Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy

Molecular Phylogenetics and Evolution

Volumn 65, Issue 2, 2012, Pages 501-509

  Lacey Knowles, L ^a   Lanier, Hayley C ^a   Klimov, Pavel B ^a   He, Qixin ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Bayesian inference; Coalescence; Gene tree; Maximum likelihood; Species tree

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPUTER SIMULATION; DNA SEQUENCE; GENETIC VARIABILITY; PHYLOGENY; STATISTICAL MODEL; UNCERTAINTY;

ALGORITHMS; BAYES THEOREM; COMPUTER SIMULATION; GENETIC VARIATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA; UNCERTAINTY;

EID: 84866147332     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.07.004     Document Type: Article

References (47)

1. Anderson D.R. Model Based Inference in the Life Sciences: A Primer on Evidence 2008, Springer, New York.
2. Brown J., Hedtke S., Lemmon A., Lemmon E. When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates. Syst. Biol. 2010, 59:145-161.
3. Burnham K.P., Anderson D.R. Model Selection and Inference: A Practical Information-Theoretic Approach 2002, Springer-Verlag, New York.
4. Carstens B.C., Knowles L.L. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 2007, 56:400-411.
5. Chung Y., Ane C. Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer. Syst. Biol. 2011, 60:261-275.
6. Cranston K.A. Summarizing gene tree incongruence at multiple phylogenetic depths. Estimating Species Trees: Practical and Theoretical Aspects 2010, 129-143. Wiley-Blackwell, Hoboken, New Jersey. L.L. Knowles, L.S. Kubatko (Eds.).
7. Cranston K.A., Hurwitz B., Ware D., Stein L., Wing R.A. Species trees from highly incongruent gene trees in rice. Syst. Biol. 2009, 58:489-500.
8. Degnan J.H., Rosenberg N.A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 2009, 1-9.
9. Delsuc F., Brinkmann H., Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 2005, 6:361-375.
10. Eckert A.J., Carstens B.C. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Mol. Phylogenet. Evol. 2008, 49:142-152.
11. Edwards S.V., Liu L., Pearl D.K. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA 2007, 104:5936-5941.
12. Felsenstein, J., 2005. PHYLIP (Phylogeny Inference Package). Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
13. Flórez-Rodríguez A., Carling M.D., Cadena C.D. Reconstructing the phylogeny of "Buarremon" brush-finches and near relatives (Aves, Emberizidae) from individual gene trees. Mol. Phylogenet. Evol. 2011, 58:297-303.
14. Harmon L.J., Weir J.T., Brock C.D., Glor R.E., Challenger W. GEIGER: investigating evolutionary radiations. Bioinformatics 2008, 24:129-131.
15. Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
16. Holder M., Sukumaran J., Lewis P. A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics. Syst. Biol. 2008, 57:814-821.
17. Huang H., He Q., Kubatko L., Knowles L. Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Syst. Biol. 2010, 59:573-583.
18. Huang H., Knowles L.L. What is the danger of the anomaly zone for empirical phylogenetics?. Syst. Biol. 2009, 58:527-536.
19. Hudson R.R. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18:247-264.
20. Huelsenbeck J.P., Ronquist F. MrBayes: bayesian inference of phylogenetic trees. Bioinformatics 2001, 17.
21. Knowles L. Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 2009, 58:463-467.
22. Knowles L.L. Sampling strategies for species tree estimation. Estimating Species Trees: Pract. Theor. Aspects 2010, 163-173. (Chapter 10).
23. Knowles L.L., Chan Y.-H. Resolving species phylogenies of recent evolutionary radiations. Ann. Mo. Bot. Gard. 2008, 95:224-231.
24. Estimating Species Trees: Practical and Theoretical Aspects 2010, Wiley and Sons, Hoboken, New Jersey. L.L. Knowles, L.S. Kubatko (Eds.).
25. Kubatko L., Carstens B., Knowles L. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25:971-973.
26. Kubatko L.S., Gibbs H.L. Estimating species relationships and taxon distinctiveness in Sistrurus rattlesnakes using multilocus data. Estimating Species Trees: Practical and Theoretical Aspects 2010, 193-207. Wiley-Blackwell, Hoboken, New Jersey. L.L. Knowles, L.S. Kubatko (Eds.).
27. Kuhner M.K., Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 1994, 11:459-468.
28. Lanier H.C., Knowles L.L. Is recombination a problem for species-tree analyses?. Syst. Biol. 2012, 61:691-701.
29. Leache A.D., Rannala B. The accuracy of species tree estimation under simulation: a comparison of methods. Syst. Biol. 2010, 60:126-137.
30. Linnen C.R. Species tree estimation for complex divergence histories. Estimating Species Trees: Practical and Theoretical Aspects 2010, 145-173. Wiley-Blackwell, Hoboken, New Jersey. L.L. Knowles, L.S. Kubatko (Eds.).
31. Liu L. BEST: bayesian estimation of species trees under the coalescent model. Bioinformatics 2008, 24:2542-2543.
32. Liu L., Yu L., Edwards S.V. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 2010, 10:302.
33. Liu L., Yu L., Kubatko L., Pearl D.K., Edwards S.V. Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol. 2009, 53:320-328.
34. Maddison W.P., Knowles L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 2006, 55:21-30.
35. Maddison, W.P., Maddison, D.R., 2009. MESQUITE: a modular system for evolutionary analysis.
36. McCormack J., Huang H., Knowles L.L. Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst. Biol. 2009, 58:501-508.
37. Philippe H., Brinkmann H., Lavrov D.V., Littlewood D.T.J., Manuel M., Wörheide G., Baurain D. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 2011, 9:e1000602.
38. Plazzi F., Ferrucci R.R., Passamonti M. Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies. BMC Bioinformatics 2010, 11:209.
39. Qiu Y., Li L., Wang B., Chen Z., Knoop V., Groth-Malonek M., Dombrovska O., Lee J., Kent L., Rest J. The deepest divergences in land plants inferred from phylogenomic evidence. Proc. Natl. Acad. Sci. 2006, 103:15511.
40. Rambaut A., Grassly N.C. SEQ-GEN: an application for the Monte Carlo simulation of DNA sequences along phylogenetic trees. Comput. Appl. Biosci. 1997, 13:235-238.
41. Robinson D.F., Foulds L.R. Comparison of phylogenetic trees. Math. Biosci. 1981, 53:131-147.
42. Schwartz R.S., Mueller R.L. Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks. BMC Evol. Biol. 2010, 10:1-21.
43. z.ast;and other methods). Sinaur Associates, Sunderland, MA.
44. Than C.V., Nakhleh L.K. Species tree inference by minimizing deep coalescenses. PLoS Comput. Biol. 2009, 5:e1000501.
45. Townsend J.P. Profiling phylogenetic informativeness. Syst. Biol. 2007, 56:222-231.
46. Townsend J.P., Leuenberger C. Taxon sampling and the optimal rates of evolution for phylogenetic inference. Syst. Biol. 2011, 60:358-365.
47. Zwickl, D.L., 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Biology. University of Texas at Austin, Austin, TX.