Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples

Molecular Biology and Evolution

Volumn 27, Issue 3, 2010, Pages 552-569

  Degiorgio, Michael ^a   Degnan, James H ^b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Anomalous gene tree; Anomaly zone; Lineage sorting; Phylogenetics; Phylogenomics; Statistical consistency

Indexed keywords

ALGORITHM; ARTICLE; CANDIDA ALBICANS; ESTIMATED SPECIES TREE; FUNGAL GENE; GENE FREQUENCY; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; PHYLOGENETIC TREE; SEQUENCE ALIGNMENT; SIMULATION; SPECIES; STATISTICAL ANALYSIS; SUPERMATRIX ROOTED TRIPLE METHOD; TAXON; THEORY;

ALGORITHMS; BAYES THEOREM; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENES, FUNGAL; MODELS, GENETIC; PHYLOGENY; SEQUENCE ALIGNMENT; SPECIES SPECIFICITY; YEASTS;

EID: 77249139678     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp250     Document Type: Article

References (63)

1. Aho AV, Sagiv Y, Szymanski TG, Ullman JD. 1981. Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J Comput. 10: 405-421.
2. Ańe C, Larget B, Baum DA, Smith SD, Rokas A. 2007. Bayesian estimation of concordance factors. Mol Biol Evol. 24: 412-426.
3. Baum BR. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon. 41:3-10.
4. Bininda-Emonds ORP. 2004. The evolution of supertrees. Trends Ecol Evol. 19:315-322.
5. Bryant D. 2003. A classification of consensus methods for phylogenies. In: Janowitz MF, Lapointe F-J, McMorris FR, Mirkin B, Roberts FS, editors. Bioconsensus. Vol.61. Providence (RI): DIMACS, AMS. p. 163-183.
6. Buckley TR, Cordeiro M, Marshall DC, Simon C. 2006. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). Syst Biol. 55: 411-425.
7. Chen D, Diao L, Eulenstein O, Fernández-Baca D, Sanderson M. 2003. Flipping: a supertree construction method. In: Janowitz MF, Lapointe F-J, McMorris FR, Mirkin B, Roberts FS, editors. Biocon-sensus. Vol.61. Providence (RI): American Mathematical Society. p. 135-160.
8. Chor B, Hendy M, Penny D. 2007. Analytic solutions for three taxon ML trees with variable rates across sites. Discrete Appl Math. 155: 750-758.
9. Chor B, Hendy M, Snir S. 2006. Maximum likelihood Jukes-Cantor triplets: analytic solutions. Mol Biol Evol. 23:626-632. (Pubitemid 43278274)
10. Chor B, Tuller T. 2005. Maximum likelihood of evolutionary trees: hardness and approximation. Bioinformatics 21:i97-i106.
11. Chung KL. 1974. A course in probability theory. 2nd ed. San Diego (CA): Academic Press.
12. Cormen TH, Leiserson CE, Rivest RL, Stein C. 2001. Introduction to algorithms. 2nd ed. Cambridge (MA): MIT Press.
13. Day W, Johnson D, Sankoff D. 1986. The computational complexity of inferring rooted phylogenies by parsimony. Math Biosci. 81: 33-42.
14. de Queiroz A, Gatesy J. 2007. The supermatrix approach to systemat-ics. Trends Ecol Evol. 22:34-41.
15. Degnan JH, DeGiorgio M, Bryant D, Rosenberg NA. 2009. Properties of consensus methods for inferring species trees from gene trees. Syst Biol. 58:35-54.
16. Degnan JH, Rosenberg NA. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2:e68.
17. Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phyloge-netic inference and the multispecies coalescent. Trends Ecol Evol. 24:332-340.
18. Degnan JH, Salter LA. 2005. Gene tree distributions under the coales-cent process. Evolution 59:24-37.
19. Edwards SV. 2009. Is a new and general theory of molecular systemat-ics emerging? Evolution 63:1-19.
20. Edwards SV, Liu L, Pearl DK. 2007. High-resolution species trees without concatenation. Proc Natl Acad Sci USA. 104:5936-5941.
21. Ewing GB, Ebersberger I, Schmidt HA, von Haeseler A. 2008. Rooted triple consensus and anomalous gene trees. BMC Evol Biol. 8:118.
22. Felsenstein J. 1978. The number of evolutionary trees. Syst Zool. 27: 27-33.
23. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer Associates.
24. Gadagkar SR, Rosenberg M, Kumar S. 2005. Inferring species phyloge-nies from multiple genes: concatenated sequence tree versus consensus gene tree. J Exp Zool. 304B:64-74.
25. Gatesy J, Baker RH. 2005. Hidden likelihood support in genomic data: can forty-five wrongs make a right? Syst Biol. 54:483-492.
26. Hedtke SM, Townsend TM, Hillis DM. 2006. Resolution of phyloge-netic conflict in large data sets by increased taxon sampling. Syst Biol. 55:522-529.
27. Hendy MD, Penny D. 1989. A framework for the quantitative study of evolutionary trees. Syst Zool. 38:297-309.
28. Holland BR, Benthin S, Lockhart PJ, Moulton V, Huber KT. 2008. Using supernetworks to distinguish hybridization from lineage-sorting. BMC Evol Biol. 8:202.
29. Jennings WB, Edwards SV. 2005. Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59:2033-2047.
30. Kolaczkowski B, Thornton JW. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.
31. Kubatko LS, Degnan JH. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol. 56: 17-24.
32. Liu L. 2008. BEST: Bayesian estimation of species trees under the coa-lescent model. Bioinformatics 24:2542-2543.
33. Liu L, Edwards SV. 2009. Phylogenetic analysis in the anomaly zone. Syst Biol. 58:452-460.
34. Liu L, Pearl DK. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol. 56:504-514.
35. Maddison WP. 1997. Gene trees in species trees. Syst Biol. 46:523-536.
36. Meng C, Kubatko LS. 2009. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. Theor Popul Biol. 75:35-45.
37. Mossel E, Vigoda E. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309:2207-2209.
38. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
39. Neyman J. 1971. Molecular studies in evolution: a source of novel statistical problems. In: Gupta SS, Yackel J, editors. Statistical decision theory and related topics. New York: Academic Press. p. 1-27.
40. Page RDM. 2002. Modified mincut supertrees. In: Guigó R, Gusfield D, editors. Lecture Notes in Computer Science. Vol.2452. Proceedings of the Second International Workshop on Algorithms in Bioinformatics (WABI, 2002), Rome, Italy, September 17-21. Berlin (Germany): Springer. p. 537-552.
41. Page RDM, Charleston MA. 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol Phylogenet Evol. 7:231-240.
42. Pamilo P, Nei M. 1988. Relationships between gene trees and species trees. Mol Biol Evol. 5:568-583.
43. Poe S, Swofford DL. 1999. Taxon sampling revisited. Nature 398: 299-300.
44. R Development Core Team 2008. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing. ISBN 3-900051-07-0.
45. Ragan MA. 1992. Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol. 1:53-58.
46. Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238. (Pubitemid 27249927)
47. Rannala B, Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656.
48. Roch S. 2006. A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. IEEE ACM Trans Comput Bioinform. 3:92-94.
49. Rokas A, Carroll SB. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol. 22:1337-1344.
50. Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
51. Rosenberg MS, Kumar S. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc Natl Acad Sci USA. 98:10751-10756.
52. Rosenberg NA. 2007. Counting coalescent histories. J Comput Biol. 14:360-377.
53. Rosenberg NA, Tao R. 2008. Discordance of species trees with their most likely gene trees: the case of five taxa. Syst Biol. 57:131-140.
54. Semple C, Steel M. 2000. A supertree method for rooted trees. Discrete Appl Math. 105:147-158.
55. Slatkin M, Pollack JL. 2008. Subdivision in an ancestral species creates asymmetry in gene trees. Mol Biol Evol. 25:2241-2246.
56. Steel M. 1992. The complexity of reconstructing trees from qualitative characters and subtrees. J Classification. 9:91-116.
57. Steel M, Rodrigo A. 2008. Maximum likelihood supertrees. Syst Biol. 57:243-250.
58. Strimmer K, von Haeseler A. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol. 13:964-969.
59. Swofford DL. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland (MA): Sinauer Associates.
60. Than C, Ruths D, Innan H, Nakhleh L. 2007. Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions. J Comput Biol. 14:517-535.
61. Willson SJ. 2009. Robustness of topological supertree methods for reconciling dense incompatible data. IEEE/ACM Trans Comput Biol Bioinform. 6:62-75.
62. Yang Z. 2000. Complexity of the simplest phylogenetic estimation problem. Proc R Soc Lond B. 267:109-116.
63. Zwickl DJ, Hillis DM. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst Biol. 51:588-598.