Estimating species trees using multiple-allele DNA sequence data

Evolution

Volumn 62, Issue 8, 2008, Pages 2080-2091

  Liu, Liang ^a   Pearl, Dennis K ^b   Brumfield, Robb T ^c   Edwards, Scott V ^a  

^a HARVARD UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

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

Indexed keywords

ALGORITHM; ALLELE; BAYESIAN ANALYSIS; COALESCENCE; DATA SET; DNA; ECOLOGICAL MODELING; GENETIC MARKER; MARKOV CHAIN; MONTE CARLO ANALYSIS; PHYLOGENETICS; POPULATION GENETICS; RECONSTRUCTION; YEAST;

ALGORITHM; ALLELE; ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BIRD; COMPUTER SIMULATION; DNA SEQUENCE; EVOLUTION; GENETICS; MONTE CARLO METHOD; PHYLOGENY; PROBABILITY; SACCHAROMYCES CEREVISIAE; SPECIES DIFFERENCE; STATISTICAL MODEL; THEORETICAL MODEL;

ALGORITHMS; ALLELES; ANIMALS; BAYES THEOREM; BIRDS; COMPUTER SIMULATION; EVOLUTION; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL; MODELS, THEORETICAL; MONTE CARLO METHOD; PHYLOGENY; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

AVES; MANACUS; SACCHAROMYCES;

EID: 47749093183     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2008.00414.x     Document Type: Article

References (56)

1. Alfaro, M. E., and M. T. Holder. 2006. The posterior and the prior in Bayesian phylogenetics. Annu. Rev. Ecol. Evol. Syst. 37 : 19 42.
2. Beaumont, M. A., and B. Rannala. 2004. The Bayesian revolution in genetics. Nat. Rev. Genet. 5 : 251 261.
3. Beerli, P. 2006. Comparison of Bayesian and maximum likelihood inference of population genetic parameters. Bioinformatics 22 : 341 345.
4. Bensch, S., D. E. Irwin, J. H. Irwin, L. Kvist, and S. Akesson. 2006. Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers. Mol. Ecol. 15 : 161 171.
5. Brumfield, R. T., and M. J. Braun. 2001. Phylogenetic relationships in bearded manakins (Pipridae; Manacus) indicate that male plumage color is a misleading taxonomic marker. Condor 103 : 248 258.
6. Brumfield, R. T., R. W. Jernigan, D. B. McDonald, and M. J. Braun. 2001. Evolutionary implications of divergent clines in an avian (Manacus; Aves) hybrid zone. Evolution 55 : 2070 2087.
7. Brumfield, R. T., L. Liu, D. E. Lum, and S. V. Edwards. in press. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data. Syst. Biol.
8. 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.
9. Cavalli-Sforza, L. L., and A. W. F. Edwards. 1964. Analysis of human evolution. Proc. XI Int. Congress Genet. 3 : 923 933.
10. Cranston, K. A., and B. Rannala. 2007. Summarizing a posterior distribution of trees using agreement subtrees. Syst. Biol. 56 : 578 590.
11. De Barro Lopes, M., J. R. Bellon, N. J. Shirley, and P. F. Ganter. 2002. Evidence for multiple interspecific hybridization in Saccharomyces sensu stricto species. FEM Yeast Res. 1 : 323 331.
12. de Queiroz, A. 1993. For consensus (sometimes). Syst. Biol. 42 : 368 372.
13. de Queiroz, A., M. J. Donoghue, and J. Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26 : 657 681.
14. Degnan, J. H., and N. A. Rosenberg. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2 : 762 768.
15. Degnan, J. H., and L. A. Salter. 2005. Gene tree distributions under the coalescent process. Evolution 59 : 24 37.
16. Edwards, S. V., L. Liu, and D. K. Pearl. 2007. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA 104 : 5936 5941.
17. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, MA.
18. Felsenstein, J. 2006. Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci Mol. Biol. Evol. 23 : 691 700.
19. Funk, D. J., and K. E. Omland. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 34 : 397 423.
20. Hasegawa, M., H. Kishino, and T. A. Yano. 1985. Dating of the human ape splitting by a molecular clock of Mitochondrial-DNA. J. Mol. Evol. 22 : 160 174.
21. Hastings, W. K. 1970. Monte-Carlo sampling methods using Markov Chains and their applications. Biometrika 57 : 97 109.
22. Hey, J., and R. Nielsen. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167 : 747 760.
23. Hey, J., and R. Nielsen. 2007. Integration within the Felsenstein equation for improved Markov Chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 104 : 2785 2790.
24. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 : 754 755.
25. 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.
26. Kingman, J. F. C. 1982. On the genealogy of large populations. Stoch. Proc. Appl. 13 : 235 248.
27. Kingman, J. F. C. 2000. Origins of the coalescent: 1974-1982. Genetics 156 : 1461 1463.
28. Kuhner, M. K., and J. Felsenstein. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11 : 459 468.
29. Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20 : 86 93.
30. Linz, S., A. Radtke, and A. von Haeseler. 2007. A likelihood framework to measure horizontal gene transfer. Mol. Biol. Evol. 24 : 1312 1319.
31. Liti, G., D. B. Barton, and E. J. Louis. 2006. Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics 174 : 839 850.
32. Liu, L. 2006. Reconstructing posterior distributions of a species phylogeny using estimated gene tree distributions. Pp. 46 49. in Ph.D dissertation. Department of Statistics. The Ohio State Univ., Columbus.
33. Liu, L., and D. K. Pearl. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56 : 504 514.
34. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46 : 523 536.
35. Maddison, W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55 : 21 30.
36. Maddison, W. P., and D. R. Maddison. 2006. Mesquite: a modular system for evolutionary analysis. Version 1.12.
37. Mossel, E., and S. Roch. 2007. Incomplete lineage sorting: consistent phylogeny estimation from multiple Loci. Available at http://arxiv.org/abs/0710. 0262 Accessed November 2, 2007 May, and P. H. Harvey. 1994. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B 344 : 305 311.
38. Newton, M. A., A. E. Raftery, A. C. Davison, M. Bacha, G. Celeux, B. P. Carlin, P. Clifford, C. Lu, M. Sherman, M. A. Tanner, et al. 1994. Approximate Bayesian-inference with the weighted likelihood bootstrap. J. R. Stat. Soc. B 56 : 3 48.
39. Nielsen, R., and M. Slatkin. 2000. Likelihood analysis of ongoing gene flow and historical association. Evolution 54 : 44 50.
40. Nilson-Tillgren, T., J. G. L. Petersen, S. Holmberg, and M. C. Kielland-Brandt. 1980. Transfer of chromosome III during Kar mediated cytoduction in yeast Carlsberg. Res. Commun. 45 : 113 117.
41. Nylander, J. A. A. 2004. MrModeltest v2. Evolutionary Biology Centre, Uppsala Univ.
42. 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.
43. Page, R. D. M. 1998. GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 14 : 819 820.
44. Page, R. D. M., and M. A. Charleston. 1997. From gene to organismal phylogeny: reconciled trees and the gene tree species tree problem. Mol. Phylogenet. Evol. 7 : 231 240.
45. Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 : 817 818.
46. Posada, D., and T. R. Buckley. 2004. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53 : 793 808.
47. Rannala, B., and Z. H. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164 : 1645 1656.
48. Rieseberg, L. H., J. Whitton, and K. Gardner. 1999. Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics 152 : 713 727.
49. Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425 : 798 804.
50. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 : 1572 1574.
51. Slowinski, J. B., A. Knight, and A. P. Rooney. 1997. Inferring species trees from gene trees: a phylogenetic analysis of the elapidae (Serpentes) based on the amino acid sequences of venom proteins. Mol. Phylogenet. Evol. 8 : 349 362.
52. Sniegowski, P. D., P. G. Dombrowski, and E. Fingerman. 2002. Saccharomyces cerevisiae and Saccharomyces paradoxus coexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics. FEMS Yeast Res. 1 : 299 306.
53. Wakeley, J. 1996. The variance of pairwise nucleotide differences in two populations with migration. Theor. Popul. Biol. 49 : 39 57.
54. Whelan, S., and N. Goldman. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18 : 691 699.
55. Wiens, J. J. 1998. Combining data sets with different phylogenetic histories. Syst. Biol. 47 : 568 581.
56. Zwickl, D. J., and M. T. Holder. 2004. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst. Biol. 53 : 877 888.