Inferring Evolutionary Rates Using Serially Sampled Sequences from Several Populations

Molecular Biology and Evolution

Volumn 20, Issue 12, 2003, Pages 2010-2018

  Rodrigo, Allen G ^a,b   Goode, Matthew ^a,b   Forsberg, Roald ^c   Ross, Howard A ^a,b   Drummond, Alexei ^a,d  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

^c AARHUS UNIVERSITY   (Denmark)

^d UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Maximum likelihood; Serial samples; Substitution rate; Subtree likelihood; Whole tree likelihood

Indexed keywords

ANALYTIC METHOD; ARTICLE; BAYES TEST; BAYES THEOREM; CLINICAL ARTICLE; DNA SEQUENCE; DRUG RESPONSE; EVOLUTIONARY RATE; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MAXIMUM LIKELIHOOD METHOD; NUCLEIC ACID BASE SUBSTITUTION; PHYLOGENETIC TREE; POPULATION GENETICS; SAMPLE; SERIAL SAMPLE; SUBSTITUTION RATE; SUBTREE LIKELIHOOD METHOD; VIRUS; VIRUS ENVELOPE; VIRUS EVOLUTION; VIRUS REPLICATION; WHOLE TREE LIKELIHOOD METHOD;

ALGORITHMS; ANTIRETROVIRAL THERAPY, HIGHLY ACTIVE; BAYES THEOREM; EVOLUTION, MOLECULAR; HIV-1; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0346095397     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg215     Document Type: Article

References (24)

1. Barnes, I., P. Matheus, B. Shapiro, D. Jensen, and A. Cooper. 2002. Dynamics of Pleistocene population extinctions in Beringian brown bears. Science 295:2267-2270.
2. Drummond, A., R. Forsberg, and A. G. Rodrigo. 2001. Estimating stepwise changes in substitution rates using serial samples. Mol. Biol. Evol. 18:1365-1371.
3. Drummond, A., G. K. Nicholls, A. G. Rodrigo, and W. Solomon. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320.
4. Drummond, A., and A. G. Rodrigo. 2000. Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA (sUPGMA). Mol. Biol. Evol. 17:1807-1815.
5. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376.
6. Finzi, D., M. Hermankova, T. Pierson et al. (15 co-authors). 1997. Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science 278:1295-1300.
7. Forsberg R., M. B. Oleksiewicz, A. M. K. Petersen, J. Hein, A. Botner, and T. Storgaard. 2001. A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease. Virology 289: 174-179.
8. Fu, Y. X. 2001. Estimating mutation rate and generation time from longitudinal samples of DNA sequences. Mol. Biol. Evol. 18:620-626.
9. Goldman, N. 1990. Maximum likelihood inferences of phylogenetic trees, with special reference to the Poisson process model of DNA substitutions and to parsimony analysis. Syst. Zool. 39:345-361.
10. Gu, X. 2001. Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18:453-464.
11. Gunthard, H. F., S. D. Frost, A. J. Leigh Brown et al. (12 co-authors). 1999. Evolution of envelope sequences of human immunodeficiency virus type 1 in cellular reservoirs in the setting of potent antiviral therapy. J. Virol. 73:9404-9412.
12. Holmes, E. C., L. Q. Zhang, P. Simmonds, C. A. Ludlam, and A. J. Leigh Brown. 1992. Convergent and divergent sequence evolution in the surface envelope glycoprotein of HIV-1 within a single infected patient. Proc. Natl. Acad. Sci. USA 89:4835-4839.
13. Lambert, D. M., P. A. Ritchie, C. D. Millar, B. Holland, A. J. Drummond, and C. Baroni. 2002. Rates of evolution in ancient DNA from Adelie penguins. Science 295:2270-2273.
14. Leitner, T., and J. Albert. 1999. The molecular clock of HIV-1 unveiled through analysis of a known transmission history. Proc. Natl. Acad. Sci. USA 96:10752-10757.
15. Leonard, J.A., R. K. Wayne, and A. Cooper. 2000. Population genetics of Ice Age brown bears. Proc. Natl. Acad. Sci. USA. 97:1651-1654.
16. Ota, R., P. J. Waddell, M. Hasegawa, H. Shimodaira, and H. Kishino. 2000. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. Mol. Biol. Evol. 17:798-803.
17. Rambaut, A. 2000. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16:395-399.
18. Rodrigo, A. G., E. G. Shpaer, E. L. Delwart, A. K. N. Iversen, M. V. Gallo, J. Brojatsch, M. S. Hirsch, B. D. Walker, and J. I. Mullins. 1999. Coalescent estimates of HIV-1 generation time in vivo. Proc. Natl. Acad. Sci. USA 96:2187-2191.
19. Rodriguez, F., J. F. Oliver, A. Marin, and J. R. Medina. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142:485-501.
20. Seo, T. K., J. L. Thorne, M. Hasegawa, and H. Kishino. 2002a. A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. Bioinformatics 18:115-123.
21. -. 2002b. Estimation of effective population size of HIV-1 within a host. A pseudomaximum-likelihood approach. Genetics 160:1283-1293.
22. Shankarappa, R., J. B. Margolick, S. J. Gange et al. (12 co-authors). 1999. Consistent viral evolutionary dynamics associated with the progression of HIV-1 infection. J. Virol. 73:10489-10502.
23. Swofford, D. L. 1999. PAUP*: phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Mass.
24. Wong, J. K., M. Hezareh, H. F. Gunthard, D.V. Havlir, C. C. Ignacio, C. A. Spina, and D. D. Richman. 1997. Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science 278:1291-1295.