Re: More evidence for Eufalconimorphae and Psittacopasserae

[Alexander Suh <asuh@uni-muenster.de>]

Hi!

evelyn sobielski schrieb am 2011-09-25:

> > Isn't that rather strange if one is interested in the
> > position of falcons?
It is, therefore I mentioned the lack of Acciptriformes in the first post of
this thread... ;-)

> [...] Coliiformes are hopeless via DNA.
If that is meant for DNA sequence analyses, I agree.
But for the previously discussed methodological reasons, this does not apply
to retroposon analyses - there, they "behave" as normal as all other sampled
birds and can be placed with moderate support. Nice.
If you doubt that, remove the taxon from the presence/absence matrix and run a
PAUP* analysis - nothing will change. :-)

> Seriemas pose much the same problem as mousebirds.
See above.

> As I said, mousebirds and _Aegotheles_ usually manage to completely
> upset at least one of the 2 major clades by their sheer presence.
As far as I know, _Aegotheles_ appears (quite consistently, both in nuclear
and mitochondrial analyses) to be the sister taxon of Apodiformes (swifts +
hummingbirds).

> 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.
That sounds like a typical BLAST artefact. Please, do not use BLAST to
identify or annotate retroposons, DNA transposons etc. as the NCBI database
does not have any consensus sequences of these to compare them to.
Just because the program tells you "part A is similar to XYZ, part B is
similar to YZ, part C is similar to human, part D is similar to protist"
doesn't mean that it's a fusion of four elements. Rather, there's nothing
similar to the full-length element deposited in the GenBank nucleotide
collection, so it'll just show whatever random similarities to GenBank
sequences there might be.

> 1. Has anyone ever tested the population genetics of
>    retroelements/transposons? (Should be possible in chicken)
To my knowledge, none have been done in birds yet (but look, for instance, at
mammals - there are plenty of studies there). This might be due to the fact
that, as far as I know, no recently active (= suitable for studies on
population level) retroposons have yet been found in chicken and zebra finch.
But, work is in progress on retroposon population genetics in a certain group
of birds. ;-)

> 2. What were the BLAST settings used in Suh et al for checking the
>    retroposon sequences against nr/nt?
None.
Retroposon sequences were identified by comparing them to the consensus
sequences available in Repbase and subsequent, thorough inspection of the
sequences by eye in comparison to a variety of known consensus sequences of
related retroposon subfamilies (especially important for defining the element
boundaries + truncations + target site duplications and for evaluating the
retroposon subfamily assignment).

> 3. What specimens were used from _Falco_? Wild or captive? If
>    captive, how many generations from the wild? (the human-like piece
>    is... odd)
... BLAST artefact?

> 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)
Retroposed sequences, once inserted in "normal" non-coding DNA, mutate just
like "normal" non-coding DNA. In such a sequence analyses (in contrast to the
clear-cut presence/absence information content of retroposon insertions), you
can expect to see the same problems ("bad behavior" of Coliiformes, short
internodes, long branch attraction, bad signal-to-noise ratio, base
composition biases, etc.) as in "normal" sequence analyses of introns.

> PNAS has a new paper about avian extinction at the K-Pg boundary.
> Looks interesting in the news, anyone seen it yet?
http://dml.cmnh.org/2011Sep/msg00104.html

Best regards,
Alex