravelling evolutionary history given that extinct
> taxa reveal patterns of 
> character evolution invisible to molecular biology.
> Finally, we argue that 
> palaeobiologists, rather than molecular biologists,
> are best placed to 
> exploit the opportunity afforded by molecular
> palaeobiology, though this 
> will require incorporating the techniques and
> approaches of molecular 
> biology into their skill-set.

Leaning a bit far out of the window I think. In
ornithology, molecular data is used for crown taxa
extensively, and after a brief period of dissent, with
the improved techniques now at our disposal it's
generally accepted. Of course, there are those who
don't go for a "total evidence" approach, proposing
"species" on barcode sequence snips from 2 specimens
without giving location data, but that's a minority.

On the other hand, molecular data is being used only
as often as it is in avian paleontology for a reason,
so I think

> Donoghue, P.C.J., and Benton, M.J. 2007. Rocks and
> clocks: calibrating the 
> Tree of Life using fossils and molecules. Trends in
> Ecology and Evolution 
> 22(8):424-431. doi: 10.1016/j.tree.2007.05.005.
> ABSTRACT: A great tradition in macroevolution and
> systematics has been the 
> ritual squabbling between palaeontologists and
> molecular biologists. But, 
> because both sides were talking past each other,
> they could never agree. 
> Practitioners in both fields should play to their
> strengths and work 
> together: palaeontologists can provide minimum
> constraints on branching 
> points in the Tree of Life with considerable
> precision, and estimate the 
> extent of unrecorded prehistory. Molecular tree
> analysts have remarkable 
> modelling tools in their armoury to convert multiple
> minimum age constraints 
> into meaningful dated trees. As we discuss here,
> work should now focus on 
> establishing reasonable, dated trees that satisfy
> rigorous assessment of the 
> available fossils and careful consideration of
> molecular tree methods: rocks 
> and clocks together are an unbeatable combination.
> Reliably dated trees 
> provide, for the first time, the opportunity to
> explore wider questions in 
> macroevolution.

is more the way to go. And this is the 3rd (at least)
major paper this year dealing methodologically with
molecular/fossil data integration and pointing out
what's not optimal at present and ways to change that,
which is very encouraging.

One remaining problem is that phylogeny analysis can't
incorporate GIS data. Theoretically, one could
approach the problem with a polar coordinate grid;
plate tectonics could thus be considered. Dispersal
barriers could be incorporated too, but that latter
thing is a major problem: there is not enough data to
give an *accurate* layout of geography in deep time.
What we have may be sufficient for crown mammals, but
for birds it's not. The data can be analyzed of
course, but not quantitatively incorporated into
phylogenetic data. (I was asked last year to
participate in a biogeographical/theoretical evolution
study, and I declined for precisely that reason: the
results would have been an outstanding and
statistically well-supported load of utter BS, because
Earth's surface was essentially treated as flat...)