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Archaeopteryx and paravian phylogenetic analyses

From: Ben Creisler

A new online paper:

Xing Xu & Diego Pol (2013)
Archaeopteryx, paravian phylogenetic analyses, and the use of
probability-based methods for palaeontological datasets.
Journal of Systematic Palaeontology (advance online publication)

Archaeopteryx, which has often been considered the earliest avialan,
is an iconic species, central to our understanding of bird origins.
However, a recent parsimony-based phylogenetic study shifted its
position from within Avialae, the group that contains modern birds, to
Deinonychosauria, the sister-taxon to Avialae. Subsequently,
probability-based methods were applied to the same dataset, restoring
Archaeopteryx to basal Avialae, suggesting these methods should be
used more often in palaeontological studies. Here we review two key
issues: arguments recently advocated for the usefulness of
probability-based methodologies in the phylogenetic reconstruction of
basal birds and their close relatives, and support for different
phylogenetic hypotheses. Our analysis demonstrates that Archaeopteryx
represents a challenging taxon to place in the phylogenetic tree, but
recent discoveries of derived theropods including basal avialans
provide increased support for the deinonychosaurian affinities of
Archaeopteryx. Most importantly, we underscore that methodological
choices should be based on the adequacy of the assumptions for
particular kinds of data rather than on the recovery of preferred or
generally accepted topologies, and that certain probability methods
should be interpreted with caution as they can grossly overestimate
character support.