Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions

Systematic Biology

Volumn 56, Issue 3, 2007, Pages 504-514

  Liu, Liang ^a,b   Pearl, Dennis K ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Bayesian hierarchical model; Coalescent theory; Gene tree; MCMC; Species tree

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; COMPUTER SIMULATION; DNA SEQUENCE; FINCH; GENETICS; MACACA; METHODOLOGY; PHYLOGENY; TIME;

ALGORITHMS; ANIMALS; BAYES THEOREM; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; FINCHES; MACACA; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

EID: 34548575126     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150701429982     Document Type: Article

References (55)

1. Altekar, G., S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist. 2004. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20:407-415. (Pubitemid 38262773)
2. Arvestad, L., A. C. Berglund., J. Lagergren., and B. Sennblad. 2004. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. RECOMB. 326-335.
3. Barlow, M., and B. G. Hall. 2002. Origin and evolution of the AmpC 0-lactamases of citrobacter freundii. Antimicrob. Agents Chemother. 46:1190-1198. (Pubitemid 34415290)
4. Buckley, T. R., M. Cordeiro, D. C. Marshall, and C. Simon. 2006. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada dugdale). Syst. Biol. 55:411- 425.
5. Bull, J. J., J. P. Huelsenbeck, C. W. Cunningham, D. L. Swofford, and P. J. Waddell. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384-397.
6. Chen, F. C, and W. H. Li. 2001. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68:444- 456.
7. Coop, G., and R. C. Griffiths. 2004. Ancestral inference on gene trees under selection. Theor. Popul. Biol. 66: 219-232. (Pubitemid 39301176)
8. Cotton, J. A., and R. D. M. Page. 2002. Going nuclear: Gene family evolution and vertebrate phylogeny reconciled. Proc. R. Soc. Lond. B. 269:1555-1561.
9. Degnan, J. H., and N. A. Rosenberg. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2:762-768. (Pubitemid 43794324)
10. Degnan, J. H., and L. Salter. 2005. Gene tree distributions under the coalescent process. Evolution 59:24-37. (Pubitemid 40181296)
11. de Queiroz, A. 1993. For consensus (sometimes). Syst Biol. 42:368-372.
12. Doyle, J. J. 1992. Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17:144-163.
13. Durand D., B. V. Halldorsson, and B. Vernot. 2006. A hybrid micromacroevolutionary approach to gene tree reconstruction. J. Comput. Biol. 13:320-335.
14. Edwards, S., and P. Beerli. 2000. Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854. (Pubitemid 32113816)
15. Edwards, S. V., L. Liu, and D.K. Pearl. 2007. High resolution species trees without concatenation. Proc. Natl. Acad. Sci. 104:5936-5941. (Pubitemid 47175637)
16. Felsenstein, J. 2004a. Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
17. Felsenstein, J. 2004b. PHYLIP (Phylogeny Inference Package). Version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
18. Fooden, J. 1980. Classification and distribution of living macaques. Pages 1-9 in The macaques: Studies in ecology, behavior, and evolution (D.G Lindburg, ed.). Van Nostrand Reinhold, New York.
19. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160- 174. (Pubitemid 16227864)
20. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
21. Huelsenbeck, J. P., D. L. Swofford, C. W. Cunningham, J. J. Bull, and P. J. Waddell. 1994. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis? Syst Biol. 43:288-291. (Pubitemid 24977983)
22. Jennings, W. B., and S.V. Edwards. 2005. Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59: 2033-2047. (Pubitemid 41384386)
23. Kluge, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25.
24. Kluge, A. G., and A. J. Wolf. 1993. Cladistics: Whaf s in a word. Cladistics. 9:183-199.
25. Kubatko, L. S., and J. H. Degnan. 2006. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56:17- 24.
26. Lartillot, N., and H. Philippe. 2005. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55:195:207.
27. Maa, J. F., D. K. Pearl, and R. Bartoszyriski. 1996. Reducing multidimensional two-sample data to one-dimensional interpoint distances. Ann. Stat. 24:1069-1074.
28. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
29. Maddison, W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst Biol. 55:21-30.
30. Minin, V., Z. Abdo, P. Joyce, and J. Sullivan. 2003. Performance-based selection of likelihood models for phylogeny estimation. Syst. Biol. 52:674-683. (Pubitemid 37365048)
31. Miyamoto, M. M., and W. M. Fitch. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44:64-76.
32. Moore, W. S. 1995 Inferring phylogenies from mtDNA variation: Mitochondrial gene trees vs. nuclear gene frees. Evolution 49:718-26.
33. Mossel, E., and E. Vigoda. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of frees. Science 309:2207-2209. (Pubitemid 41396068)
34. Nee, S., R. M. May, and P. H. Harvey. 1994. The reconstructed evolutionary process. R. Soc. Lond. Proc. Ser. B 344:77-82.
35. Newton, M. A., and A. E. Raftery. 1994. Approximate Bayesian inference by the weighted likelihood bootstrap (with discussion). J. R. Stat. Soc. Ser. B 56:3-8.
36. Nielsen, R. 1998. Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model. Theor. Popul. Biol. 53:143-151. (Pubitemid 28417977)
37. Nielsen, R., J. L. Mountain, J. P. Huelsenbeck, and M. Slatkin. 1998. Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation. Evolution 52:669-677. (Pubitemid 28324497)
38. Nixon, K. C, and J. M. Carpenter. 1996. On simultaneous analysis. Cladistics 12:221-241. (Pubitemid 126395073)
39. Nylander, J. A. A., F. Ronquist, J. P. Huelsenbeck, and J. L. Nieves Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53:47-67. (Pubitemid 38370420)
40. Page, R. D. M. 1998. GeneTree: Comparing gene and species phylogenies using reconciled trees. Bioinformatics 14:819- 820. (Pubitemid 28552117)
41. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
42. Posada, D., and K. A. Crandall. 1998. ModelTest: Testing the model of DNA substitution. Bioinformatics 14: 817-818. (Pubitemid 28552116)
43. Rannala, B., and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656. (Pubitemid 37102224)
44. Robinson, D. R, and L. R. Foulds. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147. (Pubitemid 11129084)
45. Rodrigo, A. G., M. Kellyborges, P. R. Bergquist, and P. L. Bergquist. 1993. A randomization test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. N. Z. J Bot. 31:257-268.
46. Ronquist, R, and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
47. Ronquist, F., J. P. Huelsenbeck, J. P. and P. van der Mark. 2005. MrBayes3 manual. On-line at http://mrbayes.csit.fsu.edu/mb3.l-manual.pdf.
48. Ruvolo, M. 1997. Molecular phylogeny of the hominoids: Inferences from multiple independent DNA sequence data sets. Mol. Biol. Evol. 14:248-265. (Pubitemid 27102671)
49. Simmons, M. P., C. D. Bailey, and K. C. Nixon. 2000. Phylogeny reconstruction using duplicate genes. Mol. Biol. Evol. 17:469-473. (Pubitemid 30210693)
50. Slatkin, M., and J. L. Pollack. 2006. The concordance of gene trees and species trees at two linked loci. Genetics 172:1979-1984.
51. Slowinski, J. B., and R. D. M. Page. 1999. How should species phylogenies be inferred from sequence data? Syst. Biol. 48:814 - 825. (Pubitemid 129490565)
52. Takahata, N. 1989. Gene genealogy in three related populations: Consistency probability between gene and population trees. Genetics 122:957-966.
53. Tosi, A. J., J. C. Morales, and D. J. Melnick. 2003. Paternal, maternal, and biparental molecular markers provide unique windows onto the evolutionary history of macaques monkeys. Evolution 57:1419-1435. (Pubitemid 36821253)
54. Yang, Z. 1997. On the estimation of ancestral population sizes. Genet. Res. 69:111-116.
55. Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724. (Pubitemid 27287292)