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Archaeopteryx as bird paper (free pdf)

From: Ben Creisler

The new Archaetopteryx paper in Biology Letters has been posted online and
the pdf can be downloaded for free:

Michael S. Y. Lee and Trevor H. Worthy (2011) 
Likelihood reinstates Archaeopteryx as a primitive bird. 
Biology Letters (advance online publication)
doi: 10.1098/rsbl.2011.0884 
free pdf:

The widespread view that Archaeopteryx was a primitive (basal) bird has
been recently challenged by a comprehensive phylogenetic analysis that
placed Archaeopteryx with deinonychosaurian theropods. The new phylogeny
suggested that typical bird flight (powered by the front limbs only) either
evolved at least twice, or was lost/modified in some deinonychosaurs.
However, this parsimony-based result was acknowledged to be weakly
supported. Maximum-likelihood and related Bayesian methods applied to the
same dataset yield a different and more orthodox result: Archaeopteryx is
restored as a basal bird with bootstrap frequency of 73 per cent and
posterior probability of 1. These results are consistent with a single
origin of typical (forelimb-powered) bird flight. The
Archaeopteryx?deinonychosaur clade retrieved by parsimony is supported by
more characters (which are on average more homoplasious), whereas the
Archaeopteryx?bird clade retrieved by likelihood-based methods is supported
by fewer characters (but on average less homoplasious). Both positions for
Archaeopteryx remain plausible, highlighting the hazy boundary between
birds and advanced theropods. These results also suggest that
likelihood-based methods (in addition to parsimony) can be useful in
morphological phylogenetics. 

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