On Tue, Jun 27, 2006 at 01:26:30PM +1000, Graham Turner wrote:
> Surely this study should be relegated to the junk science bin. Taxonomic
> classification is an artificial construct designed to fit animals into
> little boxes with neat labels. Trying to analyse this system probably
> says more about taxonomists than the ecology of birds.
I've appended most of the part of the paper that discusses phylogenetic
framework. Personally, I think this type of quantitative analsyis is
very intersting and is likely will to yield good explanations for many
ecological traits of birds.
Andrew
The main phylogeny used in this study was the DNA-DNA hybridization-based
phylogeny of Sibley and Ahlquist (1990). We acknowledge that there are
valid concerns regarding the methodology used by Sibley and Ahlquist
and the resulting tree topology (refs). However, theirs remains
the only phylogeny across the majority of bird families that includes
branch lengths. To examine whether the inferences we have drawn using
this phylogenetic framework could be biased because of error in the
phylogeny, we have also analyzed the data using a second phylogeny of
passerine birds (Barker et al. 2004). For the passerines, we used 100
phylogenies that had been reconstructed on the basis of pseudoreplicate
data sets of sequences from RAG-1 and RAG-2 nuclear genes and that had
been subjected to rate smoothing using penalized likelihood ...
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