a comparison of phylogenetic network methods using computer simulation使用计算机模拟系统网络的比较方法.pdfVIP

A Comparison of Phylogenetic Network Methods Using Computer Simulation 1 2 3 Steven M. Woolley *, David Posada , Keith A. Crandall ´ ´ 1 Computational Biology Program, Washington University School of Medicine, St. Louis, Missouri, United States of America, 2 Departamento de Bioquımica, Genetica e ´ Inmunologıa, Facultad de Ciencias, Universidad de Vigo, Vigo, Spain, 3 Department of Biology, Brigham Young University, Provo, Utah, United States of America Abstract 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. Principal Findings: 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 dete