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Re: Morpho v molecular (was Re: Tinamous: living dinosaurs)

Mickey Mortimer <mickey_mortimer111@msn.com> wrote:

> When the two methods consistantly give different topologies, it's always the 
> addition of new taxa and characters to morph analyses that move things closer 
> to molecular results (e.g. the recently
> discovered amphibeanean fossil with lacertid charaxcters, which molecules 
> predicted).

In the case of amphisbaenians, yes the fossil squamatan
_Cryptolacerta_ appears to back up the molecular-based placement of
amphisbaenians as the sister-group to Lacertidae.  However, correct me
if I'm wrong, but the paper that described _Cryptolacerta_ only
included a total evidence analysis (morphological characters + nuclear
gene sequences) to test its affinities.  AFAIK, there was no
morphology-only analysis.  I'm not disputing the
lacertid-amphisbaenian link; I'm merely pointing out that the
amphisbaenians are not the best example of your claim that morphology
is playing catch-up with molecules.

I think David is on the ball when he says the molecules can say
whatever they want without opposition.  There is a certain amount of
hubris in some molecular-based papers, with Waddell et al.'s 1999
review paper in Systematic Biology (which named Whippomorpha, among
other new molecular-based 'clades') being a particularly good (or bad)
example of this.  It's unfortunate that some paleontological papers
use the congruence of their morphology-based trees with
molecular-based trees as a selling point.  I think it's bad policy to
view morphological evolution (including fossil taxa) through the prism
of what the molecules say - or what we think they are saying.

> You never see more genes and sequenced taxa leading to molecular results that 
> resemble the traditional
> morphological results after all.  The changes always seem to go one way.

Hmmm... I've noticed this too (at least for mammals), and I've
wondered if this is an artifact.  With molecular-based phylogenies,
there is a limit to the number of taxa that can be sampled for
phylogenetic analysis.  So once we hit this limit, the topology of a
molecular tree is pretty much "fixed".  This gives the illusion of
stability (especially if certain nodes are well-supported,
statistically).  By contrast, new fossils are being discovered all the
time, and one 'key' fossil can radically change the topology of a
morphology-based tree.  So (again, at least for mammals)
morphology-based trees can and do change on a fairly regular basis.
So if a morphology-based tree happens to be congruent to a
molecular-based tree, is that corroboration, or coincidence?

Take the Cetartiodactyla, for example.  It contains two highly
speciose clades, Ruminantia (~180 species) and Cetacea (~90 species),
but the other clades have much fewer species (Hippopotamidae,
Camelidae, Suina).  To obtain a molecular dataset, we would compile
lots of genetic sequences for all hippopotamids, camelids, suines, and
a representative cross-section of cetacean and ruminantian species (or
you could sample *all* the cetacean and ruminantian species, but that
probably would not help resolve the relative position of either clade
better than a representative cross-section).  The resulting
molecular-based tree has effectively exhausted the possibilities for
taxon sampling.  We can try adding more sequences, but that probably
won't change the topology very much.  We could try a new algorithm,
but that calls into question the efficacy of the original analysis.

With fossils, discoveries of stem-cetaceans, and (to a lesser extent)
the discoveries and re-interpretations of certain fossil artiodactyl
taxa, have guided our views on how whales evolved.  Future discoveries
will undoubtedly provide further insights.  Remember that despite all
the confidence molecular biologists had in a whale-artiodactyl clade,
it wasn't until _Artiocetus_ turned up - the proto-whale with the
artiodactyl-style ankle - that we had hard evidence (quite literally)
to support this link.