A Survey of Combinatorial Methods for Phylogenetic Networks

Overview

Journal Genome Biol Evol

Publisher Oxford University Press

Specialties Biology
Genetics
Molecular Biology

Date 2010 Nov 18

PMID 21081312

Citations 59

Authors

Daniel H Huson

Celine Scornavacca

Affiliations

Soon will be listed here.

Abstract

The evolutionary history of a set of species is usually described by a rooted phylogenetic tree. Although it is generally undisputed that bifurcating speciation events and descent with modifications are major forces of evolution, there is a growing belief that reticulate events also have a role to play. Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal gene transfer, or recombination. In this article, we give an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation.

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References

Rokas A, Williams B, King N, Carroll S . Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 2003; 425(6960):798-804. DOI: 10.1038/nature02053. View

Song Y . A concise necessary and sufficient condition for the existence of a galled-tree. IEEE/ACM Trans Comput Biol Bioinform. 2006; 3(2):186-91. DOI: 10.1109/TCBB.2006.15. View

Bandelt H, Forster P, Sykes B, Richards M . Mitochondrial portraits of human populations using median networks. Genetics. 1995; 141(2):743-53. PMC: 1206770. DOI: 10.1093/genetics/141.2.743. View

Bryant D, Moulton V . Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol. 2003; 21(2):255-65. DOI: 10.1093/molbev/msh018. View

Dress A, Huson D . Constructing splits graphs. IEEE/ACM Trans Comput Biol Bioinform. 2006; 1(3):109-15. DOI: 10.1109/TCBB.2004.27. View

Makarenkov V . T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics. 2001; 17(7):664-8. DOI: 10.1093/bioinformatics/17.7.664. View

Planet P, Kachlany S, Fine D, DeSalle R, Figurski D . The Widespread Colonization Island of Actinobacillus actinomycetemcomitans. Nat Genet. 2003; 34(2):193-8. DOI: 10.1038/ng1154. View

Jin G, Nakhleh L, Snir S, Tuller T . Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics. 2007; 23(2):e123-8. DOI: 10.1093/bioinformatics/btl313. View

Grunewald S, Forslund K, Dress A, Moulton V . QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets. Mol Biol Evol. 2006; 24(2):532-8. DOI: 10.1093/molbev/msl180. View

10.

Griffiths R, Marjoram P . Ancestral inference from samples of DNA sequences with recombination. J Comput Biol. 1996; 3(4):479-502. DOI: 10.1089/cmb.1996.3.479. View

11.

Huson D, Dezulian T, Klopper T, Steel M . Phylogenetic super-networks from partial trees. IEEE/ACM Trans Comput Biol Bioinform. 2006; 1(4):151-158. DOI: 10.1109/TCBB.2004.44. View

12.

Bandelt H, Forster P, Rohl A . Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999; 16(1):37-48. DOI: 10.1093/oxfordjournals.molbev.a026036. View

13.

Parida L, Mele M, Calafell F, Bertranpetit J . Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns. J Comput Biol. 2008; 15(9):1133-54. DOI: 10.1089/cmb.2008.0065. View

14.

van Iersel L, Kelk S, Rupp R, Huson D . Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters. Bioinformatics. 2010; 26(12):i124-31. PMC: 2881387. DOI: 10.1093/bioinformatics/btq202. View

15.

Gusfield D, Bansal V, Bafna V, Song Y . A decomposition theory for phylogenetic networks and incompatible characters. J Comput Biol. 2007; 14(10):1247-72. PMC: 2581772. DOI: 10.1089/cmb.2006.0137. View

16.

Doolittle W . Phylogenetic classification and the universal tree. Science. 1999; 284(5423):2124-9. DOI: 10.1126/science.284.5423.2124. View

17.

Song Y, Hein J . Constructing minimal ancestral recombination graphs. J Comput Biol. 2005; 12(2):147-69. DOI: 10.1089/cmb.2005.12.147. View

18.

Gusfield D, Eddhu S, Langley C . Efficient reconstruction of phylogenetic networks with constrained recombination. Proc IEEE Comput Soc Bioinform Conf. 2006; 2:363-74. View

19.

Wagele J, Mayer C . Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects. BMC Evol Biol. 2007; 7:147. PMC: 2040160. DOI: 10.1186/1471-2148-7-147. View

20.

Tofigh A, Hallett M, Lagergren J . Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Trans Comput Biol Bioinform. 2011; 8(2):517-35. DOI: 10.1109/TCBB.2010.14. View