Assessing approaches for inferring species trees from multi-copy genes

Systematic Biology

Volumn 64, Issue 2, 2015, Pages 325-339

  Chaudhary, Ruchi ^a,b   Boussau, Bastien ^c   Burleigh, J Gordon ^b   Fernández Baca, David ^a  

^a Iowa State University   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c UNIVERSITÉ LYON 1   (France)

Author keywords

Deep coalescence; Gene duplication; Gene loss; Gene tree parsimony; MulRF; Njst; PHYLDOG

Indexed keywords

CLASSIFICATION; COMPUTER PROGRAM; COMPUTER SIMULATION; DNA SEQUENCE; GENE DELETION; GENE DUPLICATION; PHYLOGENY; PROCEDURES; STANDARDS;

CLASSIFICATION; COMPUTER SIMULATION; GENE DELETION; GENE DUPLICATION; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84927677112     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu128     Document Type: Article

References (71)

1. Åkerborg O., Sennblad B., Arvestad L., Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc. Natl Acad. Sci. USA 106:5714-5719.
2. Ané C., Larget B., Baum D.A., Smith S.D., Rokas A. 2007. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 24:1575.
3. Arvestad L., Berglund A.-C., Lagergren J., Sennblad B. 2003. Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19:i7-i15.
4. Arvestad L., Berglund A.-C., Lagergren J., Sennblad B. 2004. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), New York, NY, USA: ACM. P. 326-335.
5. Arvestad L., Lagergren J., Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J. ACM 56:1-44.
6. Bansal M.S., Burleigh J.G., Eulenstein O. 2010. Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. BMC Bioinform. 11:S42.
7. Bansal M.S., Burleigh J.G., Eulenstein O., Wehe A. 2007. Heuristics for the gene-duplication problem: a Θ(n) speed-up for the local search. Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007), Berlin Heidelberg: Springer-Verlag. P. 238-252.
8. Beiko R.G., Doolittle W.F., Charlebois R.L. 2008. The impact of reticulate evolution on genome phylogeny. Syst. Biol. 57:844-856.
9. Boussau B., Szöllo{combining double acute accent}si G.J., Duret L., Gouy M., Tannier E., Daubin V. 2012. Genome-scale coestimation of species and gene trees. Genome Res. 23:323-330.
10. Burleigh J.G., Bansal M.S., Eulenstein O., Hartmann S., Wehe A., Vision T.J. 2011. Genome-scale phylogenetics: Inferring the plant tree of life from 18,896 gene trees. Syst. Biol. 60:117-125.
11. Burleigh J.G., Bansal M.S., Eulenstein O., Vision T.J. 2010. Inferring species trees from gene duplication episodes. Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, New York, NY, USA: ACM. P. 198-203.
12. Burleigh J.G., Bansal M.S., Wehe A., Eulenstein O. 2009. Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants. J. Comput. Biol. 16:1071-1083.
13. Chaudhary R., Bansal M.S., Wehe A., Fernández-Baca D., Eulenstein O. 2010. igtp: a software package for large-scale gene tree parsimony analysis. BMC Bioinform. 11:574.
14. Chaudhary R., Burleigh J.G., Fernández-Baca D. 2012. Fast local search for unrooted Robinson-Foulds supertrees. IEEE/ACM Transact. Comput. Biol. Bioinform. 9:1004-1013.
15. Chaudhary R., Burleigh J.G., Fernández-Baca D. 2013. Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. Algorithm. Mol. Biol. 28:8.
16. Chaudhary R., Fernández-Baca D., Burleigh J.G. 2014. MulRF: a software package for phylogenetic analysis using multi-copy gene trees. Bioinformatics doi:10.1093/bioinformatics/btu648.
17. Cotton J.A., Page R.D.M. 2003. Gene tree parsimony vs. uninode coding for phylogenetic reconstruction. Mol. Phylogenet. Evol. 29:298-308.
18. Crosby R.W., Williams T.L. 2012. A fast algorithm for computing the quartet distance for large sets of evolutionary trees. Proceedings of the 8th international conference on Bioinformatics Research and Applications (ISBRA 2012), Berlin Heidelberg: Springer-Verlag. P. 60-71.
19. Degnan J.H., Rosenberg N.A. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24:332-340.
20. Feller W. 1968. An introduction to probability theory and its applications. Vol. 1, 3rd ed. Hoboken, New Jersey, USA: John Wiley & Sons, Inc.
21. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
22. Felsenstein J. 1993. Retree software. http://evolution.genetics.washington.edu/phylip/doc/retree.html.
23. Ganapathy G. 2006. Algorithms and heuristics for combinatorial optimization in phylogeny. [PhD. thesis]. Austin: University of Taxas.
24. Ge F., Wang L.-S., Kim J. 2005. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol. 3:909-914.
25. Goodman M., Czelusniak J., Moore G.W., Romero-Herrera A.E., Matsuda G. 1979. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Biol. 28:132-163.
26. Górecki P., Burleigh J.G., Eulenstein O. 2011. Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. BMC Bioinform. 12:S15.
27. Górecki P., Burleigh J.G., Eulenstein O. 2012. GTP supertrees from unrooted gene trees: linear time algorithms for NNI based local searches. Proceedings of the 8th International Conference on Bioinformatics Research and Applications (ISBRA 2012), Berlin Heidelberg: Springer-Verlag. P. 102-114.
28. Guigó R., Muchnik I., Smith T.F. 1996. Reconstruction of ancient molecular phylogeny. Mol. Phylogenet. Evol. 6:189-213.
29. Hahn M.W. 2007. Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biol. 8:R141.
30. Heled J., Drummond A.J. 2010. Bayesian inference of species trees from multilocus data. J. Mol. Biol. Evol. 27:570-580.
31. Holton T.A., Pisani D. 2010. Deep genomic-scale analyses of the metazoa reject coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol. Evol. 2:310-324.
32. Katz L.A., Grant J.R., Parfrey L.W., Burleigh J.G. 2012. Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life. Syst. Biol. 61:653-660.
33. Knowles L.L. 2009. Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 58:463-467.
34. Kubatko L.S., Carstens B.C., Knowles L.L. 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25:971-973.
35. Kubatko L.S., Degnan J.H. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56:17-24.
36. Liu L. 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24:2542-2543.
37. Liu L., Pearl D.K. 2007. Species trees from gene trees: reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56:504-514.
38. Liu L., Yu L. 2011. Estimating species trees from unrooted gene trees. Syst. Biol. 60:661-667.
39. Liu L., Yu L., Edwards S.V. 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 10:302.
40. Liu L., Yu L., Kubatko L., Pearl D.K., Edwards S.V. 2009. Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol. 53:320-328.
41. Ma B., Li M., Zhang L. 2000. From gene trees to species trees. SIAM J. Comput. 30:729-752.
42. Maddison W.P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
43. Maddison W.P., Knowles L.L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
44. Maddison W.P., Maddison D. 2009. Mesquite: a modular system for evolutionary analysis. version 2.6. http://mesquiteproject.org.
45. Medina E.M., Jones G.W., Fitzpatrick D.A. 2011. Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom. J. Mol. Evol. 73:116-133.
46. Mossel E., Vigoda E. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309:2207-2209.
47. Near T.J., Eytan R.I., Dornburg A., Kuhn K.L., Moore J.A., Davis M.P., Wainwright P.C., Friedman M., Smith W.L. 2012. Resolution of ray-finned fish phylogeny and timing of diversification. Proc. Natl Acad. Sci. USA 109:13698-13703.
48. Ness R.W., Graham S.W., Barrett S.C.H. 2011. Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family pontederiaceae. J. Mol. Biol. Evol. 28:3009-3018.
49. Page R. D.M., Charleston M. A. 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7:231-240.
50. Penny D., White W.T., Hendy M.D., Phillips M.J. 2008. A bias in ML estimates of branch lengths in the presence of multiple signals. Mol. Biol. Evol. 25:239-242.
51. Puigbò P., Garcia-Vallvé S., McInerney J.O. 2007. TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics 23:1556-1558.
52. Rambaut A., Grassly N.C. 1997. Seq-Gen: an application for the Monte-Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
53. Rasmussen M.D., Kellis M. 2011. A Bayesian approach for fast and accurate gene tree reconstruction. J. Mol. Biol. Evol. 28:273-290.
54. Rasmussen M.D., Kellis M. 2012. Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Res. 22:755-765.
55. Robinson D.F., Foulds L. R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
56. Sanderson M.J., McMahon M.M. 2007. Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evol. Biol. 7:S3.
57. Sjöstrand J., Tofigh A., Daubin V., Arvestad L., Sennblad B., Lagergren J. forthcoming. A Bayesian method for analyzing lateral gene transfer. Syst. Biol.
58. Slowinski J.B., Knight A., Rooney A.P. 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.
59. Slowinski J.B., Page R.D.M. 1999. How should species phylogenies be inferred from sequence data? Syst. Biol. 48:814-825.
60. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
61. Sukumaran J., Holder M.T. 2010. DendroPy: a python library for phylogenetic computing. Bioinformatics 26:1569-1571.
62. Swenson M.S., Barbançon F., Warnow T., Linder C.R. 2010. A simulation study comparing supertree and combined analysis methods using SMIDGen. Algorithm. Mol. Biol. 5:8.
63. Szöllo{combining double acute accent}si G.J., Boussau B., Abby S.S., Tannier E., Daubin V. 2012. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc. Natl. Acad. Sci. USA 109:17513-17518.
64. Than C.V., Rosenberg N.A. 2011. Consistency properties of species tree inference by minimizing deep coalescences. J. Comput. Biol. 18:1-15.
65. Wainwright P.C., Smith W.L., Price S.A., Tang K.L., Sparks J.S., Ferry L.A., Kuhn K.L., Eytan R.I., Near T.J. 2012. The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Syst. Biol. 61:1001-1027.
66. Wehe A., Bansal M.S., Burleigh J.G., Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24:1540-1541.
67. Wehe A., Burleigh J.G. 2010. Scaling the gene duplication problem towards the tree of life. Proceedings of the ISCA 2nd International Conference on Bioinformatics and Computational Biology, BICoB-2010, March 24-26, 2010. (H. Al-Mubaid, ed.) ISCA, Honolulu, Hawaii, USA: Sheraton Waikiki Hotel. P. 133-138.
68. Whidden C., Zeh N., Beiko R.G. forthcoming. Supertrees based on the subtree prune-and-regraft distance. Syst. Biol.
69. Yu Y., Warnow T., Nakhleh L. 2011a. Algorithms for MDC-based multi-locus phylogeny inference. Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2011), Berlin Heidelberg: Springer-Verlag. p. 531-545.
70. Yu Y., Warnow T., Nakhleh L. 2011b. Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles. J. Comput. Biol. 18:1543-1559.
71. Zhang L. 2011. From gene trees to species trees II: species tree inference by minimizing deep coalescence events. IEEE/ACM Transact. Comput. Biol. Bioinform. 8:1685-1691.