Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data

BMC Evolutionary Biology

Volumn 14, Issue 1, 2014, Pages

  Fourment, Mathieu ^a   Holmes, Edward C ^a  

^a University of Sydney   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DATA SET; DIVERGENCE; EVOLUTIONARY BIOLOGY; GENE; GENE EXPRESSION; INFLUENZA; ROOT; SIMULATION;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPUTER SIMULATION; EVOLUTION; GENETICS; INFLUENZA VIRUS B; MOLECULAR EVOLUTION; PHYLOGENY; STATISTICAL MODEL;

BAYES THEOREM; BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; INFLUENZA B VIRUS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY;

EID: 84905373684     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/s12862-014-0163-6     Document Type: Article

References (26)

1. A nonparametric approach to estimating divergence times in the absence of rate constancy. MJ Sanderson, Mol Biol Evol 1997 14 1218 1231 10.1093/oxfordjournals.molbev.a025731 (Pubitemid 27523135)
2. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. MJ Sanderson, Mol Biol Evol 2002 19 101 109 10.1093/oxfordjournals.molbev.a003974 11752195 (Pubitemid 34008052)
3. Estimating the rate of evolution of the rate of molecular evolution. JL Thorne, H Kishino, IS Painter, Mol Biol Evol 1998 15 1647 1657 10.1093/oxfordjournals.molbev.a025892 9866200 (Pubitemid 28550989)
4. Conjugate Gibbs sampling for Bayesian phylogenetic models. N Lartillot, J Comput Biol 2006 13 1701 1722 10.1089/cmb.2006.13.1701 17238840 (Pubitemid 46175705)
5. Bayesian estimation of divergence times from large sequence alignments. S Guindon, Mol Biol Evol 2010 27 1768 1781 10.1093/molbev/msq060 20194424
6. A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times. Z Yang, Acta Zool Sin 2004 50 645 656
7. Dating phylogenies with hybrid local molecular clocks. S Aris-Brosou, PLoS One 2007 2 879 10.1371/journal.pone.0000879 17849008 (Pubitemid 351425669)
8. Relaxed phylogenetics and dating with confidence. AJ Drummond, SYW Ho, MJ Phillips, A Rambaut, PLoS Biol 2006 4 699 710 10.1371/journal.pbio.0040088
9. Bayesian random local clocks, or one rate to rule them all. AJ Drummond, MA Suchard, BMC Biol 2010 8 114 10.1186/1741-7007-8-114 20807414
10. A hierarchical Bayesian model for calibrating estimates of species divergence times. TA Heath, Syst Biol 2012 61 793 809 10.1093/sysbio/sys032 22334343
11. LJ Eshelman, The CHC adaptive search algorithm: how to do safe search when engaging in nontraditional genetic recombination Morgan Kaufmann Publisher, San Mateo, CA 1991
12. Automated phylogenetic detection of recombination using a genetic algorithm. SL Kosakovsky Pond, D Posada, MB Gravenor, CH Woelk, SDW Frost, Mol Biol Evol 2006 23 1891 1901 10.1093/molbev/msl051 16818476 (Pubitemid 44412875)
13. A genetic algorithm approach to detecting lineage-specific variation in selection pressure. SL Kosakovsky Pond, SDW Frost, Mol Biol Evol 2005 22 478 485 10.1093/molbev/msi031 (Pubitemid 40299496)
14. B Efron, RJ Tibshirani, An introduction to the bootstrap Chapman and Hall, New York 1993
15. Evolutionary trees from DNA-sequences-a maximum-likelihood approach. J Felsenstein, J Mol Evol 1981 17 368 376 10.1007/BF01734359 7288891 (Pubitemid 11016207)
16. BEAST: Bayesian evolutionary analysis by sampling trees. AJ Drummond, A Rambaut, BMC Evol Biol 2007 7 214 10.1186/1471-2148-7-214 17996036 (Pubitemid 351253125)
17. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. G Baele, P Lemey, T Bedford, A Rambaut, MA Suchard, AV Alekseyenko, Mol Biol Evol 2012 29 2157 2167 10.1093/molbev/mss084 22403239
18. The evolutionary dynamics of human influenza B virus. R Chen, EC Holmes, J Mol Evol 2008 66 655 663 10.1007/s00239-008-9119-z 18504518
19. Differentiation of influenza B virus lineages Yamagata and Victoria by real-time PCR. B Biere, B Bauer, B Schweiger, J Clin Microbiol 2010 48 1425 1427 10.1128/JCM.02116-09 20107085
20. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. VN Minin, EW Bloomquist, MA Suchard, Mol Biol Evol 2008 25 1459 1471 10.1093/molbev/msn090 18408232 (Pubitemid 351882020)
21. Sampling-through-time in birth-death trees. T Stadler, J Theor Biol 2010 267 396 404 10.1016/j.jtbi.2010.09.010 20851708
22. Tracer. http://tree.bio.ed.ac.uk/software/tracer/ [http://tree.bio.ed.ac. uk/software/tracer/]
23. Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus. M Worobey, GZ Han, A Rambaut, Proc Natl Acad Sci U S A 2014 111 8107 8112 10.1073/pnas.1324197111 24778238
24. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. M dos Reis, Z Yang, Mol Biol Evol 2011 28 2161 2172 10.1093/molbev/msr045 21310946
25. Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy. JO Wertheim, M Fourment, SL Kosakovsky Pond, Mol Biol Evol 2012 29 451 456 10.1093/molbev/msr266 22045998
26. Yersinia pestis and the Plague of Justinian 541-543 AD: a genomic analysis. DM Wagner, J Klunk, M Harbeck, A Devault, N Waglechner, JW Sahl, J Enk, DN Birdsell, M Kuch, C Lumibao, D Poinar, T Pearson, M Fourment, B Golding, JM Riehm, DJ Earn, S Dewitte, JM Rouillard, G Grupe, I Wiechmann, JB Bliska, PS Keim, HC Scholz, EC Holmes, H Poinar, Lancet Infect Dis 2014 14 319 326 10.1016/S1473-3099(13)70323-2 24480148