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Coelurosaurian phylogeny: model-based methods and parsimony



A new paper that may be of interest to the list:

Spencer MR, Wilberg EW 2013 Efficacy or convenience? Model-based
approaches to phylogeny estimation using morphological data.
Cladistics doi:10.1111/cla.12018

Model-based approaches (e.g. maximum likelihood, Bayesian inference)
are widely used with molecular data, where they might be more
appropriate than maximum parsimony for estimating phylogenies under
various models of molecular evolution. Recently, there has been an
increase in the application of model-based approaches with
morphological (mainly fossil) data; however, there is some doubt as to
the effectiveness of the model of morphological evolution. The input
parameters (prior probabilities) for the model are unclear,
particularly when concerned with unobserved character states. Despite
this, some systematists are suggesting superiority of these
model-based methods over maximum parsimony based on, for example,
increased resolution or, in the current study, the preferred
phylogenetic placement of an iconic taxon. Here, we revisit a recently
published analysis implying such superiority and document the
discrepancies between parsimony-based and model-based approaches to
phylogeny estimation. We find that although some taxa are shifted back
to their "traditional" phylogenetic placement, other clades are
disturbed. The model-based phylogenies are better resolved; however,
due to the lack of an appropriate model of morphological evolution,
the increase in resolving power is probably not meaningful. Similarly,
some of the preferred phylogenetic positions of taxa, particularly of
labile taxa such as _Archaeopteryx_, are based solely on analyses
employing maximum parsimony as the optimality criterion. Poor
resolution and labile taxa indicate a need for further examination of
the morphology and not a change in method.


Of course, since it's published in _Cladistics_, certain things are to
be expected (there is an obvious effort to play down the well-known
drawbacks of parsimony, such as its susceptibility to long-branch
attraction), but overall it's a pretty decent review of the subject.
The authors run an implied-weighting analysis of Xu et al.'s (2011)
dataset, and the results are less controversial than in the previous
analyses of the same matrix (Xu et al. 2011; Lee & Worthy 2011):
_Archaeopteryx_ is recovered as an avialan and tyrannosauroids are
monophyletic. _Haplocheirus_ is outside _Maniraptoriformes_, though.


*Refs:*

Lee MSY, Worthy TH 2011 Likelihood reinstates _Archaeopteryx_ as a
primitive bird. Biol Lett 8(2): 299-303

Xu X, You H-L, Du K, Han F-L 2011 An Archaeopteryx-like theropod from
China and the origin of Avialae. Nature 475(7357): 465-70

-- 
David Černý