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

David Marjanovic <david.marjanovic@gmx.at> wrote:

> Maybe it's all their predecessors that suffered from this instead, and
> Hackett et al. and Harshman et al. finally got it right...! :-)
> Wouldn't be the first time. It took till 2001 till somebody finally found
> the mice & rats as rodents and not as the sister-group(s!) to all other
> placentals anymore.

This brings to mind something else that concerns me.  Are molecular
phylogenies tested and re-tested by the addition of new taxa (when
possible) and/or new sequence data until the tree "looks right".
Obviously the position of rats and mice as basal placentals was
"wrong", because our intuition sent up a red flag on this one.  So too
with the basal position of Passeriformes (songbirds) within crown
Aves.  So the analyses were re-done with new data, and these taxa
ended up in a position that was not obviously "wrong" - rats and mice
happily nested inside Rodentia, and Passeriformes content as derived
Aves.  All is right with the world, and we can move on.

But what if the whale/hippo/ruminantian clade is also "wrong"?  How
would we know?  If we've exhausted the option of taxon sampling, is
stringing together even more gene sequences going to resolve the
problem if the gene sequences themselves are the problem?

With a morphology-based analysis, there is at least the advantage that
the fossil record spits up new taxa every now and then.  Often these
aren't the "right" taxa (insofar as they don't help resolve any
outstanding phylogenetic questions); but fossils occasionally do fill
in hitherto missing gaps.  So-called "missing links".  At the very
least, new discoveries allow phylogenetic hypotheses to be tested by
the addition of new taxa and/or characters states.  Look at how
informative taxa like _Guanlong_ and _Eotyrannus_ and _Dilong_ have
been in resolving tyrannosaur affinities, and documenting *how*
advanced tyrannosaurids came to be.  With the entire whale-artiodactyl
thing, the discoveries of various stem-whales has proven to be an
enormous boon in understanding how whales evolved.  Fossil data has
corroborated the link between whales and artiodactyls; but it's been
less helpful in linking whales to hippos, and not helpful at all in
linking whales+hippos to ruminantians.  So why are so many folks
assuming that the molecules must be "right", and it's the morphology
that's lagging behind?

With turtles, I think we've hit a wall in relying on molecular-based
phylogenies to tell us where turtles came from.  IMHO, the fossil
record is our only hope.

> But we all know that losing flight is much easier that regaining it.

In birds, yes.  But apparently stick insects (Phasmatodea) have
regained flight (and wings) more than once from a flightless/wingless
state (Whiting et al. 2003;  Nature. 421:264-267.)

I'm not suggesting that birds have the same developmental or
phenotypic plasticity as arthropods.... but stick insects show it can
be done.

The major reason for loss of flight in birds is a shift to an insular
environment.  On these islands there is no selective pressure to
retain flight, or to regain it.  (Unless a new predator suddenly comes
along, like cats or rats or humans, and the poor bird goes extinct...
but by then it's too late.)

But could a bird that recently lost the power of flight regain flight
ability?  Could a flightless bird like a kakapo or a kagu give rise to
a secondarily volant descendant?  The fact is, we really don't know.
Given the right circumstances, and if the flight apparatus had not
completely atrophied (as it has in modern ratites), or taken on a
specialized, non-aerodynamic function (like subaquatic locomotion as
in penguins, or a weapon as in _Xenicibis_), then I think it is
theoretically possible for a bird to regain flight.  It may actually
have happened - but I doubt we would know about it.  If tinamous are
nested inside the ratite clade, then we just don't know if the
tinamous are secondarily volant, or if flight was lost multiple times
by ratites (the hypothesis favored by Harshman et al. [2008], for the
same reason that David gave.)

An avian flight apparatus that represents a substantial drawdown in
flight ability such that flapping flight is no longer possible, but
the wings are still capable of flapping, might mimic the incipient
avian flight apparatus in most respects.