Transition between Stochastic Evolution and Deterministic Evolution in the Presence of Selection: General Theory and Application to Virology

Microbiology and Molecular Biology Reviews - Tập 65 Số 1 - Trang 151-185 - 2001
Igor M. Rouzine1, Allen G. Rodrigo2, John M. Coffin1
1Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts 02111,1 and
2School of Biological Sciences, University of Auckland, Auckland, New Zealand2

Tóm tắt

SUMMARYWe present here a self-contained analytic review of the role of stochastic factors acting on a virus population. We develop a simple one-locus, two-allele model of a haploid population of constant size including the factors of random drift, purifying selection, and random mutation. We consider different virological experiments: accumulation and reversion of deleterious mutations, competition between mutant and wild-type viruses, gene fixation, mutation frequencies at the steady state, divergence of two populations split from one population, and genetic turnover within a single population. In the first part of the review, we present all principal results in qualitative terms and illustrate them with examples obtained by computer simulation. In the second part, we derive the results formally from a diffusion equation of the Wright-Fisher type and boundary conditions, all derived from the first principles for the virus population model. We show that the leading factors and observable behavior of evolution differ significantly in three broad intervals of population size, N. The “neutral limit” is reached when N is smaller than the inverse selection coefficient. When N is larger than the inverse mutation rate per base, selection dominates and evolution is “almost” deterministic. If the selection coefficient is much larger than the mutation rate, there exists a broad interval of population sizes, in which weakly diverse populations are almost neutral while highly diverse populations are controlled by selection pressure. We discuss in detail the application of our results to human immunodeficiency virus population in vivo, sampling effects, and limitations of the model.

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Tài liệu tham khảo

Abramowitz M. Stegun I. Handbook of mathematical functions. 1964 National Bureau of Standards New York N.Y

10.1128/jvi.64.12.6221-6233.1990

10.1038/376125a0

Burns D. P. Desrosiers R. C. Envelope sequence variation, neutralizing antibodies, and primate lentivirus persistence.Curr. Top. Microbiol. Immunol.1881994185219

10.1128/jvi.65.4.1843-1854.1991

10.1038/348454a0

10.1017/S0016672397002954

10.1016/S0960-9822(07)00416-2

10.1099/0022-1317-75-11-3249

10.1097/00042560-199605010-00002

10.1038/374569a0

10.1128/jvi.68.10.6672-6683.1994

Donis R. O. Muller's ratchet and flu virus.Science2531991308309

10.1073/pnas.89.13.6015

Eigen M. Biebricher C. K. Sequence space and quasispecies distribution RNA genetics Domingo E. Holland J. J. Ahlquist P. III 1988 3 22 CRC Press, Inc. Boca Raton, Fla

10.1006/jmbi.1998.2366

10.1093/genetics/78.2.737

10.1017/S0370164600023993

10.1017/S0370164600044886

10.1128/jvi.66.10.6175-6180.1992

10.1146/annurev.immunol.17.1.625

10.1126/science.274.5289.985

Haldane J. B. S. A mathematical theory of natural and artificial selection.Trans. Camb. Philos. Soc.2319241941

10.1017/S0305004100015644

10.1038/373123a0

Holland J. J. De La Torre J. C. Steinhauer D. A. RNA virus populations as quasispecies.Curr. Top. Microbiol. Immunol.1761992120

10.1073/pnas.89.11.4835

Hudson R. R. Boos D. B. Kaplan N. L. A statistical test for detecting geographic subdivision.Mol. Biol. Evol.91992138151

Karlin S. McGregor J. On some stochastic models in genetics Stochastic models in medicine and biology. Gurland J. 1964 245 271 University of Wisconsin Press Madison

10.1006/viro.1993.1503

10.1093/genetics/39.3.280

10.1073/pnas.41.3.144

10.1101/SQB.1955.020.01.006

10.1093/genetics/47.6.713

10.2307/3211856

10.1139/g89-009

Kimura M. Population genetics molecular evolution and the neutral theory. Selected papers. 1994 The University of Chicago Press Chicago Ill

10.1093/genetics/61.3.763

10.1016/0304-4149(82)90011-4

10.2307/3213548

10.1007/BF01457949

10.1006/tpbi.1997.1299

10.1128/jvi.67.7.3951-3960.1993

10.1128/jvi.70.3.2038-2043.1996

10.1073/pnas.94.5.1862

10.1128/jvi.71.6.4284-4295.1997

10.1073/pnas.88.10.4280

10.1128/jvi.69.11.6911-6916.1995

10.1128/jvi.69.8.5087-5094.1995

Mayers D. L. McCutchan F. E. Sandersbuell E. E. Merritt L. I. Dilworth S. Fowler A. K. Marks C. A. Ruiz N. M. Richman D. D. Roberts C. R. Burke D. S. Characterization of HIV isolates arising after prolonged zidovu-dine therapy.J. Acquired Immune Defic. Syndr.51992749759

10.1016/0022-5193(71)90058-0

10.1098/rspb.1958.0054

10.1086/280418

10.1086/282771

10.1093/genetics/145.2.519

Nietfield W. Bauer M. Fevrier M. Maier R. Holzwarth B. Frank R. Maier B. Riviere Y. Meyerhans A. Sequence constraints and recognition by CTL of an HLA-B27-restricted HIV-1 gag epitope.J. Immunol.154199521892197

10.1017/S0016672300033619

10.1128/jvi.70.9.6414-6417.1996

10.1128/jvi.69.11.6805-6809.1995

10.1128/jvi.69.5.2869-2872.1995

10.1007/BF02111283

10.1126/science.271.5255.1582

Raikh M. E. Ruzin I. M. Transmittance fluctuations in randomly non-uniform barriers and incoherent mesoscopics Quantum phenomena in mesoscopic systems. Altshuler B. L. Lee P. A. Webb R. A. 1991 301 354 North Holland Amsterdam The Netherlands

10.1128/JVI.72.1.113-120.1998

Rodrigo A. G. Felsenstein J. Coalescent approaches to HIV population genetics Molecular evolution of HIV. Crandall K. 1999 233 272 John Hopkins University Press Baltimore Md

10.1073/pnas.96.5.2187

10.1073/pnas.96.19.10758

10.1128/JVI.73.10.8167-8178.1999

10.1006/viro.1995.1548

Seibert S. A. Howell C. Y. Hughes M. K. Hughes A. L. Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1).Mol. Biol. Evol.121995803813

10.1128/JVI.73.12.10489-10502.1999

Shklovski B. I. Efros A. L. Electronic properties of doped semiconductors. 1984 Springer-Verlag KG Berlin Germany

10.1084/jem.170.6.2023

Wain-Hobson S. Sala M. Drift and conservatism in RNA virus evolution: are they adapting or merely changing? Origin and evolution of viruses. Domingo E. Webster R. Holland J. 1999 115 140 Academic Press Ltd. London United Kingdom

10.1214/aoms/1177704463

10.1016/0040-5809(75)90020-9

10.1038/373117a0

10.1073/pnas.87.24.9938

10.1016/0042-6822(91)90767-6

10.1093/genetics/16.2.97

10.1073/pnas.31.12.382

10.2307/1931666

10.1073/pnas.94.4.1264

10.1128/jvi.70.12.8879-8887.1996

10.1128/JVI.73.1.855-860.1999

10.1128/jvi.67.6.3345-3356.1993

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Microbiology and Molecular Biology Reviews

Tập 65 Số 1

151-185

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