This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
January-March 2004 (vol. 1 no. 1)
pp. 13-23
ASCII Text
x 
 
Bernard M.E. Moret, Luay Nakhleh, Tandy Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth Timme, "Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 1, pp. 13-23, January-March, 2004.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2004.10,
author = {Bernard M.E. Moret and Luay Nakhleh and Tandy Warnow and C. Randal Linder and Anna Tholse and Anneke Padolina and Jerry Sun and Ruth Timme},
title = {Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {1},
number = {1},
issn = {1545-5963},
year = {2004},
pages = {13-23},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2004.10},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IS - 1
SN - 1545-5963
SP13
EP23
EPD - 13-23
A1 - Bernard M.E. Moret,
A1 - Luay Nakhleh,
A1 - Tandy Warnow,
A1 - C. Randal Linder,
A1 - Anna Tholse,
A1 - Anneke Padolina,
A1 - Jerry Sun,
A1 - Ruth Timme,
PY - 2004
KW - Phylogenetic networks
KW - reticulate evolution
KW - error metric
KW - Robinson-Foulds
KW - bipartitions
KW - tripartitions.
VL - 1
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.

[1] L. Addario-Berry, M.T. Hallett, and J. Lagergren, Toward Identifying Lateral Gene Transfer Events Proc. Eighth Pacific Symp. Biocomputing (PSB '03), pp. 279-290, 2003.
[2] H.J. Bandelt and A.W.M. Dress, Split Decomposition: A New and Useful Approach to Phylogenetic Analysis of Distance Data Molecular Phylogenetics and Evolution, vol. 1, pp. 242-252, 1992.
[3] H.J. Bandelt, V. Macaulay, and M.B. Richards, Median Networks: Speedy Construction and Greedy Reduction, One Simulation, and Two Case Studies from Human mtDNA Molecular Phylogenetics and Evolution, vol. 16, pp. 8-28, 2000.
[4] D. Bryant and V. Moulton, NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks Proc. Second Int'l Workshop Algorithms in Bioinformatics (WABI '02), pp. 375-391, 2002.
[5] R.C. Griffiths and P. Marjoram, Ancestral Inference from Samples of DNA Sequences with Recombination J. Computational Biology, vol. 3, pp. 479-502, 1996.
[6] M.T. Hallett and J. Lagergren, New Algorithms for the Duplication-Loss Model Proc. Fourth Ann. Int'l Conf. Computational Molecular Biology (RECOMB '00), pp. 138-146, 2000.
[7] M.T. Hallett and J. Lagergren, Efficient Algorithms for Lateral Gene Transfer Problems Proc. Fifth Ann. Int'l Conf. Computational Molecular Biology (RECOMB '01), pp. 149-156, 2001.
[8] M.T. Hallett, J. Lagergren, and A. Tofigh, Simultaneous Identification of Duplications and Lateral Transfers Proc. Eighth Ann. Int'l Conf. Computational Molecular Biology (RECOMB '04), pp. 347-356, 2004.
[9] D.M. Hillis, J.J. Bull, M.E. White, M.R. Badgett, and I.J. Molineux, Experimental Approaches to Phylogenetic Analysis Systematic Biology, vol. 42, pp. 90-92, 1993.
[10] D.M. Hillis and J.P. Huelsenbeck, Signal, Noise, and Reliability in Molecular Phylogenetic Analyses J. Heredity, vol. 83, pp. 189-195, 1992.
[11] R.R. Hudson, Properties of the Neutral Allele Model with Intergenic Recombination Theoretical Population Biology, vol. 23, pp. 183-201, 1983.
[12] D.H. Huson, SplitsTree: A Program for Analyzing and Visualizing Evolutionary Data Bioinformatics, vol. 14, no. 1, pp. 68-73, 1998.
[13] W.P. Maddison, Gene Trees in Species Trees Systematic Biology, vol. 46, no. 3, pp. 523-536, 1997.
[14] V. Makarenkov, T-REX: Reconstructing and Visualizing Phylogenetic Trees and Reticulation Networks Bioinformatics, vol. 17, no. 7, pp. 664-668, 2001.
[15] V. Makarenkov and P. Legendre, From a Phylogenetic Tree to a Reticulated Network J. Computational Biology, vol. 11, no. 1, pp. 195-212, 2004.
[16] L. Nakhleh, J. Sun, T. Warnow, R. Linder, B.M.E. Moret, and A. Tholse, Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods Proc. Eighth Pacific Symp. Biocomputing (PSB '03), pp. 315-326, 2003.
[17] L. Nakhleh, T. Warnow, and C.R. Linder, Reconstructing Reticulate Evolution in Species Theory and Practice Proc. Eighth Ann. Int'l Conf. Computational Molecular Biology (RECOMB '04), pp. 337-346, 2004.
[18] A. Piccolboni and D. Gusfield, On the Complexity of Fundamental Computational Problems in Pedigree Analysis Technical Report CSE-99-8, UC Davis, Dept. of Computer Science, 1999.
[19] D. Posada and K.A. Crandall, The Effect of Recombination on the Accuracy of Phylogeny Estimation J. Molecular Evolution, vol. 54, no. 3, pp. 396-402, 2002.
[20] D. Posada, K.A. Crandall, and E.C. Holmes, Recombination in Evolutionary Genomics Ann. Rev. Genetics, vol. 36, pp. 75-97, 2002.
[21] L.H. Rieseberg, The Role of Hybridization in Evolution Old Wine in New Skins Am. J. Botany, vol. 82, no. 7, pp. 944-953, 1995.
[22] L.H. Rieseberg, S.J.E. Baird, and K.A. Gardner, Hybridization, Introgression, and Linkage Evolution Plant Molecular Biology, vol. 42, no. 1, pp. 205-224, 2000.
[23] L.H. Rieseberg and R.D. Noyes, Genetic Map-Based Studies of Reticulate Evolution in Plants Trends in Plant Science, vol. 3, no. 7, pp. 254-259, 1998.
[24] D.R. Robinson and L.R. Foulds, Comparison of Phylogenetic Trees Math. Biosciences, vol. 53, pp. 131-147, 1981.
[25] F.J. Rohlf, Phylogenetic Models and Reticulations J. Classification, vol. 17, no. 2, pp. 185-189, 2000.
[26] K. Strimmer and V. Moulton, Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models Molecular Biology and Evolution, vol. 17, pp. 875-881, 2000.
[27] K. Strimmer, C. Wiuf, and V. Moulton, Recombination Analysis Using Directed Graphical Models Molecular Biology and Evolution, vol. 18, no. 1, pp. 97-99, 2001.
[28] D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis, Phylogenetic Inference Molecular Systematics, D.M. Hillis, B.K. Mable, and C. Moritz, eds., pp. 407-514, Sinauer Assoc., 1996.

Index Terms:
Phylogenetic networks, reticulate evolution, error metric, Robinson-Foulds, bipartitions, tripartitions.
Citation:
Bernard M.E. Moret, Luay Nakhleh, Tandy Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth Timme, "Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 1, pp. 13-23, Jan.-March 2004, doi:10.1109/TCBB.2004.10
Usage of this product signifies your acceptance of the Terms of Use.