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Re: Taxon sampling in cladistic analyses - some results from DNA



Hi!

evelyn sobielski schrieb am 2011-09-13:
> [...]
> For the following, if I say "robust" I mean "including resilience to
> changes in taxon sample". Otherwise I say "strong" or similar. The
> two are most assuredly NOT the same.
> (The retroposon signal for Eufaconimorphae is *strong*. Its
> robustness has not been tested at all, and this is is why I think the
> paper should not have been published yet.)
;-) Please, have a close look at the retroposon data (character matrix in
Supplementary Table S1 of the paper) - as there is no conflicting signal in
the data set regarding the monophyly of Eufalconimorphae, you can remove as
many taxa as you like and still get the same result.

> Mousebirds, then, are perhaps the #1 avian taxon which can only be
> permitted into a mol analysis to test for destabilizing effects.
> Until the reason for their odd behavior is known, it is dangerous to
> include them "for completeness". Furthermore I do not think that
> until this has happened, it is impossible to resolve their affinities
> based on molecular data. All you will end up with is a huge load of
> "phylogenetic signal" that may almost all be invented whole cloth.
Thankfully, in retroposon phylogenies, one doesn't have the problem of long
branch attraction (LBA) or destabilizing effects when adding certain taxa. In
the light of this, I think it's worth to at least consider that mousebirds
could be the sister taxon of the remaining "landbirds" (Picocoraciae + trogons
+ Accipitriformes sensu lato + owls + seriemas + Eufalconimorphae).
The support is not strong (only 2 retroposon insertions), but as the typical
caveats of sequence analyses (LBA, bad signal to noise ratio, a lot of
homoplasy, etc.) do not apply to retroposon insertions, there seems to be at
least a moderate but clear phylogenetic signal for this hypothesis.

> [...]. you can tell in advance which taxa are
> troublemaker candidates. For molecular analyses, there are obvious
> cases like parrots sister to storks (OCD dataset)
Guess why (so far) only concatenated sequence analyses (of multiple nuclear
genes) have yielded the first congruences in neoavian relationships. Have a
look at the single gene analyses of Ericson et al. (2006, Supplementary
Information) in comparison to their "main" tree. The single gene analyses
yielded some weird results (e.g., Otididae + Turnicidae; Phaethontidae +
Rhynochetidae); their "main" tree didn't (i.e., Turnicidae witin
Charadriiformes, Rhynochetidae sister to Eurypygidae). Thus, the only chance
to accomodate the very low signal content in sequence analyses is to use a lot
of (independently evolving) loci.

> As regards transposable elements, any such analysis has to deal with
> the caveats mentioned in the fallout of the "Pegasoferae" case before
> drawing any conclusions.
This incongruency is most likely caused by incomplete lineage sorting (no type
of molecular data is "immune" to this, thus, the more loci one studies, the
better), given that the internodes at the base of Laurasiatheria are very very
short (quite comparable to the earliest branches of the neoavian radiation).
Nevertheless, Nishihara et al.'s (2006) retroposon support for Pegasoferae is
relatively strong.

> [...]. I am not certain that interspecific variation is markedly
> higher here than interspecific variation. They are called not
> "transposable" without a reason - if you find one at a particular
> position in a particular species, you cannot per se assume it's
> present just the same in the sister *individual* to the one
> sequenced. [...]
Retroposons are not DNA transposons, hence: no "cut and paste".
Additionally, as most retroposon insertions definitely are non-functional
(thus, no selection pressure on the host genome for "acquiring" or "losing"
them at a certain intronic or intergenic locus), the chance of precise
excision or parallel insertion is very very low.
If these two things would not be the case, I'm quite sure that there would be
lots of incongruences within/among retroposon analyses. But after dozens of
studies and hundreds of published retroposon markers (plus tens of thousand
experimentally checked ones) there is no evidence that refutes that retroposon
insertions are almost homoplasy-free. Maybe it's time to trust the work that
has been done in the last fifteen years. :-)

Best regards,
Alex

References:
- Ericson, P. G. P. et al. Diversification of Neoaves: integration of
molecular sequence data and fossils. Biol. Lett. 2, 543–547 (2006).
- Nishihara, H., Hasegawa, M., and Okada, N.: Pegasoferae, an
unexpected mammalian clade revealed by tracking ancient
retroposon insertions. Proc. Natl. Acad. Sci. 103: 9929–9934 (2006).