The structure of allelic diversity in the presence of purifying selection

Theoretical Population Biology

Volumn 81, Issue 2, 2012, Pages 144-157

  Desai, Michael M ^a,b   Nicolaisen, Lauren E ^a,b   Walczak, Aleksandra M ^c   Plotkin, Joshua B ^d  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c CNRS   (France)

^d UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Allelic diversity; Ewens sampling formula; Linkage; Purifying selection

Indexed keywords

ALLELE; EMPIRICAL ANALYSIS; FITNESS; MOLECULAR ANALYSIS; MUTATION; NATURAL SELECTION; NUMERICAL MODEL; POPULATION GENETICS; SAMPLING;

ALLELE; ARTICLE; COMPARATIVE STUDY; FITNESS; GENETIC LINKAGE; GENETIC VARIABILITY; GENETICS; HUMAN; POISSON DISTRIBUTION; POPULATION DYNAMICS; PROBABILITY; REPRODUCTIVE FITNESS;

ALLELES; GENETIC FITNESS; GENETIC LINKAGE; GENETIC VARIATION; HUMANS; PHYSICAL FITNESS; POISSON DISTRIBUTION; POPULATION DYNAMICS; PROBABILITY;

EID: 84856535119     PISSN: 00405809     EISSN: 10960325     Source Type: Journal    
DOI: 10.1016/j.tpb.2011.12.002     Document Type: Article

References (42)

1. Abramowitz M., Stegun I.A. Handbook of Mathematical Functions 1965, Dover, New York.
2. Barton N.H., Etheridge A.M. The effect of selection on genealogies. Genetics 2004, 166:1115-1131.
3. Betancourt A.J., Welch J.J., Charlesworth B. Reduced effectiveness of selection caused by a lack of recombination. Current Biology 2009, 19:655-660.
4. Charlesworth B. The effect of background selection against deleterious mutations on weakly selected, linked variants. Genetical Research 1994, 63:213-227.
5. Charlesworth B., Morgan M.T., Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics 1993, 134:1289-1303.
6. Charlesworth D., Charlesworth B., Morgan M.T. The pattern of neutral molecular variation under the background selection model. Genetics 1995, 141:1619-1632.
7. Comeron J.A., Kreitman M. Population, evolutionary and genomic consequences of interference selection. Genetics 2002, 161:389-410.
8. Comeron J.M., Williford A., Kliman R.M. The hill-robertson effect: evolutionary consequences of weak selection and linkage in finite populations. Heredity 2008, 100:19-31.
9. Etheridge A.M., Griffiths R.C. A coalescent dual process in a moran model with genic selection. Theoretical Population Biology 2009, 75:320-330.
10. Etheridge A.M., Griffiths R.C., Taylor J.E. A coalescent dual process in a moran model with genic selection, and the lambda coalescent limit. Theoretical Population Biology 2010, 78:77-92.
11. Ethier S.N., Kurtz T.G. The infinitely-many alleles model with selection as a measure-valued diffusion. Stochastic Models in Biology, Lecture Notes in Biomathematics 1987, 70:72-86.
12. Ethier S.N., Kurtz T.G. Convergence to fleming-viot processes in the weak atomic topology. Stochastic Processes and their Applications 1994, 54:1-27.
13. Ewens W.J. The sampling theory of selectively neutral alleles. Theoretical Population Biology 1972, 3:87-112.
14. Ewens W.J. Mathematical Population Genetics: I. Theoretical Introduction 2004, Springer, New York, NY.
15. Ewens W.J., Li W.-H. Frequency spectra of neutral and deleterious alleles in a finite population. Journal of Mathematical Biology 1980, 10:155-166.
16. Gordo I., Navarro A., Charlesworth B. Muller's ratchet and the pattern of variation at a neutral locus. Genetics 2002, 161:835-848.
17. Griffiths R.C. Allele frequencies with genic selection. Journal of Mathematical Biology 1983, 17:1-10.
18. Grote M.N., Speed T.P. Approximate ewens formulae for symmetric overdominance selection. Annals of Applied Probability 2002, 12:637-663.
19. Hahn M.W. Toward a selection theory of molecular evolution. Evolution 2008, 62:255-265.
20. Haigh J. The accumulation of deleterious genes in a population-Muller's ratchet. Theoretical Population Biology 1978, 14:251-267.
21. Hartl D.L. A Primer of Population Genetics 1988, Sinauer Associates, Sunderland, MA.
22. Hermisson J., Redner O., Wagner H., Baake E. Mutation-selection balance: ancestry, load, and maximum principle. Theoretical Population Biology 2002, 62:9-46.
23. Hudson R., Kaplan N. Gene trees with background selection. Non-Neutral Evolution: Theories and Molecular Data 1994, 140-153. Chapman and Hall, New York. B. Golding (Ed.).
24. Hudson R., Kaplan N. Deleterious background selection with recombination. Genetics 1995, 141:1605-1617.
25. Joyce P. Robustness of the ewens sampling formula. Journal of Applied Probability 1995, 32:609-622.
26. Joyce P., Tavare S. The distribution of rare alleles. Journal of Mathematical Biology 1995, 33:602-618.
27. Kaiser V.B., Charlesworth B. The effects of deleterious mutations on evolution in non-recombining genomes. Trends in Genetics 2009, 25:9-12.
28. Kaplan N.L., Darden T., Hudson R.R. The coalescent process in models with selection. Genetics 1988, 120:819-829.
29. Karlin S., McGregor J. Addendum to a paper of W. Ewens. Theoretical Population Biology 1972, 3:113-116.
30. Kimura M., Maruyama T. The mutational load with epistatic gene interactions in fitness. Genetics 1966, 54:1337-1351.
31. Li W.-H. Maintenance of genetic variability under mutation and selection pressures in a finite population. PNAS 1977, 74:2509-2513.
32. Li W.-H. Maintenance of genetic variability under the joint effect of mutation, selection and random drift. Genetics 1978, 90:349-382.
33. Li W.-H. Maintenance of genetic variability under the pressure of neutral and deleterious mutations in a finite population. Genetics 1979, 92:647-667.
34. Lohse K., Harrison R.J., Barton N.H. A general method for calculating likelihoods under the coalescent process. Genetics 2011, 189:977-987.
35. McVean G.A.T., Charlesworth B. The effects of hill-robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 2000, 155:929-944.
36. Nordborg M., Charlesworth B., Charlesworth D. The effect of recombination on background selection. Genetical Research 1996, 67:159-174.
37. O'Fallon B.D., Seger J., Adler F.R. A continuous-state coalescent and the impact of weak selection on the structure of gene genealogies. Molecular Biology and Evolution 2010, 27:1162-1172.
38. Sawyer S.A., Hartl D.L. Population genetics of polymorphism and divergence. Genetics 1992, 132:1161-1176.
39. Seger J., Smith W.A., Perry J.J., Hunn J., Kaliszewska Z.A., Sala L.L., Pozzi L., Rowntree V.J., Adler F.R. Gene genealogies strongly distorted by weakly interfering mutations in constant environments. Genetics 2010, 184:529-545.
40. Walczak A.M., Nicolaisen L.E., Plotkin J.B., Desai M.M. The structure of genealogies in the presence of purifying selection: an effective coalescent theory. Genetics 2011, 10.1534/genetics.111.134544.
41. Watterson G.A. The homozygosity test of neutrality. Genetics 1978, 88:405-417.
42. Williamson S., Orive M.E. The genealogy of a sequence subject to purifying selection at multiple sites. Molecular Biology and Evolution 2002, 19:1376-1384.