Maximum likelihood analyses of 3,490 rbcl sequences: Scalability of comprehensive inference versus group-specific taxon sampling

Evolutionary Bioinformatics

Volumn 2010, Issue 6, 2010, Pages 73-90

  Stamatakis, Alexandros ^a   Göker, Markus ^b   Grimm, Guido W ^c  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^c SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

Author keywords

Many taxon analyses; Phylogenetic inference; RAxML; Taxon jackknifing

Indexed keywords

RIBULOSEBISPHOSPHATE CARBOXYLASE;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; CORRELATION ANALYSIS; FEASIBILITY STUDY; INTERMETHOD COMPARISON; JACKKNIFE TEST; MAXIMUM LIKELIHOOD METHOD; MOLECULAR PHYLOGENY; MULTIGENE FAMILY; PHYLOGENETIC TREE; PROBABILITY; SAMPLING; SCALE UP; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; TAXONOMIC IDENTIFICATION;

EID: 77955475480     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: None     Document Type: Article

References (62)

1. Zwickl DJ. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion. Austin: University of Texas at Austin; 2006.
2. Stamatakis A, Ludwig T, Meier H. RAxML-III: A fast program for Maximum Likelihood-based inference of large phylogenetic trees. Bioinformatics. 2005;21:456-63.
3. Stamatakis A. RAxML-VI-HPC: Maximum-Likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22: 2688-90.
4. Stamatakis A, Blagojevic F, Antonopoulos CD, Nikolopoulos DS. Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM Cell. Journal of VLSI Signal Processing Systems. 2007;48:271-86.
5. Minh BQ, Vinh LS, von Haeseler A, Schmidt HA. pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies. Bioinformatics. 2005;21:3794-96.
6. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696-704.
7. Hordijk W, Gascuel O. Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics. 2005;21:4338-47.
8. Jobb G, von Haeseler A, Strimmer K. Treefinder: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol. 2004;4:18.
9. Huelsenbeck JP, Ronquist F. MrBayes: Bayesian inference of phylogeny. Bioinformatics. 2001;17:754-55.
10. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19:1572-74.
11. Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 2008;452:745-49.
12. McMahon MM, Sanderson MJ. Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Syst Biol. 2006;55: 818-36.
13. Gueidan C, Roux C, Lutzoni F. Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Verrucariales, Ascomycota). Mycol Res. 2007;111:1145-68.
14. Jansen RK, Cai Z, Raubeson LA, et al. (16 co-authors). Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A. 2007;104:19369-74.
15. Hackett SJ, Kimball RT, Reddy S, et al. (18 co-authors). A phylogenomic study of birds reveals their evolutionary history. Science. 2008;320:1763-68.
16. Yoon HS, Grant J, Tekle YI, et al. (10 co-authors). Broadly sampled multigene trees of eukaryotes. BMC Evol Biol. 2008;8:14.
17. Gee H. Ending incongruence. Nature. 2003;425:782.
18. Philippe H, Snell EA, Bapteste E, Lopez P, Holland PWH, Casane D. Phylogenomics of Eukaryotes: Impact of missing data on large alignments. Mol Biol Evol. 2004;21:1740-52.
19. Jeffroy O, Brinkmann H, Delsuc F, Philippe H. Phylogenomics: the beginning of incongruence? Trends Genet. 2006;22:225-31.
20. Mc Guire JA, Witt CC, Altshuler DL, Remsen JV Jr. Phylogenetic systematics and biogeography of humming birds:Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Syst Biol. 2007;56:837-56.
21. Kolokotronis SO. Molecular evolution of Elephantidae and their tuberculosis pathogens. New York: Columbia University; 2008.
22. Smith SA, Beaulieu JM, Donoghue MJ. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol Biol. 2009;9:37.
23. Ripplinger J, Sullivan J. Does choice in model selection affect maximum likelihood analysis? Syst Biol. 2008;57:76-85.
24. Tavare S. Some probabilistic and statistical problems on the analysis of DNA sequences. Lect Math Life Sci. 1986;17:57-86.
25. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites. J Mol Evol.1994;39:306-14.
26. Ott M, Zola J, Aluru S, Stamatakis A. Large-scale Maximum Likelihoodbased phylogenetic analysis on the IBM BlueGene/L. On-Line Procceedings of IEEE/ACM Supercomputing Conference. 2007. Available at: http://www.sc07.supercomputing.org/schedule/pdf/pap271.pdf
27. Stamatakis A, Ott M. Exploiting fine-grained parallelism in the phylogenetic likelihood function with MPI, Pthreads, and OpenMP: A performance study. Proceedings of third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008). 2008:424-35.
28. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783-91.
29. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 2008;57:758-71.
30. Bininda-Emonds ORP, Brady SG, King J, Sanderson MJ. Scaling of accuracy in extremely large phylogenetic trees. Procceedings of Pacific Symposium on Biocomputing. 2001;6:547-58.
31. Moret BME, Roshan U, Warnow T. 2002. Sequence-length requirements for phylogenetic methods. In: Goos G. Hartmanis J. van Leeuwen J, eds. Procceedings of Algorithms in Bioinformatics: Second International Workshop, WABI 2002. Heidelberg, New York: Springer; 2002: 343-56. Lecture Notes in Computer Science; Vol. 2452.
32. Yang Z. Statistical properties of the Maximum Likelihood method of phylogenetic estimation and comparison with distance matrix methods. Syst Biol. 1994;43:329-42.
33. Goloboff PA, Catalano SA, Marcos Mirande J, et al. (7 co-authors). Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups. Cladistics. 2009;25:211-30.
34. Zwickl DJ, Hillis DM. Increased taxon sampling greatly reduces phylogenetic error. Syst Biol. 2002;51:588-98.
35. Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of live. Nat Rev Genet. 2005;6:361-75.
36. Graham SW, Olmstead RG, Barrett SCH. Rooting phylogenetic trees with distant outgroups: A case study from the Commelinoid monocots. Mol Biol Evol. 2002;19:1769-81.
37. Savolainen V, Chase MW, Hoot SB, et al. (10 co-authors). Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst Biol. 2000;49:306-62.
38. Stevens PF. 2001 onwards. Angiosperm Phylogeny Website. Version 8, June 2007 (and more or less continuously updated since). Available at: http://www.mobot.org/MOBOT/research/APweb/welcome.html. Accessed October 10 2009.
39. Angiosperm Phylogeny Group II. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot J Linn Soc. 2003;141:399-436.
40. Hilu KW, Borsch T, Müller K, et al. (16 co-authors). Angiosperm phylogeny based on matK sequence information. Am J Bot. 2003;90:1758-76.
41. Davies JT, Barradough TG, Chase MW, et al. (6 co-authors). Darwin's abominable mystery: Insights from a supertree of the angiosperms. Proc Natl Acad Sci U S A. 2004;101:1904-09.
42. Soltis PS, Soltis DE. The origin and diversification of angiosperms. Am J Bot. 2004;91:1614-26.
43. Qiu YL, Dombrovska O, Lee J, et al. (20 co-authors). Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. Int J Plant Sci. 2005;166:815-42.
44. Soltis DE, Gitzendanner MA, Soltis PS. A 567-taxon data set for angiosperms: The challenges posed by Bayesian analyses of large data sets. Int J Plant Sci. 2007;168:137-57.
45. Sanderson MJ, Wojciechowski MF, Hu J-M, Sher Khan T, Brady SG. Error, bias, and long-branch attraction in data of two chloroplast photosystem genes in seed plants. Mol Biol Evol. 2005;17:782-97.
46. Rydin C, Källersjö M. Taxon sampling and seed plant phylogeny. Cladistics. 2002;18:485-513.
47. Lanyon SM. Detecting internal inconsistencies in distance data. Syst Zool. 1985;34:397-403.
48. Stamatakis A. Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective. Procceedings of 20th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS 2006). 2006; no page numbers [Proceedings on CD].
49. Efron B, Halloran E, Holmes S. Bootstrap confidence levels for phylogenetic trees. Proc Natl Acad Sci U S A. 1996;93:13429.
50. Swofford DL. PAUP*: Phylogenetic analysis using parsimony (*and other methods). 4 ed. Champaign, USA: Sinauer Associates; 2002.
51. Huson DH, Dezulian T, Rausch C, Richter D, Rupp R. Dendroscope 0.22: Visualization of large trees. Tübingen: University of Tübingen, ZBIT, Department Algorithms in Bioinformatics. 2007.
52. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23:254-67.
53. Holland B, Moulton V. Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees. In: Benson G, Page R, eds. Algorithms in Bioinformatics: Third International Workshop, WABI, Budapest, Hungary. Proceedings. Berlin, Heidelberg, Stuttgart: Springer Verlag; 2003:165-76.
54. Grimm GW, Renner SS, Stamatakis A, Hemleben V. A nuclear ribosomal DNA phylogeny of Acer inferred with maximum likelihood, splits graphs, and motif analyses of 606 sequences. Evol Bioinform. 2:7-22.
55. Holland B, Huber KT, Moulton V, Lockhart PJ. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol Biol Evol. 2004;21:1459-61.
56. Nandi OI, Chase MW, Endress PK. A combined cladistic analysis of angiosperms using rbcL and non-molecular data sets. Ann MO Bot Gard. 1998;85:137-212.
57. Qiu YL, Lee JH, Bernasconi-Quadroni F, et al. (10 co-authors). The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature. 1999;402:404-07.
58. Soltis DE, Senters AE, Zanis MJ, et al. (9 co-authors). Gunnerales are sister to other core eudicots: Implications for the evolution of pentamery. Am J Bot. 2003;90:461-70.
59. Kim S, Soltis DE, Soltis PS, Zanis MJ, Suh Y. Phylogenetic relationships among early-diverging eudicots based on four genes: were the eudicots ancestrally woody? Mol Phylogenet Evol. 2004;31:16-30.
60. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How Many Bootstrap Replicates are Necessary? Proceedings of RECOMB 2009, Springer Lecture Notes in Bioinformatics. 2009;5541:184-200.
61. Stamatakis A, Komornik Z, Berger SA. Evolutionary Placement of Short Sequence Reads on Multi-Core Architectures. Accepted for publication at 8th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-10). PDF: http://wwwkramer.in.tum.de/exelixis/pubs/ Exelixis-RRDR-2009-2.pdf
62. Berger SA, Stamatakis A. Evolutionary Placement of Short Sequence Reads, Exelixis Rapid Research Dissemination Report 2009-3, TU Munich, November 2009. PDF: http://wwwkramer.in.tum.de/exelixis/pubs/Exelixis- RRDR-2009-3.pdf