Models, algorithms and programs for phylogeny reconciliation

Briefings in Bioinformatics

Volumn 12, Issue 5, 2011, Pages 392-400

  Doyon, Jean Philippe ^a   Ranwez, Vincent ^b   Daubin, Vincent ^c,d   Berry, Vincent ^e  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b ISEM Laboratory   (France)

^c UNIVERSITÉ DE LYON   (France)

^d LABORATOIRE DE BIOMÉTRIE ET BIOLOGIE EVOLUTIVE   (France)

^e UNIV MONTPELLIER   (France)

Author keywords

Gene duplication; Lateral gene transfer; Loss; Parsimony; Phylogeny; Probability; Reconciliation

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; GENE DUPLICATION; GENOME; GENOMICS; HORIZONTAL GENE TRANSFER; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; SPECIES DIFFERENCE;

ALGORITHMS; ANIMALS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE TRANSFER, HORIZONTAL; GENOME; GENOMICS; HUMANS; MODELS, GENETIC; PHYLOGENY; SPECIES SPECIFICITY;

EID: 80053210637     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbr045     Document Type: Article

References (70)

1. Bansal M, Eulenstein O. The multiple gene duplication problem revisited. Bioinformatics 2008;24(13): i132-8.
2. Treangen T, Rocha E. Horizontal transfer, not duplication, drives the expansion of protein families in Prokaryotes. PLoS Genet 2011;7(1):e1001284.
3. Boussau B, Daubin V. Genomes as documents of evolutionary history. Trends Ecol Evol 2010;25:224-32.
4. Goodman M, Czelusniak J, Moore G, et al. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst Zool 1979;28(2):132-63.
5. Guigo R, Muchnik I, Smith T. Reconstruction of ancient molecular phylogeny. Mol Phylogenet Evol 1996;6(2): 189-213.
6. Page R. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst Biol 1994;43(1):58.
7. Abby S, Tannier E, Gouy M, et al. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics 2010;11(1):324.
8. Beiko R, Hamilton N. Phylogenetic identification of lateral genetic transfer events. BMC Evol Biol 2006;6(1):15.
9. Nakhleh L, Ruths F, Wang LS. RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. Proc 11th Int Comput Combinatorics Conf 2005. (LNCS 3595): 84-93.
10. Dufayard J-F, Duret L, Penel S, et al. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 2005;21(11):2596-603.
11. Storm C, Sonnhammer E. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 2002;18(1):92.
12. Van Der Heijden R, Snel B, Van Noort V, et al. Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics 2007;8(1):83.
13. Wapinski I, Pfeffer A, Friedman N, et al. Natural history and evolutionary principles of gene duplication in fungi. Nature 2007;449(7158):54-61.
14. Zmasek C, Eddy S. RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 2002;3(1):14.
15. Chen F, Mackey A, Vermunt J, et al. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE 2007;2(4):e383.
16. Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 2009;5(1):e1000262.
17. Rivera A, Pankey M, Plachetzki D, et al. Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. BMC Evol Biol 2010; 10(1):123.
18. David LA, Alm EJ. Rapid evolutionary innovation during an Archaean genetic expansion. Nature 2011;469(7328): 93-6.
19. Akerborg O, Sennblad B, Arvestad L, et al. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci USA 2009;106(14):5714-9.
20. Durand D, Halldórsson B, Vernot B. A hybrid micro-macroevolutionary approach to gene tree reconstruction. J Comput Biol 2006;13(2):320-35.
21. Rasmussen M, Kellis M. A bayesian approach for fast and accurate gene tree reconstruction. Mol Biol Evol 2011;28(1): 273-90.
22. Wapinski I, Pfeffer A, Friedman N, et al. Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics 2007;23(13):i549.
23. Sanderson M, McMahon M. Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evol Biol 2007;7(Suppl 1):S3.
24. Page R, Charleston M. Trees within trees: phylogeny and historical associations. Trends Ecol Evol 1998; 13(9):356-9.
25. Nieberding C, Jousselin E, Desdevises Y. The use of co-phylogeographic patterns to predict the nature of interactions, and vice-versa. In: Morand S, Krasnov B, (eds). The Geography of Host-parasite Interactions. New York: Oxford University Press, 2010.
26. Brooks D, Ferrao A. The historical biogeography of co-evolution: emerging infectious diseases are evolutionary accidents waiting to happen. J Biogeography 2005;32(8): 1291-9.
27. Bonizzoni P, Vedova G, Dondi R. Reconciling a gene tree to a species tree under the duplication cost model. Theor Comput Sci 2005;347(1-2):36-53.
28. Górecki P, Tiuryn J. DLS-trees: a model of evolutionary scenarios. Theor Comput Sci 2006;359(1-3):378-99.
29. Zhang L. On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. J Comput Biol 1997;4(2): 177-87.
30. Mirkin B, Muchnik I, Smith T. A biologically consistent model for comparing molecular phylogenies. J Comput Biol 1995;2(4):493-507.
31. Zmasek C, Eddy S. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 2001;17(9):821.
32. Bender MA, Farach-Colton M. The LCA Problem Revisited. In: Gonnet H. Gaston, Daniel Panario, Alfredo Viola (eds). Proceedings of the 4th Latin American Symposium on Theoretical Informatics (LATIN '00). London, UK: Springer-Verlag, 2000;88-94.
33. Arvestad L, Berglund A, Lagergren J, et al. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. Proc Eighth annu Int Conf Res Comput Mol Biol 2004;326-35.
34. Doyon JP, Chauve C, Hamel S. Space of gene/species trees reconciliations and parsimonious models. J Comput Biol 2009;16(10):1399-418.
35. Chauve C, El-Mabrouk N. New perspectives on gene family evolution: losses in reconciliation and a link with supertrees. Res Comput Mol Biol 2009;5541:46-58.
36. Tofigh A. Using trees to capture reticulate evolution, lateral gene transfers and cancer progression. PhD thesis. Sweden: KTH Royal Institute of Technology, 2009.
37. Hahn M. Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biol 2007;8(7):R141.
38. Berglund-Sonnhammer AC, Steffansson P, Betts M, et al. Optimal gene trees from sequences and species trees usinga soft interpretation of parsimony. J Mol Evol 2006;63(2): 240-50.
39. Chang W, Eulenstein O. Reconciling gene trees with apparent polytomies. Proc COCOON 2006 (LNCS 4112): p. 235-44.
40. Vernot B, Stolzer M, Goldman A, et al. Reconciliation with non-binary species trees. J Comput Biol 2008;15(8): 981-1006.
41. Wapinski I, Pfeffer A, Friedman N, et al. Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics 2007;23(13):i549.
42. Arvestad L, Berglund AC, Lagergren J, et al. Bayesian gene/ species tree reconciliation and orthology analysis using MCMC. Bioinformatics 2003;19(Suppl 1):i7-15.
43. Novozhilov A, Karev G, Koonin E. Biological applications of the theory of birth-and-death processes. Brief Bioinform 2006;7(1):70.
44. Arvestad L, Lagergren J, Sennblad B. The gene evolution model and computing its associated probabilities. J ACM 2009;56(2):1-44.
45. Sennblad B, Lagergren J. Probabilistic orthology analysis. Syst Biol 2009;58(4):411.
46. Sennblad B, Lagergren J. PrimeGEM - probabilitic orthology analysis. 2009. http://prime.sbc.su.se/primeGEM (8 September 2011, date last accessed).
47. Doyon JP, Hamel S, Chauve C. An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework. IEEE/ACM Trans Comput Biol Bioinformat 2011;99 (PrePrints).
48. Górecki P, Burleigh GJ, Eulenstein O. Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. BMC Bioinformatics 2011; 12(Suppl 1):S15.
49. Górecki P, Eulenstein O. DrML - Maximum Likelihood Estimation in the Duplication Loss Model 2010. http://bioputer.mimuw.edu.pl/_gorecki/drml (8 September 2011, date last accessed).
50. Csu00 rü s M, Miklós I. Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Mol Biol Evol 2009;26(9):2087.
51. Kumar S. Molecular clocks: four decades of evolution. Nat Rev Genet 2005;6(8):654-62.
52. Rasmussen M, Kellis M. Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes. Genome Res 2007; 17(12):1932.
53. De Bie T, Cristianini N, Demuth J, et al. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 2006;22(10):1269-71.
54. Ovadia Y, Fielder D, Conow C, et al. The cophylogeny reconstruction problem is NP-complete. J Comput Biol 2011;18:59-65.
55. Tofigh A, Hallett M, Lagergren J. Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Trans Comput Biol Bioinform 2011;8:517-35.
56. Charleston M, Perkins S. Traversing the tangle: algorithms and applications for cophylogenetic studies. J Biomed Inform 2006;39(1):62-71.
57. Merkle D, Middendorf M. Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information. Theory Biosci 2005;123(4):277-99.
58. Libeskind-Hadas R, Charleston M. On the computational complexity of the reticulate cophylogeny reconstruction problem. J Comput Biol 2009;16(1):105-17.
59. Doyon JP, Scornavacca C, Szö llo00 si GJ, et al. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. Proc 14th Int Conf Res Comput Mol Biol (RECOMB-CG) 2011. Volume 6398 of LNCS; 93-108.
60. Merkle D, Middendorf M, Wieseke N. A parameteradaptive dynamic programming approach for inferring cophylogenies. BMC Bioinformatics 2010;11(Suppl 1):S60.
61. Charleston M. Jungles: a new solution to the host/parasite phylogeny reconciliation problem. Mathl Biosci 1998;149(2): 191-223.
62. Rasmussen M. SPIMAP - Species Informed Maximum A Posteriori Gene Tree Reconstruction. 2011. http://compbio.mit.edu/spimap (8 September 2011, date last accessed).
63. Akerborg O, Sennblad B, Arvestad L, et al. PrIME-GSR: a Bayesian integrated model for genes, sequences, and rates. 2008. http://prime.sbc.su.se/primeGSR (8 September 2011, date last accessed).
64. Akerborg O, Sennblad B, Lagergren J. Birth-death prior on phylogeny and speed dating. BMC Evol Biol 2008;8:77.
65. Charleston MA, Page RDM. TreeMap 3 program. 2002. http://sydney.edu.au/engineering/it/_mcharles/software/ treemap/treemap3.html (8 September 2011, date last accessed).
66. Zmasek C, Eddy S. 2010. http://www.phylosoft.org/forester/applications/sdi (8 September 2011, date last accessed).
67. Doyon JP, Hamel S, Chauve C. Korak - Exploring the Space of Reconciliations and Probabilistic Framework. http://www.lirmm.fr/_doyon/Korak (8 September 2011, date last accessed).
68. Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009;25:2286-8.
69. Sanderson M. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 2003;19(2):301.
70. Conow C, Fielder D, Ovadia Y, et al. Jane: a new tool for the cophylogeny reconstruction problem. Algorithms Mol Biol 2010;5:16.