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Re: More evidence for Eufalconimorphae and Psittacopasserae

> > Although the taxon sampling is a bit patchy (e.g., no
> representatives of
> > Acciptriformes and Strigiformes)

You need at least 2 of _Sagittarius_, _Pandion_ and elanids plus 2 of 
eagle/hawk/buteo. One of _Sagittarius_/_Pandion_ will usually go rogue.

> Isn't that rather strange if one is interested in the
> position of falcons?

Coliiformes and _Aegotheles_ (haven't seen _Steatornis_) give the strongest 
bogus signal. Coliiformes are hopeless via DNA. But the framework now exists 
for morph. _Aegotheles_ is... funny. I wouldn't be surprised if _Steatornis_ 
was no better. Something the entire base of the cypselomorphs has a high 
probability to be rogue (Apodiforms are the only thing I could get to clade 

Seriemas pose much the same problem as mousebirds. Their relationship based on 
DNA is simply not to be taken seriously. They were one of the *major* Pg 
radiations, so this needs to be reanalyzed. You could leave out fossils *if* 
they behaved predictably on DNA, but they don't. (Any more seriema DNA is 
gladly appreciated though) They are not major upsetters though.

Psittaciforms, accipitrids, falconids and passerines are in the same major 
clade it looks. Strigiforms probably too. Other than these, "picocoracines". It 
looks like 2 subsequent radiations, one is the basal split of Neoavesa into - 
basically - Aequornithes and "higher landbirds" and *perhaps* 2-3 more distinct 
lineages surviving from that time.  Some taxa are "weird" though - all 
"Metaves", essentially, though *most* do in fact reliably go in one clade or 
the other for *most* loci. The second radiation is very explosive and somewhat 
obfuscated (but not usually destabilized) in Aequornithes by ciconiids etc, in 
the other clade by upupiforms. 
As I said, mousebirds and _Aegotheles_ usually manage to completely upset at 
least one of the 2 major clades by their sheer presence.
I woudn't trust anything that doesn't compare the tree with and without them.

Falconids tend to turn up close to passerines, and perhaps reliably so. 
Psittaciforms are perhaps more often among Aequornithes than close to 
falconids, and if not rogue they are usually closer to accipitrids.

NWvultures clade irregularly, with about even likelihood for them to turn up 
next to falconids, accipitrids or within Aequornithes. Removing them, however, 
usually has little effect on the tree.

Both radiations must have occurred in the late K. We have some fossils which 
very much look as if they'd turn out on one "side" of charadriiforms, 
Aequornithes etc. or the "opposite" one, so the basal radiation of these was 
very likely already ongoing. 

There are regions all over the genome where oligo-indels "happen", i.e. they 
are not repaired (conspicuous in an alignment because there are many oligo-gaps 
and consensus is low).
There are other regions where there is a higher probability of long indels 
(usually ins rather than dels). They are rarely phylogenetically informative 
per se. A certain insert (and perhaps deletion) may consist of several 
independent elements; I found one of the retroposons apparently a fusion of 4 
elements, 2 of which were ubiquitious in Neornithes, 1 has human(?) and 1 was 
likely protist.

In strigiforms, it *may* be necessary to always sample _Phodilus_.

I have not found a viable solution for cypselomorphs yet. This and the low 
taxon sampling among "picocoracines" is the present obstacle on resolving the 
"higher landbirds". And of course, either the tree with a mousebird or without 
one (two doesn't help either, not even when both genera are sampled) or neither 
may be true. We cannot tell.

The two most common taxa to stand basal in Neoaves (mis-rooting to 
Galloanseres/paleognaths) are passeriforms and columbiforms. I haven't really 
checked what the latter are closest to when you unroot Neoaves (passeriforms 
are usually close to something "higher landbird", not rarely to falcons), but 
IIRC they *might* be Aequornithes. (Need to add charadriiiforms and some more 
Aequornithes to the sample now.

1. Has anyone ever tested the population genetics of retroelements/transposons? 
(Should be possible in chicken)
2. What were the BLAST settings used in Suh et al for checking the retroposon 
sequences against nr/nt?
3. What specimens were used from _Falco_? Wild or captive? If captive, how many 
generations from the wild? (the human-like piece is... odd)
4. What does a cladistic analysis of the more widespread transposons' sequence 
say? (Some of the more ubiquitious long transposons seem to carry significant 
phylogenetic signal)

There is something odd in the pattern of rogue taxa. Can't lay my finger on it, 
but in some cases I could fix it by sampling a close relative instead. In these 
cases there were often massive indels in the rogue taxa (in one trochiline 
genus there was 1 rogue and 1 unrogue sp.). Not finding them in close relatives 
would mean that such indels, which are assumed to persist in situ through 
evolutionary time with high probability, don't. 


PNAS has a new paper about avian extinction at the K-Pg boundary. Looks 
interesting in the news, anyone seen it yet?