A survey of combinatorial methods for phylogenetic networks

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 23-35

  Huson, Daniel H ^a   Scornavacca, Celine ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

Combinatorics; Molecular; Networks; Phylogeny; Reticulate events

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; HUMAN; MOLECULAR EVOLUTION; PHYLOGENY;

ANIMALS; EVOLUTION, MOLECULAR; HUMANS; MODELS, GENETIC; PHYLOGENY;

EID: 79954427560     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evq077     Document Type: Review

References (75)

1. Bandelt H-J. 1994. Phylogenetic networks. Verhandlungen des Naturwissenschaftlichen Vereins in Hamburg. 34:51-71.
2. Bandelt H-J, Dress A. 1993. A relational approach to split decomposition. In: Opitz O, Lausen B, Klar R, editors. Information and classification. Berlin (Germany): Springer. pp. 123-131.
3. Bandelt H-J, Dress AWM. 1992. A canonical decomposition theory for metrics on a finite set. Adv Math. 92:47-105.
4. Bandelt H-J, Forster P, Rö hl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16:37-48. (Pubitemid 29024937)
5. Bandelt HJ, Forster P, Sykes BC, Richards MB. 1995. Mitochondrial portraits of human population using median networks. Genetics. 141(2):743-753.
6. Baroni M, Semple C, Steel M. 2006. Hybrids in real time. Syst Biol. 55(1):46-56.
7. Bokhari S, Janies D. 2008. Reassortment networks for investigating the evolution of segmented viruses. IEEE/ACM Trans Comput Biol Bioinform. 7(2):288-298.
8. Bordewich M, Linz S, St. John K, Semple C. 2007. A reduction algorithm for computing the hybridization number of two trees. Evol Bioinform. 3:86-98.
9. Bordewich M, Semple C. 2007. Computing the minimum number of hybridisation events for a consistent evolutionary history. Discrete Appl Math. 155(8):914-928. (Pubitemid 46436152)
10. Bryant D, Moulton V. 2004. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol. 21(2):255-265. (Pubitemid 38314614)
11. Buneman P. 1971. The recovery of trees from measures of dissimilarity. In: Hodson FR, Kendall DG, Tautu P, editors. Mathematics in the archaeological and historical sciences. Edinburgh: Edinburgh University Press. pp. 387-395.
12. Casado F, Bonvicino CR, Seuanez HN. 2007. Phylogeographic analyses of Callicebus lugens (Platyrrhini, Primates). J Hered. 98(1):88-92. (Pubitemid 47355534)
13. Castrucci M, et al. 1993. Genetic reassortment between avian and human influenza A viruses in Italian pigs. Virology. 193(1): 503-506.
14. Choy C, Jansson J, Sadakane K, Sung W-K. 2005. Computing the maximum agreement of phylogenetic networks. Theor. Comput. Sci. 335(1):93-107. (Pubitemid 40574419)
15. Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Mol Ecol. 9:1657-1659.
16. Delwiche CF, Palmer JD. 1996. Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol Biol Evol. 13:873-882. (Pubitemid 26240091)
17. Dessimoz C, Margadant D, Gonnet GH. 2008. DLIGHT-lateral gene transfer detection using pairwise evolutionary distances in a statistical framework. In: Vingron, Martin; Wong, Limsoon, editors. RECOMB 2008. Research in Computational Molecular Biology: Proceedings of the 12th International Conference on Research in Computational Molecular Biology (RECOMB), Volume 4955 of LNCS; Singapore. Berlin (Heidelberg): Springer. pp. 315-330.
18. Disotell T. 2003. Discovering human history from stomach bacteria. Genome Biol. 4(5):213.
19. Doolittle WF. 1999. Phylogenetic classification and the Universal Tree. Science. 284:2124-2128. (Pubitemid 29297466)
20. Doyon J, et al. 2010. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. In: Tannier, Eric, Editors. RECOMB-CG 2010. Research in Computational Molecular Biology: Proceedings of the 14th International Conference on Research in Computational Molecular Biology (RECOMB), Volume 6398 of LNCS. Ottawa, Canada. Berlin (Heidelberg): Springer. p.*
21. Dress AWM, Huson DH. 2004. Constructing splits graphs. IEEE/ACM Trans Comput Biol Bioinform. 1(3):109-115. (Pubitemid 40325598)
22. Ebersberger I, et al. 2007. Mapping human genetic ancestry. Mol Biol Evol. 24(10):2266-2276. (Pubitemid 47574726)
23. Excoffier L, Smouse P. 1994. Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics. 136:343-359. (Pubitemid 24016698)
24. Grass Phylogeny Working Group. 2001. Phylogeny and subfamilial classification of the grasses (Poaceae). Ann Mo Bot Gard. 88(3):373-457.
25. Griffiths RC, Marjoram P. 1996. Ancestral inference from samples of DNA sequences with recombination. J Comput Biol. 3:479-502. (Pubitemid 27063414)
26. Griffiths RC, Marjoram P. 1997. An ancestral recombination graph. In: Donnelly P, Tavaré S, editors. Progress in population genetics and human evolution, volume 87 of IMA volumes of mathematics and its applications. Berlin (Germany): Springer. p. 257-270.
27. Grünewald SKF, Dress AWM, Moulton V. 2007. QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets. Mol Biol Evol. 24(2):532-538. (Pubitemid 46204385)
28. Gusfield D. 2005. Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination. J Comput Syst Sci. 70:381-398. (Pubitemid 40391416)
29. Gusfield D, Bansal V. 2005. A fundamental decomposition theory for phylogenetic networks and incompatible characters. In: Miyano S, et al., editors. RECOMB 2005. Research in Computational Molecular Biology: Proceedings of the Ninth International Conference on Research in Computational Molecular Biology (RECOMB), Volume 3500 of LNCS; Cambridge: Berlin (Heidelberg): Springer. p. 217-232. (Pubitemid 41420666)
30. Gusfield D, Bansal V, Bafna V, Song YS. 2007. A decomposition theory for phylogenetic networks and incompatible characters. J Comput Biol. 14(10):1247-1272. (Pubitemid 350249340)
31. Gusfield D, Eddhu S, Langley C. 2003. Efficient reconstruction of phylogenetic networks with constrained recombinations. In: CSB 2003. Proceedings of the IEEE Computer Society Conference on Bioinformatics (CSB); Stanford. Los Alamitos (CA): IEEE Computer Society. p. 363.
32. Hein J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J Mol Evol. 36:396-405. (Pubitemid 23121907)
33. Hein J, Schierup MH, Wiuf C. 2005. Gene genealogies, variation and evolution: a primer in coalescent theory. Oxford: Oxford University Press.
34. Holland B, Huber K, Moulton V, Lockhart PJ. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol Biol Evol. 21:1459-1461. (Pubitemid 38823749)
35. Holland B, Moulton V. 2003. Consensus networks: a method for visualizing incompatibilities in collections of trees. In: Benson G, Page R, editors. Benson, Gary, Page, Roderic, editors. WABI 2003; Budapest, Hungary. Heidelberg (Germany). Algorithms in bioinformatics. Proceedings of the Third International Workshop on Algorithms in Bioinformatics (WABI), Volume 2812. Springer. p. 165-176.
36. Huber KT, Oxelman B, Lott M, Moulton V. 2006. Reconstructing the evolutionary history of polyploids from multilabeled trees. Mol Biol Evol. 23(9):1784-1791. (Pubitemid 44309772)
37. Huson D, Rupp R. 2008. Summarizing multiple gene trees using cluster networks. Crandall, Keith, Lagergren, Jens, editors. WABI 2008; Budapest, Hungary. Heidelberg (Germany). Algorithms in Bioinformatics: Proceedings of the Eighth International Workshop on Algorithms in Bioinformatics (WABI), Volume 5251 of LNBI. p. 211-225.
38. Huson D, Scornavacca C. 2011. Dendroscope 2-a program for computing and drawing rooted phylogenetic trees and networks [Internet]. Software Available from: www.dendroscope.org.
39. Huson DH. 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics. 14(10):68-73. (Pubitemid 28397727)
40. Huson DH. 2007. Split networks and reticulate networks. In: Gascuel O, Steel MA, editors. Reconstructing evolution: new mathematical and computational advances. Oxford: Oxford University Press. p. 247-276.
41. Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23:254-267. (Pubitemid 43100040)
42. Huson DH, Dezulian T, Klö pper T, Steel MA. 2004. Phylogenetic supernetworks from partial trees. IEEE/ACM Trans Comput Biol Bioinform. 1(4):151-158.
43. Huson DH, Klö pper T, Lockhart PJ, Steel MA. 2005. Reconstruction of reticulate networks from gene trees. In: Miyano S, et al., editors. RECOMB 2005. Research in Computational Molecular Biology: Proceedings of the Ninth International Conference on Research in Computational Molecular Biology (RECOMB), Volume 3500 of LNCS; Cambridge, USA; Berlin (Heidelberg): Springer. p. 233-249. (Pubitemid 41420667)
44. Huson DH, Klö pper TH. 2005. Computing recombination networks from binary sequences. Bioinformatics. 21(Suppl 2):ii159-ii165. (Pubitemid 41535443)
45. Huson DH, Rupp R, Berry V, Gambette P, Paul C. 2009. Computing galled networks from real data. Bioinformatics. 25(12):i85-i93.
46. Huson DH, Rupp R, Scornavacca C. 2011. Phylogenetic networks: concepts, algorithms and applications. Cambridge, UK: Cambridge University Press.
47. Jansson J, Sung W-K. 2006. Inferring a level-1 phylogenetic network from a dense set of rooted triplets. Theor. Comput. Sci. 363(1):60-68. (Pubitemid 44508784)
48. Jin G, Nakhleh L, Snir S, Tuller T. 2006a. Efficient parsimony-based methods for phylogenetic network reconstruction. ECCB 2006. Proceedings of the 5th European Conference on Computational Biology (ECCB), Volume 23 of Bioinformatics; Eilat, Israel. Oxford, UK. p. e123-e128.
49. Jin G, Nakhleh L, Snir S, Tuller T. 2006b. Maximum likelihood of phylogenetic networks. Bioinformatics. 22(21):2604-2611. (Pubitemid 44642598)
50. Jin G, Nakhleh L, Snir S, Tuller T. 2007. Inferring phylogenetic networks by the maximum parsimony criterion: a case study. Mol Biol Evol. 24(1):324-337. (Pubitemid 46026305)
51. Kanj IA, Nakhleh L, Than C, Xia G. 2008. Seeing the trees and their branches in the network is hard. Theor Comput Sci. 401(1-3):153-164.
52. Kivisild T, et al. 1999. Deep common ancestry of Indian and western Eurasian mtDNA lineages. Curr Biol. 9:1331-1334.
53. Linder CR, Rieseberg LH. 2004. Reconstructing patterns of reticulate evolution in plants. Am J Bot. 91:1700-1708. (Pubitemid 43193727)
54. Maddison WP. 1997. Gene trees in species trees. Syst Biol. 46(3):523-536.
55. Makarenkov V. 2001. T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics. 17(7):664-668. (Pubitemid 32707593)
56. Morrison D. 2005. Networks in phylogenetic analysis: new tools for population biology. Int J Parasitol. 35(5):567-582.
57. Morrison D. 2010. Phylogenetic networks in systematic biology (and elsewhere). In: Mohan R, editor. Research advances in systematic biology. Trivandrum (India): Global Research Network. p. 1-48.
58. O'Donnell K, Kistler H, Tacke B, Casper H. 2000. Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of fusarium graminearum, the fungus causing wheat scab. Proc Natl Acad Sci U S A. 97(14):7905-7910. (Pubitemid 30460746)
59. Parida L, Melé M, Calafell F, Bertranpetit J. 2008. Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns. J Comput Biol. 15(9):1133-1153.
60. Planet PJ, Kachlany SC, Fine DH, DeSalle R, Figurski DH. 2003. The widespread colonization island of Actinobacillus actinomycetemcomitans. Nat Genet. 34:193-198. (Pubitemid 36666931)
61. Rieseberg LH. 1997. Hybrid origins of plant species. Annu Rev Ecol Evol Syst. 28:359-389. (Pubitemid 28012297)
62. Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 425:798-804. (Pubitemid 37355944)
63. Sneath P. 1975. Cladistic representation of reticulate evolution. Syst Zool. 24(3):360-368.
64. Song YS. 2006. A concise necessary and sufficient condition for the existence of a galled-tree. IEEE/ACM Trans Comput Biol Bioinform. 3(2):186-191.
65. Song YS, Hein J. 2005. Constructing minimal ancestral recombination graphs. J Comput Biol. 12(2):147-169. (Pubitemid 40444585)
66. Song YS, Wu Y, Gusfield D. 2005. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. Bioinformatics. 21:413-422.
67. Syvanen M. 1985. Cross-species gene transfer; implications for a new theory of evolution. J Theor Biol. 112(2):333-343. (Pubitemid 15160996)
68. Templeton AR, Crandall KA, Sing CF. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics. 132:619-633.
69. To T-H, Habib M. 2009. Level-k phylogenetic networks are constructable from a dense triplet set in polynomial time. Combinatorial Pattern Matching. In: Kucherov, Gregory, Ukkonen, Esko, editors. CPM 2009. Proceeding of the 20th Annual Symposium Combinatorial Pattern Matching (CPM), Volume 5577 of LNCS Lille, France: Heidelberg (Germany). p. 275-288.
70. Tofigh A, Hallet M, Lagergren J. 2010. Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Trans Comput Biol Bioinform. 99.
71. van Iersel L, Kelk S, Rupp R, Huson D. 2010. Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters. ISMB 2010. Proceedings of the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Volume 26 of Bioinformatics; Global Boston, USA. Oxford (UK). p. i124-i131.
72. Wagele J, Mayer C. 2007. Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects. BMC Evol Biol. 7(1):147.
73. Wang L, Ma B, Li M. 2000. Fixed topology alignment with recombination. Discrete Applied Mathematics. 104(1-3):281-300.
74. Whidden C, Beiko R, Zeh N. 2010. Fast FPT algorithms for computing rooted agreement forests: theory and experiments. In: Festa, Paola, editors. SEA 2010. Proceedings of the 9th International Symposium on Experimental Algorithms (SEA), Volume 6049 of LNCS. Naples, Italy: Heidelberg (Germany). p. 141-153.
75. Whitfield J, Cameron S, Huson D, Steel M. 2008. Filtered Z-closure supernetworks for extracting and visualizing recurrent signal from incongruent gene trees. Syst Biol. 57(6):939-947.