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RE: Molecular clocks and avian diversification

--- Guy Leahy <xrciseguy@sbcglobal.net> schrieb:

>  Mol Biol Evol. 2006 Sep;23(9):1731-40. Epub 2006
> Jun
> 14.  Links 
> A mitogenomic timescale for birds detects variable
> phylogenetic rates of molecular evolution and
> refutes
> the standard molecular clock.Pereira SL, Baker AJ. 
> Department of Natural History, Royal Ontario Museum,
> Toronto, Ontario, Canada. sergio.pereira@utoronto.ca

Wow, thanks aplenty. This shall prove most useful 

> at the Cretaceous/Tertiary boundary. We identified
> fossils that are useful as time constraints within
> vertebrates. Our timescale reveals that rates of
> molecular evolution vary across genes and among taxa
> through time, thereby refuting the widely used
> mitogenomic or cytochrome b molecular clock in
> birds.
> Moreover, the 5-Myr divergence time assumed between
> 2
> genera of geese (Branta and Anser) to originally
> calibrate the standard mitochondrial clock rate of
> 0.01 substitutions per site per lineage per Myr
> (s/s/l/Myr) in birds was shown to be underestimated
> by
> about 9.5 Myr. 

Major ouch time!

> We found
> no support for the hypothesis that the molecular
> clock
> in birds "ticks" according to a constant rate of
> substitution per unit of mass-specific metabolic
> energy rather than per unit of time, as recently
> suggested. 

What a pity. It was more reasonable than Pauling's
original suggestion. Still, Leach's Storm-petrel and
the flak Penhallurick and Wink got suggested that it
was indeed not so - for some reason, molecular clocks
in seabirds appear to tick slower.

> Our analysis advances knowledge of rates
> of
> DNA evolution across birds and other vertebrates and
> will, therefore, aid comparative biology studies
> that
> seek to infer the origin and timing of major
> adaptive
> shifts in vertebrates.

A nice way of putting what a biomedical researcher
seeking major founding would without doubt have called
"...will revolutionize our understanding of..."

Well, as I understand it, there was (and and I'm
leaving paleognaths out here!) the anseriform lineage
which existed as very distinct by the C/T boundary (as
indicated by Vegavis), and the Galliform lineage which
is inferred to have done so too. The "Galloanseres" I
find weakly supported by evidence at present; they may
be an artifact of traditional cladistics being limited
to dichotomous splits* and an underlying ancestral
morphology largely obliterated by the odd adaptational

Apart from that, I strongly presume that there have
been some significant splits in the other Neognathae
during the Late(st) Cretaceous. How one would call
these lineages - pan-Ciconiiformes a la Sibley/Ahquist
seems to be deprecated, finally, and whether it's the
proposed Metaves and Coronaves is another matter - is
unresolved, and also whether or not some species-poor
"oddball" lineages split off that early - the overall
evolutionary pattern suggests it may very well have
been so. What seems fairly certain is that what was
formerly called "higher landbirds", i.e.
more-or-less-perching-adapted smallish birds including
passerines might just barely have constituted a
distinct lineage 65 mya, and at any rate was
apparently precluded from significant radiation by the
Enantiornithes which fairly certainly occupied the
major landbird niches. I find the supposed "Cretaceous
parrot mandible" (UCMP 143274 IIRC) far too spurious
to accept, especially as there is no indication that
bill morphology was anything but the last major
psittaciform feature to evolve.

In the end, one gets a pattern of neognath
diversification at the C/T boundary that is not all
too different from 19th-century phenetic
classifications a la Bonaparte (walking birds",
"wading birds", "swimming birds" etc), or at least
closer to that than to the all-orders-are-equal lineup
used for lack of a better alternative: waterfowl were
present and well-evolved, and gamefowl most probably
too, and apart from that probably 2 major lineages and
perhaps the occasional species-poor oddball, with the
major lineages in the early stages of radiation.

Still, I think the "graculavids" have their merit -
not as a true lineage, but as a form taxon in the
truest sense: an ecological state a whole bunch of
modern bird lineages passed through during the Latest

Trying to find major and robust symplesiomorphies of
the (tentative, as of yet) large branches of
Neornithes has proven to be very frustrating. But I
think we're getting close - this year has the best
odds yet to be seen in future time as the year where
it all started to come together (I am spending far too
much time to read MPE and MBE papers these days).

Ideally, in the absence of a usable fossil record,
molecules should suggest phylogenies which then should
be verified by morphological characters. The latter
are very liable to misinterpretation on their own, and
the former are notorious for giving bad dates by now.
One needs at least 2 differing approaches to eliminate
method-specific errors. The procellarids, for example,
showed how a molecular phylogeny can suggest which
morphological characters are robust for reconstructing
the phylogeny in aloneage and which ones are shaped by
high adaptive pressures.

Regards... and many many thanks!


* In reality, the time it takes for lineages to
diverge may be long enough in relation to overall
radiation speed for that assumption not to hold true,
and certain groups may not adhere to it at all.
Consider the mallard and its relatives: we know that
the moa-nalos of Hawai'i are probably derived from
some Pacific Black Duck ancestor - a subpopulation or
even just vagrants of one species -  but we also known
that in all probability, the split between the latter
and the mallard, and more so the split between the
mallard and the American Black and Mexican Ducks will
more likely than not disappear without any lasting
evolutionary trace. Then you have the sadly extinct
Marianas duck which was a good phylospecies on grounds
of allopatry which nonetheless evolved - probably
entirely during the Holocene - as a hybrid swarm
between vagrant mallards and Pacific Blacks. In
conclusion, the present state of speciation in the
mallard group is not necessarily significant in
evolutionary time, with gene pools only incompletely
separated - but that did not prevent part of that
half-diverged gene pool to give rise to the moa-nalos
which were physically incapable of being submerged
back into that common gene pool. The conclusion is
that cladistics is incapable to correctly represent
the evolutionary relationships between species in the
genus Anas (cladistics would argue for all moa-nalos
to be retained in Anas, even in Anas sensu stricto
i.e. the mallard and its allies, but that's really
underplaying their adaptations waaaay).

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