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Re: Molecular clocks and avian diversification

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!

It's embarrassing that anyone used this as late as 2006. (It has recently been refuted, I think in the latest paper on the phylogeny of Neornithes.)

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

What a pity.


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..."

Where's the revolution?

Instead, let me doubt the dates. A Permian date for the basal divergence of the crown of Archosauria is suspect. An Early Cretaceous date for the basal divergence of Neornithes is highly suspect. And so on... I've recently done some molecular dating; some programs let you fiddle with several parameters that can greatly influence the results, others seem to have them inbuilt and inalterable...

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),

What's so "very distinct" about it?

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

So you think there was a trichotomous split?!?

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

I have not yet seen evidence for this. The low diversity of "graculavids" -- the Cretaceous ones all come from New Jersey -- doesn't argue for it...

* 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.

Don't confuse cladogenesis ( = any halfway permanent split of a population in two) and speciation. Those aren't the same... except under some species concepts...

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).

Cladistics is the method to find phylogenetic trees, nothing more. It does not tell you how to classify. Classification is a separate problem. (Well, it's an entirely artificial non-problem, but that's another story...)