Cladistics paper - comments please

[gkw@amnet.net.au]

The most recent issue of PLoS Computational Biology has a paper
http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030051
on the reliability and accuracy of methods used to assess phylogenetic trees.
Abstract:
Metrics of phylogenetic tree reliability, such as parametric bootstrap 
percentages or Bayesian posterior probabilities, represent internal 
measures of the topological reproducibility of a phylogenetic tree, while 
the recently introduced aLRT (approximate likelihood ratio test) assesses 
the likelihood that a branch exists on a maximum-likelihood tree. Although 
those values are often equated with phylogenetic tree accuracy, they do not 
necessarily estimate how well a reconstructed phylogeny represents 
cladistic relationships that actually exist in nature. The authors have 
therefore attempted to quantify how well bootstrap percentages, posterior 
probabilities, and aLRT measures reflect the probability that a deduced 
phylogenetic clade is present in a known phylogeny. The authors simulated 
the evolution of bacterial genes of varying lengths under biologically 
realistic conditions, and reconstructed those known phylogenies using both 
maximum likelihood and Bayesian methods. Then, they measured how frequently 
clades in the reconstructed trees exhibiting particular bootstrap 
percentages, aLRT values, or posterior probabilities were found in the true 
trees. The authors have observed that none of these values correlate with 
the probability that a given clade is present in the known phylogeny. The 
major conclusion is that none of the measures provide any information about 
the likelihood that an individual clade actually exists. It is also found 
that the mean of all clade support values on a tree closely reflects the 
average proportion of all clades that have been assigned correctly, and is 
thus a good representation of the overall accuracy of a phylogenetic tree.

My understanding of cladistics is too weak to properly evaluate this paper, 
so I would be very interested in the opinions of list members who do 
understand as to the findings and their applicability (if any), to the 
methodology and interpretation of dinosaur phylogenetic trees, particularly 
with regard to the ability of such trees to accurately predict "real" 
relationships.
thanks
Graeme Worth