Recovering the treelike trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis

Journal of Computational Biology

Volumn 20, Issue 2, 2013, Pages 93-112

  Roch, Sebastien ^a,c   Snir, Sagi ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF HAIFA   (Israel)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

lateral gene transfer; phylogenetic reconstruction; quartet reconstruction

Indexed keywords

BACTERIAL GENOME; BACTERIUM; BIOLOGICAL MODEL; CLASSIFICATION; CONFERENCE PAPER; EVOLUTION; GENETICS; HORIZONTAL GENE TRANSFER; PHYLOGENY; STATISTICAL MODEL;

BACTERIA; BIOLOGICAL EVOLUTION; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY;

EID: 84873603321     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0234     Document Type: Conference Paper

References (58)

1. Arvestad, L., Lagergren, J., and Sennblad, B. 2009. The gene evolution model and computing its associated probabilities. J. ACM 56(2), Article 7.
2. Athreya, K.B., and Ney, P.E. 1972. Branching processes. Springer-Verlag, New York. Die Grundlehren der mathematischen Wissenschaften, Band 196.
3. Bandelt, H.-J., and Dress, A. 1986. Reconstructing the shape of a tree from observed dissimilarity data. Adv. Appl. Math. 7, 309-343.
4. Bansal, M.S., Banay, G., Gogarten, J.P., et al. 2011. Detecting highways of horizontal gene transfer. J. Comput. Biol. 18, 1087-1114.
5. Bapteste, E., Susko, E., Leigh, J., et al. 2005. Do orthologous gene phylogenies really support tree-thinking? BMC Evol. Biol. 5, 33.
6. Baum, B. 1992. Combining trees as a way of combining data sets for phylogenetic inference. Taxon 41, 3-10.
7. Beiko, R., Harlow, T., and Ragan, M. 2005. Highways of gene sharing in prokaryotes. Proc. Natl. Acad. Sci. USA 102, 14332-14337.
8. Berry, V., and Gascuel, O. 2001. Inferring evolutionary trees with strong combinatorial evidence. Theor. Comput. Sci. 240, 271-298.
9. Buneman, P. 1971. The recovery of trees from measures of dissimilarity, 387-395 In Hodson, F., Kendall, D., and Tautu, P., eds. Anglo-Romanian Conference on Mathematics in the Archaeological and Historical Sciences, Edinburgh University Press, Mamaia, Romania.
10. Chung, Y., and Ane, C. 2011. Comparing two bayesian methods for gene tree/species tree reconstruction: Simulations with incomplete lineage sorting and horizontal gene transfer. Syst. Biol. 60, 261-275.
11. Csürös, M., and Miklós, I. 2006. A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer. In RECOMB, 206-220.
12. Dagan, T, and Martin, W. 2006. The tree of one percent. Genome Biol. 7, 118.
13. Daskalakis, C., and Roch, S. 2010. Alignment-free phylogenetic reconstruction. In RECOMB, 123-137.
14. Daskalakis, C., Mossel, E., and Roch, S. 2011. Evolutionary trees and the ising model on the bethe lattice: a proof of steel's conjecture. Probab. Theory Rel. 149, 149-189.
15. Degnan, J.H., and Rosenberg, N.A. 2009. Gene tree discordance, phylogenetic inference and the multispecies coa-lescent. Trends Ecol. Evol. 24, 332-340.
16. Delsuc, F., Brinkmann, H., and Philippe, H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6, 361-375.
17. Dewhirst, F.E., Shen, Z., Scimeca, et al. 2005. Discordant 16S and 23S rRNA gene phylogenies for the Genus Helicobacter: Implications for phylogenetic inference and systematics. J. Bacteriol. 187, 6106-6118.
18. Doolittle, W., and Bapteste, E. 2007. Pattern pluralism and the tree of life hypothesis. Proc. Natl. Acad. Sci. USA 104, 2043-2049.
19. Eisen, J.A., and Fraser, C.M. 2003. Phylogenomics: Intersection of evolution and genomics. Science 300, 1706-1707.
20. Erdös, P.L., Steel, M.A., Székely, L.A., et al. 1999a. A few logs suffice to build (almost) all trees (part 1). Random Struct. Algor., 14, 153-184.
21. Erdös, P.L., Steel, M.A., Székely, L.A., et al. 1999b. A few logs suffice to build (almost) all trees (part 2). Theor. Comput. Sci. 221, 77-118.
22. Galtier, N. 2007. A model of horizontal gene transfer and the bacterial phylogeny problem. Syst. Biol. 56, 633-642.
23. Galtier, N., and Daubin, V. 2008. Dealing with incongruence in phylogenomic analyses. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363, 4023-4029.
24. Ge, F., Wang, L., and Kim, J. 2005. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol. 3, e316.
25. Gogarten, J.P., Doolittle, W.F., and Lawrence, J.G. 2002. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19, 2226-2238.
26. Gogarten, J.P., and Townsend, J.P. 2005. Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Micro. 3, 679-687.
27. Huson, D.H., Rupp, R., and Scornavacca, C. 2010. Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, Cambridge.
28. Jin, G., Nakhleh, L., Snir, S., et al. 2006. Maximum likelihood of phylogenetic networks. Bioinformatics 22, 2604-11.
29. Jin, G., Nakhleh, L., Snir, S., et al. 2009. Parsimony score of phylogenetic networks: Hardness results and a linear-time heuristic. IEEE/ACM Trans. Comput. Biology Bioinform. 6, 495-505.
30. Joly, S., McLenachan, P.A., and Lockhart, P.J. 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am. Nat. 174, E54-E70.
31. Kim, J., and Salisbury, B.A. 2001. A tree obscured by vines: Horizontal gene transfer and the median tree method of estimating species phylogeny. In Pacific Symposium on Biocomputing, 571-582.
32. Koonin, E. 2007. The biological big bang model for the major transitions in evolution. Biol. Direct 2, 21.
33. Koonin, E.V., Puigbo, P., and Wolf, Y.I. 2011. Comparison of phylogenetic trees and search for a central trend in the forest of life. J. Comput. Biol. 18, 917-924.
34. Kubatko, L.S. 2009. Identifying hybridization events in the presence of coalescence via model selection. Syst. Biol. 58, 478-488.
35. Lindvall, T. 1992. Lectures on the Coupling Method. Wiley, New York.
36. Maddison, W.P. 1997. Gene trees in species trees. Syst. Biol. 46, 523-536.
37. Meng, C., and Kubatko, L.S. 2009. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. Theor. Popul. Biol. 75, 35-45.
38. Mossel, E. 2004. Phase transitions in phylogeny. Trans. Amer. Math. Soc. 356, 2379-2404.
39. Motwani, R., and Raghavan, P. 1995. Randomized algorithms. Cambridge University Press, Cambridge.
40. Puigbo, P., Wolf, Y., and Koonin, E. 2009. Search for a 'tree of life' in the thicket of the phylogenetic forest. J. Biol. 8, 59.
41. Puigbo, P., Wolf, Y.I., and Koonin, E.V. 2010. The tree and net components of prokaryote evolution. Genome Biol. Evol. 2, 745-756.
42. Ragan, M. 1992. Matrix representation in reconstructing phylogenetic-relationships among the eukaryotes. Biosystems 28, 47-55.
43. Ragan, M.A., and Beiko, R.G. 2009. Lateral genetic transfer: open issues. Philos. Trans. R. Soc. Lond. B Biol. Sci. 364, 2241-2251.
44. Rannala, B., and Yang, Z. 1996. Probability distribution of molecular evolutionary trees: A new method of phyloge-netic inference. J. Mol. Evol. 43, 304-311.
45. Roch, S., and Snir, S. 2012. Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis. In RECOMB, 224-238.
46. Schouls, L.M., Schot, C.S., and Jacobs, J.A. 2003. Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. J. Bacteriol. 185, 7241-7246.
47. Semple, C., and Steel, M. 2003. Phylogenetics. Vol. 22 in Mathematics and its Applications series. Oxford University Press, New York.
48. Smets, B.F., and Barkay, T. 2005. Horizontal gene transfer: perspectives at a crossroads of scientific disciplines. Nat. Rev. Micro. 3, 675-678.
49. Snir, S., and Rao, S. 2010. Quartets maxcut: A divide and conquer quartets algorithm. IEEE/ACM Trans. Comput. Biology Bioinform. 7, 704-718.
50. Snir, S., and Rao, S. 2012. Quartet maxcut: A fast algorithm for amalgamating quartet trees. Mol. Phylogenet. Evol. 62, 1-8.
51. Steel, M. 1992. The complexity of reconstructing trees from qualitative characters and subtress. J. Classif. 9, 91-116.
52. Suchard, M.A. 2005. Stochastic models for horizontal gene transfer. Genetics 170, 419-431.
53. Than, C., Ruths, D., Innan, H., et al. 2007. Confounding factors in hgt detection: Statistical error, coalescent effects, and multiple solutions. J. Comput. Biol. 14, 517-535.
54. van Berkum, P., Terefework, Z., Paulin, L., et al. 2003. Discordant phylogenies within the rrn loci of rhizobia. J. Bacteriol. 185, 2988-2998.
55. Yap, W.H., Zhang, Z., and Wang, Y. 1999. Distinct types of rrna operons exist in the genome of the Actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J. Bacteriol. 181, 5201-5209.
56. Yu, Y., Than, C., Degnan, J.H., et al. 2011. Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Syst. Biol. 60, 138-149.
57. Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., et al. 2006. Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. Genome Res. 16, 1099-1108.
58. Zhaxybayeva, O., Lapierre, P., and Gogarten, J. 2004. Genome mosaicism and organismal lineages. Trends Genet. 20, 254-260.