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Re: Genes show Neoaves branching before K/Pg extinction

Is the inclusion of hard upper  bounds (maximum age constraints) a
> common practice in molecular dating?

Hard or not hard, upper bounds _should_ be included much more often than they are. I've published on this (Laurin & me 2006, Syst. Biol.).

Many recent papers (e.g. Brown  & van Tuinen 2011; Ronquist et al.
> 2012) use probability distributions with a minimum at the age of a
> fossil and a long low-probability tail instead of a hard maximum,
> which seems to make sense,

It does (and wasn't available to us in 2006). But the paper we're discussing didn't do that; it used minima without any maxima.

given that maximum ages cannot  be estimated from the fossil record
> without making some dubious assumptions.

Well, in a few cases the fossil record is good enough that absence of evidence is evidence of absence. Same ref as above.

Yes, but that's exactly what I  meant, too: if the ratite morphology
> originated more than once, the group diagnosed by the possession of
> that morphology is polyphyletic (it's a union of several
> monophyletic groups) rather than paraphyletic (a monophyletic group
> minus another monophyletic group). Paraphyly and polyphyly cannot be
> distinguished using a tree topology alone. If you don't want to
> speculate about ancestral states, all that you can say is that
> ratites are non-monophyletic.

You imply that Ratitae is defined by character states...

So it can happen in at  least one group of insects. But could it
>> happen in birds? Could something like the modern kagu (which has
>> muscles that are too weak for powered flight, but it still glides)
>> give rise to powered fliers millions of years in the future?

I think so, but that would require an absence of competitors and rather weird selection pressures. So,

I don't call for discounting it  automatically, I'm just implying
> it's highly unlikely --

I agree.

The oldest known paleognaths  are lithornithids, which were rather
> strong fliers (expectable if the last common ancestor of paleognaths
> could fly, suspicious if it could not).

To be fair, we have no clue about their phylogenetic position(s) within Palaeognathae.

Madagascan aepyornithids are  apparently nested in the Australasian
> ratite clade, and the same might be true for the South American
> _Diogenornis_

You don't think *D.* is a rhea?

Elżanowski (1995), for example,  provided a nice list of cranial
> characters in which ostriches either have the same state as neognaths
> or are intermediate between neognaths and all remaining paleognaths.

...Wow. I had no idea!

If there is something  problematic about the interrelationships of
> paleognaths, it's the position of tinamous, not the placement of the
> root -- and incomplete lineage sorting is probably a bigger problem
> than both substitution saturation and inadequate taxon sampling.
> Smith et al. (2012) argued that the base of non-ostrich paleognaths
> is not a hard polytomy because of the total lack of support for one
> of three possible topologies in their data set -- the one with
> tinamous being sister to a rhea/kiwi/casuariid clade. However, that's
> the topology recovered by Haddrath and Baker with both their 10-gene
> and the 27-gene data sets, so the possibility of non-ostrich
> paleognaths being a hard polytomy cannot be ruled out. The extremely
> short internodes in the relevant region of the tree would be
> consistent with it.

...And _that_ immediately brings the incomplete lineage sorting among laurasiatherians to mind. I think we're looking at very fast radiations into the empty world of the early Paleocene.