Test of genetical isochronism for longitudinal samples of DNA sequences

Genetics

Volumn 176, Issue 1, 2007, Pages 327-342

  Liu, Xiaoming ^a   Fu, Yun Xin ^a  

^a UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA ANALYSIS; DNA SEQUENCE; EXPERIMENTAL DESIGN; GENE MUTATION; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; SAMPLE SIZE; BIOLOGICAL MODEL; GENETIC PROCEDURES; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE;

RNA VIRUSES;

BASE SEQUENCE; EVOLUTION, MOLECULAR; GENETIC TECHNIQUES; MODELS, GENETIC;

EID: 34548569323     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.065037     Document Type: Article

References (23)

1. ACHAZ, G., S. PALMER, M. KEARNEY, F. MALDARELLI, J. W. MELLORS et al., 2004 A robust measure of HIV-1 population turnover within chronically infected individuals. Mol. Biol. Evol. 21: 1902-1912.
2. DRUMMOND, A., and A. G. RODRIGO, 2000 Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA. Mol. Biol. Evol. 17: 1807-1815.
3. DRUMMOND, A., R. FORSBERG and A. G. RODRIGO, 2001 The inference of stepwise changes in substitution rates using serial sequence samples. Mol. Biol. Evol. 18: 1365-1371.
4. DRUMMOND, A. J., 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.
5. DRUMMOND, A. J., O. G. PYBUS, A. RAMBAUT, R. FORSBERG and A. G. RODRIGO, 2003 Measurably evolving populations. Trends Ecol. Evol. 18: 481-488.
6. EWENS, W. J., and G. R. GRANT, 2005 Statistical Methods in Bioinformatics: An Introduction. Springer, New York.
7. FELSENSTEIN, J., 1992 Estimating effective population size from samples of sequences: a bootstrap Monte Carlo integration method. Genet. Res. 60: 209-220.
8. FU, Y. X., 1994 A phylogenetic estimator of effective population-size or mutation-rate. Genetics 136: 685-692.
9. FU, Y. X., 1995 Statistical properties of segregating sites. Theor. Popul. Biol. 48: 172-197.
10. FU, Y. X., 2001 Estimating mutation rate and generation time from longitudinal samples of DNA sequences. Mol. Biol. Evol. 18: 620-626.
11. FU, Y. X., and W. H. LI, 1999 Coalescing into the 21st century: an overview and prospects of coalescent theory. Theor. Popul. Biol. 56: 1-10.
12. GRIFFITHS, R. C., and S. TAVARE, 1994 Simulating probability-distributions in the coalescent. Theor. Popul. Biol. 46: 131-159.
13. HUDSON, R. R., 1983 Testing the constant-rate neutral allele model with protein-sequence data. Evolution 37: 203-217.
14. HUDSON, R. R., D. D. BOOS and N. L. KAPLAN, 1992 A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9: 138-151.
15. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 1995 Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
16. RAMBAUT, A., 2000 Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16: 395-399.
17. RODRIGO, A. G., E. G. SHPAER, E. L. DELWART, A. K. N. IVERSEN, M. V. GALLO et al., 1999 Coalescent estimates of HIV-1 generation time in vivo. Proc. Natl. Acad. Sci. USA 96: 2187-2191.
18. RODRIGO, A. G., M. GOODE, R. FORSBERG, H. A. ROSS and A. DRUMMOND, 2003 Inferring evolutionary rates using serially sampled sequences from several populations. Mol. Biol. Evol. 20: 2010-2018.
19. SEO, T. K., J. L. THORNE, M. HASEGAWA and H. KISHINO, 2002a Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach. Genetics 160: 1283-1293.
20. SEO, T. K., J. L. THORNE, M. HASEGAWA and H. KISHINO, 2002b A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. Bioinformatics 18: 115-123.
21. TAJIMA, F., 1983 Evolutionary relationship of DNA-sequences in finite populations. Genetics 105: 437-460.
22. WAKELEY, J., and J. HEY, 1997 Estimating ancestral population parameters. Genetics 145: 847-855.
23. WATTERSON, G. A., 1975 Number of segregating sites in genetic models without recombination. Theor. Popul. Biol. 7: 256-276.