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