"What is 'long-branch attarction' and how susceptible are the 3 major
methods of phylogenetic reconstruction to it?" 
Thanks a bundle to anyone who can help. 
---SuperNerdGirl



Cladistic parsimony(or maximum parsimony) is a method of phylogenetic
inference in the construction of cladograms. Cladograms are branching
tree like structures used to represent lines of descent based on one or
more evolutionary change(s). Cladistic parsimony is used to support the
hypothesis(es) that require the fewest evolutionary changes. It should
be noted that for some types tree, it will consistantly produce the
wrong results regardless of how much data is collected(This is called
long-branch attraction).

Using computer simulation to generate sequence data for protein
families, we studied the influence of among site rate variation on the
performance of phylogenetic reconstruction. The following methods for
phylogenetic reconstruction were compared: maximum likelihood,
parsimony, and distance-matrix analyses. Three different tree topologies
were used to explore the effect of long branch attraction with data that
incorporated substitution bias and different degrees of among site rate
variation. 

While all methods showed errors due to long branch attraction under
extreme conditions, maximum likelihood was by far the most successful in
accurately resolving deep phylogenies

"It's uncertain whether intelligence has any long term survival value.
Bacteria do quite well with it."

Stephen Hawking
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