Fast Dating Using Least-Squares Criteria and Algorithms

Systematic Biology

Volumn 65, Issue 1, 2016, Pages 82-97

  To, Thu Hien ^a   Jung, Matthieu ^a,b   Lycett, Samantha ^c   Gascuel, Olivier ^a  

^a UNIV MONTPELLIER   (France)

^b UNIVERSITÉ DE STRASBOURG   (France)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Active set method; algorithms; computer simulations; dating; influenza (H1N1); least squares; linear algebra; molecular clock; serial data; substitution rate estimation; temporal precedence constraints; viruses

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETICS; INFLUENZA A VIRUS (H1N1); MOLECULAR EVOLUTION; PHYLOGENY; REGRESSION ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; INFLUENZA A VIRUS, H1N1 SUBTYPE; LEAST-SQUARES ANALYSIS; MODELS, GENETIC; PHYLOGENY; SOFTWARE;

EID: 84960356372     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syv068     Document Type: Article

References (60)

1. Akerborg O., Sennblad B., Lagergren J. 2008. Birth-death prior on phylogeny and speed dating. BMC Evol. Biol. 8:77.
2. Akerborg O., Sennblad B., Arvestad L., Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis.PNAS 106(14):5714-5719.
3. Ayres D.L., Darling A., Zwickl D.J., Beerli P., Holder M.T., Lewis P.O., Huelsenbeck J.P., Ronquist F., Swofford D.L., Cummings M.P., Rambaut A., Suchard M.A. 2012. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst. Biol. 61(1):170-173.
4. Battistuzzi F.U., Filipski.A, Hedges S.B., Kumar S. 2010. Performance of relaxed-clockmethods in estimating evolutionary divergence times and their credibility intervals. Mol. Biol. Evol. 27(6):1289-1300.
5. Bello G., Passaes C.P., Guimarães M.L., Lorete R.S., Matos Almeida S.E., Medeiros R.M., Alencastro P.R., Morgado M.G. 2008. Origin and evolutionary history of HIV-1 subtype C in Brazil. AIDS 22: 1993-2000.
6. Bertsekas D.P. 1999. Nonlinear programming. Cambridge, MA:Athena Scientific.
7. Boyd S., Vandenberghe L. 2004. Convex optimization, Chapter 5:244. Cambridge: Cambridge University Press.
8. Britton T., Anderson C.L., Jacquet D., Lundqvist S., Bremer K. 2007. Estimating divergence times in large phylogenetic trees. Syst. Biol. 56(5):741-752.
9. Christman M.C., Kedwaii A., Xu J., Donis R.O., Lu G. 2011. Pandemic (H1N1) 2009 virus revisited: an evolutionary retrospective. Infect. Genet. Evol. 11:803-811.
10. Desper R., Gascuel O. 2002. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J. Comput. Biol. 19(5):687-705.
11. Douzery E.J., Delsuc F., Stanhope M.J., Huchon D. 2003. Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations. J. Mol. Evol. 57(1 Suppl):S201-S213.
12. Doyon J.P., Ranwez V., Daubin V., Berry V. 2011. Models, algorithms and programs for phylogeny reconciliation. Brief. Bioinform. 12(5): 392-400.
13. Drummond A., Rodrigo A. 2000. Reconstruction genealogies of serial samples under the assumption of a molecular clock using serialsample UPGMA. Mol. Biol. Evol., 17(12):1807-1815.
14. Drummond A.J., Pybus O.G., Rambaut A., Forsberg R., Rodrigo A.G. 2003a. Measurably evolving populations. Trends Ecol. Evol. 18: 481-488.
15. Drummond A., Pybus O.G., Rambaut A. 2003b. Inference of viral evolutionary rates from molecular sequences. Adv. Parasitol. 54: 331-358.
16. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88.
17. Drummond A.J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
18. Drummond A.J., Suchard M.A., Xie D., Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29(8):1969-1973.
19. Felsenstein, J. 1989. PHYLIP - phylogeny inference package (Version 3.2). Cladistics 5:164-166.
20. Fitch W.M., Margoliash E. 1967. Construction of phylogenetic trees. Science 155:279-284.
21. Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14(7): 685-695.
22. Grenfell B.T., Pybus O.G., Gog J.R., Wood J.L., Daly J.M., Mumford J.A., Holmes E.C. 2004. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303:327-332.
23. Guindon S. 2010. Bayesian estimation of divergence times from large sequence alignments. Mol. Biol. Evol. 27:1768-1781.
24. Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to infer large phylogenies by maximum-likelihood. Syst. Biol. 52(5):696-704.
25. Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321.
26. Hedge J., Lycett S.J., Rambaut A. 2013. Real-time characterization of the molecular epidemiology of an influenza pandemic. Biol. Lett. 9:5 20130331.
27. Hedges S.B., Kumar S., editors. 2009. The timetree of life. New York: Oxford University Press.
28. Jetz W., Thomas G.H., Joy J.B., Redding D.W., Hartmann K., Mooers A.O. 2014. Global distribution and conservation of evolutionary distinctness in birds. Curr. Biol. 24(9):919-930.
29. Lambert D.M., Ritchie P.A., Millar C.D., Holland B., Drummond A.J., Baroni C. 2002. Rates of evolution in ancient DNA from Adelie penguins. Science 295:2270-2273.
30. Langley C.H., Fitch W. 1974. An examination of the constancy of the rate of molecular evolution. J. Mol. Evol. 3:161-177.
31. Lefort V., Desper R., Gascuel O. 2015 (forthcoming). FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol. Biol. Evol. 32:2798-2800.
32. Lemey P., Suchard M., Rambaut A. 2009. Reconstructing the initial global spread of a human influenza pandemic: A Bayesian spatial- temporal model for the global spread of H1N1pdm. PLoS Curr. 1:RRN1031.
33. Lepage T., Bryant D., Philippe H. Lartillot N. 2007. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 24:2669-2680.
34. Mourad R., Chevennet F., Dunn D.T. Fearnhill E., Delpech V., Asboe D., Gascuel O., Hue S. 2015. A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK. AIDS 500:15-00106.
35. Murty K.G. 1988. Linear complementarity, linear and nonlinear programming. Sigma Series in Applied Mathematics, Vol. 3. Berlin: Heldermann Verlag. p. 447-448
36. Nocedal J., Wright S.J. 2006. Numerical optimization. 2nd ed., Chapter 16. Springer-Verlag, Berlin, New York. p. 455-468
37. O'Meara, O.T. 2000. Introduction to quadratic forms. Berlin and New York: Springer-Verlag.
38. Posada D., Crandall K.A. 2001. Evaluation of methods for detecting recombination fromDNAsequences: Computer simulations. PNAS 98(24):13757-13762.
39. Rambaut A. 2000. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16(4):395-399.
40. Rambaut A. 2007. Path-O-Gen web server: http://tree.bio.ed.ac.uk/software/pathogen/
41. 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.
42. Rambaut A., Holmes E. 2009. The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic. PLoS Curr. 1:RRN1003.
43. Rannala B., Yang Z. 2007. Inferring speciation times under an episodic molecular clock. Syst. Biol. 56(3):453-466.
44. Rasmussen M.D., Kellis M. 2012. Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Res. 22(4):755-765.
45. Ronquist F., Klopfstein S., Vilhelmsen L., Schulmeister S., Murray D.L., Rasnitsyn A.P. 2012. A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera. Syst. Biol. 61(6):973-999.
46. Saitou N., Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4(4):406-425.
47. Sanderson M.J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1218-1231.
48. Sanderson M.J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
49. Sanderson M.J. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics. 19(2):301-302.
50. Shankarappa R., Margolick J. B., Gange S. J., Rodrigo A. G., Upchurch D., Farzadegan H., Gupta P., Rinaldo C. R., Learn G. H., He X., Huang X.L., Mullins J.I. 1999. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73:10489-10502.
51. Smith S. A., O'Meara B.C. 2012. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28:2689-2690.
52. Sokal R., Michener C. 1958. A statistical method for evaluating systematic relationships. Kans. Univ. Sci. Bull. 38:1409-1438.
53. Stadler T. 2010. Sampling-through-time in birth-death trees. J. Theor. Biol. 267:396-404.
54. Tarjan R. E. 1983. Data structures and network algorithms. Philadelphia: SIAM.
55. Tamura K., Battistuzzi F.U., Billing-Ross P., Murillo O., Filipski A., Kumar S. 2012. Estimating divergence times in large molecular phylogenies. PNAS 109:19333-19338.
56. Thorne J.L., Kishino H., Painter S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15(12): 1647-1657.
57. Thorne J.L., Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51(5):689-702.
58. Volz E.M., Koelle K., Bedford T. 2013. Viral phylodynamics. PLoS Comput. Biol. 9:e1002947.
59. Xia X., Yang Q. 2011. A distance-based least-square method for dating speciation events. Mol. Phylogenet. Evol. 59:342-353.
60. Yang Z., O'Brien J.D., Zheng X., Zhu H.Q., She Z.S. 2007. Tree and rate estimation by local evaluation of heterochronous nucleotide data. Bioinformatics 23(2):169-176.