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Re: Mesozoic roots of parrots and passerine birds
> This paper also propose the
> split between falcons and hawks:
> A Phylogenomic Study of Birds Reveals Their Evolutionary
> Shannon J. Hackett, et al. Science 320, 1763
> (2008); DOI:
This and the others cited all use beta-fibrinogen intron 7 data, which is
suspected to carry a strong bogus phylogenetic signal. They cannot be taken at
face value, until the data have been reanalyzed.
See here: http://www.biomedcentral.com/1471-2148/8/20
(Give me some 15 more months, and I'll probably have done that ;-) )
Same problem as with transposons: indels were once believed to be entirely
nonhomoplasious, but they are apparently anything but that. I don't know which
it was, but one mammal study found a signal-noise ratio of 1.5 among about a
If you look at Supplement 1 of the present paper, you'll find that support for
Eufalconimorphae rests mainly on the J-class retroposons, and that comparison
across taxa is otherwise highly incomplete. It looks as if they took the
retroposon set of the zebrafinch and sequenced other birds until they had
enough data to "prove" Eufalconimorphae. But verificationism hasn't been an
acceptable scientific methodology 100 years ago! You need to look for data
which REFUTE your hypothesis, and if you can find none, THEN you're cool. (It
is also interesting that their data does not support monophyly of either
Cypselomorphae and Mirandornithes)
The bottom line is that non-sequence molecular data presents similar problems
as sequence data turned out to be 20 years ago (see e.g.
http://www.springerlink.com/content/1l5c766g0cptp6fv/). But while we have by
now worked out the source of bias and bad SNR in sequence data, the use of
non-sequence molecular data is too recent to have done so. In 10 years, we can
use such markers and really yield robust results, but until then it is mnrely
clear that these genomic events are not as random as they seem. So one *can* of
course use the data, but "robust" and "definite" are terms one should not use
to describe the results. Except if the SNR is 0 (i.e. the data are just random
noise) - and possibly even then -, today's phylogenetic analyses WILL ALWAYS
resolve a phylogeny.
See e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577343/ for some of the
current research in this direction. This is about a comparatively
well-understood transposon, yet it took 10 years or more to clarify at least
the basics of its target site preference.
In short, until J-class retroposons are proven to insert at random sites, these
results are evidence but not proof.