A comparison of phylogenetic network methods using computer simulation.
BACKGROUND
We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper bound, median-joining, reduced median joining and minimum spanning network) compared to standard tree approaches, (neighbor-joining and maximum parsimony) in the presence and absence of recombination.


RESULTS
In the absence of recombination, all methods recovered the correct topology and branch lengths nearly all of the time when the substitution rate was low, except for minimum spanning networks, which did considerably worse. At a higher substitution rate, maximum parsimony and union of maximum parsimony trees were the most accurate. With recombination, the ability to infer the correct topology was halved for all methods and no method could accurately estimate branch lengths.


CONCLUSIONS
Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel algorithms developed in the future.
Woolley
Steven M
SM
Computational Biology Program, Washington University School of Medicine, St. Louis, Missouri, United States of America. stevenwoolley@wustl.edu
Posada
David
D
Crandall
Keith A
KA
D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D003196:Computer Graphics; D003198:Computer Simulation; D019143:Evolution, Molecular; D005189:False Positive Reactions; D005821:Genetic Techniques; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D011995:Recombination, Genetic; D015203:Reproducibility of Results; D016415:Sequence Alignment