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Re: Genes show Neoaves branching before K/Pg extinction



Hi!

> One major problem here: how do we know that ancestral-state
> reconstruction is correct?
I think that's one of the reasons why Haddrath & Baker added retroposon data -
because their character polarization very well corroborates the sequence-based
rooting of paleognaths and the basal position of _Struthio_. No noise in the
signal here. :-)

> The fact that moa were not fully sampled for RT may be a reason (or
> THE reason), but I still wonder how many RT one would have expected
> for a moa-tinamou clade, given their prevalence on the other branches
> of the paleognath subtree, and taking into account branch length. Or,
> to put it another way, how unexpected zero-RT support for
> moa+tinamous is.
Given that the starting point of their retroposon analyses were CR1 libraries
from emu, ostrich, great spotted, kiwi and lesser rhea, the lack of support
for moa + tinamous is not unexpected at all. I assume that if they had done a
tinamou and/or a moa library, they might have found retroposon markers for
that clade. (Same with the support for Aequornithes, by the way.)

The "skew" of the phylogenetic distribution of retroposon markers is not only
dependent on the branch length (and sample size), but also on the genomes that
you take as a basis for your study. E.g., let's assume you would study human
retroposons - you would not expect to be able to use that human retroposon
information to resolve rodent phylogeny. ;-)

I think their study pretty much solves the biggest "paleognath problem" - the
hitherto controversial ratite nonmonophyly.

Best wishes,
Alex



evelyn sobielski schrieb am 2012-09-14:

> > > Polyphyly. Ratites could be paraphyletic only if the
> > last common
> > > ancestor of all paleognaths were a ratite, too -- a
> > large flightless
> > > bird with a keel-less sternum.

> One major problem here: how do we know that ancestral-state
> reconstruction is correct? I have found (in sequence analyses) that
> rooting paleognaths correctly (and *knowing* it is correct) is almost
> impossible due to saturation. Sometimes it is clearly visible; this
> is the case when passerines turn up basal among neognaths. Otherwise,
> one can only note that the internal phylogeny of paleognaths (if you
> unroot them) is constant between loci, but if rooted it differs
> between loci.

> Arguably RT might fix this, and the fact that they found 5 RT
> supporting _Struthio_ as basal among paleognaths is in line with
> this. But the tinamou-moa "clade" is unsupported by RT, particularly
> since the preceding node (the one excluding _Struthio_) has a large
> number of supporting RT.  (cf. Fig. 4 of the paper)

> The fact that moa were not fully sampled for RT may be a reason (or
> THE reason), but I still wonder how many RT one would have expected
> for a moa-tinamou clade, given their prevalence on the other branches
> of the paleognath subtree, and taking into account branch length. Or,
> to put it another way, how unexpected zero-RT support for
> moa+tinamous is. Compare the Neoaves part of the tee, which looks as
> good as anything, and though RT are sparse here, their distribution
> is *not* conspicuously skewed (e.g. we don't have 5-RT support for
> Aequornithes).

> The first phenomenon, BTW, might be the reason they only sampled one
> galliform. I found that getting cracids and phasianids to clade based
> on sequence data is quite tough already due to saturation. Often, the
> cracid will wind up in Anseriformes. Anhimids have a similar problem.

> (To analyze sequences, I use PhyML latest version, with GTR and 10
> rate categories, autoaligned in SeaView but with much manual
> correction as non-mt loci hardly align correctly over a wide taxo
> sample due to indels.)

> In a nutshell, I have not found any locus to date (I checked all
> those for which a sufficient taxonomic sample for "higher landbirds"
> is available) that can be expected to root reliably once you get deep
> into the Mesozoic.


> The paleognath problem, from what I have seen, can only be solved by:
> 1. reconstructing a consensus *internal* phylogeny (unrooted) from
>    molecular data.
> 2. morph analysis adding fossils, even if fragentary (partition
>    dataset if necessary).
> 3. Testing the consensus of 1. + 2. against various outgroup/locus
>    combinations; you will find different rootpoints (= ancestral-state
>    reconstructions), probably even for different outgroups *within the
>    same locus*.
> 4. Analyze the pattern of rootpoints found in 4 and hope anything
>    worthwhile turns up. E.g. clustering of rootpoints for various
>    Galloanseres, with rootpoints for e.g. waders as outgroup outside
>    this cluster, and for e.g. owls even further away.
> (5. Wait for a konservat fossil of a Cenomanian-Turonian paleognath.)

> The only shortcut I can think of: do a pure morph analysis using
> cranial characters *only* (well *maybe* throw in TMT and/or TBT) and
> including any and all K material available, no matter how
> fragmentary, as well as any and all early Pg material especially for
> paleognaths and Galloanseres.

> It is easy to forget (one would think looking at the literature) that
> with the usual mutation rates, the null hypothesis is "around the
> K-Pg boundary, noise exceeds signal for most avian loci; my 100 Ma
> signal is essentially swamped by noise and any attempts to recover it
> will yield artefacts, perhaps more artefacts than signal." To presume
> you can simply go and root paleognaths with Galloanseres and expect
> it to be dependably correct is unrealistic, given that 2 Galliformes
> + 2 Anseriformes do not clade correctly in many situations unless
> forced.


> Regards,

> Eike