Research Article: Invariant based quartet puzzling

Date Published: December 6, 2012

Publisher: BioMed Central

Author(s): Joseph P Rusinko, Brian Hipp.


First proposed by Cavender and Felsenstein, and Lake, invariant based algorithms for phylogenetic reconstruction were widely dismissed by practicing biologists because invariants were perceived to have limited accuracy in constructing trees based on DNA sequences of reasonable length. Recent developments by algebraic geometers have led to the construction of lists of invariants which have been demonstrated to be more accurate on small sequences, but were limited in that they could only be used for trees with small numbers of taxa. We have developed and tested an invariant based quartet puzzling algorithm which is accurate and efficient for biologically reasonable data sets.

We found that our algorithm outperforms Maximum Likelihood based quartet puzzling on data sets simulated with low to medium evolutionary rates. For faster rates of evolution, invariant based quartet puzzling is reasonable but less effective than maximum likelihood based puzzling.

This is a proof of concept algorithm which is not intended to replace existing reconstruction algorithms. Rather, the conclusion is that when seeking solutions to a new wave of phylogenetic problems (super tree algorithms, gene vs. species tree, mixture models), invariant based methods should be considered. This article demonstrates that invariants are a practical, reasonable and flexible source for reconstruction techniques.

Partial Text

Given that ML models are known to reconstruct the correct quartet trees with very high accuracy, the fact that BSI-puzzling performs comparably with ML-puzzling in most circumstances is somewhat surprising and encouraging. We see this as evidence that invariant based models of reconstruction may play an important role in practical phylogenetic reconstruction in addition to the role they currently play in helping to understand the theoretical possibilities of phylogenetic reconstruction problems

The authors declare that they have no competing interests.

JR designed the algorithm and simulation studies. BH designed and tested the software. Both authors drafted the manuscript. Both authors read and approved the final manuscript.




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