Genetic Diversity in the Interference Selection Limit

PLoS Genetics

Volumn 10, Issue 3, 2014, Pages

  Good, Benjamin H ^a,b   Walczak, Aleksandra M ^c   Neher, Richard A ^d   Desai, Michael M ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c LABORATOIRE DE PHYSIQUE STATISTIQUE   (France)

^d MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME; INTERFERENCE SELECTION; MOLECULAR EVOLUTION; MUTATION; PURIFYING SELECTION; REPRODUCTIVE FITNESS; GENETIC LINKAGE; GENETIC POLYMORPHISM; GENETICS; HUMAN; POPULATION GENETICS;

EVOLUTION, MOLECULAR; GENETIC LINKAGE; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; MUTATION; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SELECTION, GENETIC;

EID: 84897428561     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004222     Document Type: Article

References (86)

1. Barrick JE, et al. (2009) Genome evolution and adaptation in a long-term experiment with Es-cherichia coli. Nature 461: 1243-1247.
2. Lang GI, Rice DP, Hickman MJ, Sodergren E, Weinstock GM, et al. (2013) Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 500: 571-574.
3. Andersen EC, Gerke JP, Shapiro JA, Crissman JR, Ghosh R, et al. (2012) Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nature Genetics 44: 285-290.
4. Begun DJ, Aquadro CF, (1992) Levels of naturally occuring dna polymorphism correlate with recombination rates in D. melanogaster. Nature 356: 519-520.
5. Sella G, Petrov DA, Przeworski M, Andolfatto P, (2009) Pervasive natural selection in the Drosophila genome? PLoS Genetics 5: e1000495.
6. McVicker G, Gordon D, Davis C, Green P, (2009) Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet 5: e1000471.
7. Lohmueller KE, Albrechtsen A, Li Y, Kim SY, Korneliussen T, et al. (2011) Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genetics 7: e1002326.
8. Sawyer SA, Hartl DL, (1992) Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
9. Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, et al. (2002) The cost of inbreeding in Arabidopsis. Nature 416: 531-534.
10. Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, et al. (2005) Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Nat Acad Sci 102: 7882-7887.
11. Keightley PD, Eyre-Walker A, (2007) Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177: 2251-2261.
12. Boyko AR, Williamson SH, Indap AR, Degenhardt JD, R D Hernandez e, (2008) Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 4: e1000083.
13. Neher RA, (2013) Genetic draft, selective interference, and population genetics of rapid adaptation. Annual Review of Ecology, Evolution, and Systematics 44: 195-215.
14. Bustamante CD, Wakeley J, Sawyer S, Hartl DL, (2001) Directional selection and the site-frequency spectrum. Genetics 159: 1779-1788.
15. Messer PW, Petrov DA, (2013) Frequent adaptation and the mcdonald-kreitman test. Proc Natl Acad Sci 110: 8615-8620.
16. Charlesworth B, Morgan MT, Charlesworth D, (1993) The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
17. Smith JM, Haigh J, (1974) Hitch-hiking effect of a favorable gene. Genet Res 23: 23-35.
18. Cutter AD, Payseur BA, (2013) Genomic signatures of selection at linked sites: unifying the disparity among species. Nat Rev Gen 14: 262-274.
19. Barraclough TG, Fontaneto D, Ricci C, Herniou EA, (2007) Evidence for inefficient selection against deleterious mutations in cytochrome oxidase i of asexual bdelloid rotifers. Mol Biol Evol 24: 1952-1962.
20. Bartolomé C, Charlesworth B, (2006) Evolution of amino-acid sequences and codon usage on the Drosophila miranda neo-sex chromosomes. Genetics 174: 2033-2044.
21. Betancourt AJ, Welch JJ, Charlesworth B, (2009) Reduced effectiveness of selection caused by a lack of recombination. Current Biology 19: 655-660.
22. Seger J, Smith WA, Perry JJ, Hunn J, Kaliszewska ZA, et al. (2010) Gene geneologies strongly distorted by weakly interfering mutations in constant environments. Genetics 184: 529-545.
23. Subramanian S, (2012) The abundance of deleterious polymorphisms in humans. Genetics 190: 1579-1583.
24. O'Fallon B, (2013) Purifying selection causes widespread distortions of genealogical structure on the human x chromosome. Genetics 194: 485-492.
25. McVean GAT, Charlesworth B, (2000) The effects of hill-robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 155: 929-944.
26. Comeron JM, Kreitman M, (2002) Population, evolutionary, and genomic consequences of interference selection. Genetics 161: 389-410.
27. Przeworski M, Charlesworth B, Wall JD, (1999) Genealogies and weak purifying selection. Mol Biol Evol 16: 246-252.
28. Williamson S, Orive ME, (2002) The genealogy of a sequence subject to purifying selection at multiple sites. Mol Biol Evol 19: 1376-1384.
29. Kaiser VB, Charlesworth B, (2008) The effects of deleterious mutations on evolution in nonrecombining genomes. Trends in Genetics 25: 9-12.
30. Wilson Sayres MA, Lohmueller KE, Nielsen R, (2014) Natural selection reduced diversity on human y chromosomes. PLoS Genet 10: e1004064.
31. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by dna polymorphism. Genetics 123: 585-595.
32. Haigh J, (1978) The accumulation of deleterious genes in a population. Theor Pop Biol 14: 251-267.
33. Kaplan N, Darden T, Hudson R, (1988) The coalescent process in models with selection. Genetics 1988: 819-829.
34. Hudson RR, Kaplan NL, (1995) Deleterious background selection with recombination. Genetics 141: 1605-1617.
35. Nordborg M, Charlesworth B, Charlesworth D, (1996) The effect of recombination on background selection. Genet Res 67: 159-174.
36. Walczak AM, Nicolaisen LE, Plotkin JB, Desai MM, (2012) The structure of genealogies in the presence of purifying selection: a fitness-class coalescent. Genetics 190: 753-779.
37. Nicolaisen LE, Desai MM, (2012) Distortions in genealogies due to purifying selection. Molecular Biology and Evolution 29: 3589-3600.
38. Nicolaisen LE, Desai MM, (2013) Distortions in genealogies due to purifying selection and recombination. Genetics 195: 221-230.
39. Charlesworth D, Charlesworth B, Morgan MT, (1995) The pattern of neutral molecular variation under the background selection model. Genetics 141: 1619-1632.
40. Hudson RR, Kaplan NL (1994) Gene trees with background selection. In: Evolution: Theories and Molecular Data, London: Chapman & Hall. pp. 140-153.
41. Gordo I, Navarro A, Charlesworth B, (2002) Muller's ratchet and the pattern of variation at a neutral locus. Genetics 161: 835-848.
42. Zeng K, Charlesworth B, (2011) The joint effects of background selection and genetic recombination on local gene genealogies. Genetics 189: 251-266.
43. Barton N, Etheridge AM, (2004) The effect of selection on genealogies. Genetics 166: 1115-1131.
44. Neher RA, Hallatschek O, (2013) Genealogies in rapidly adapting populations. Proc Nat Acad Sci 110: 437-442.
45. Sargsyan O, Wakeley J, (2008) A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organsisms. Theoretical Popululation Biology 74: 104-114.
46. Santiago E, Caballero A, (1998) Effective size and polymorphism of linked neutral loci in populations under directional selection. Genetics 149: 2105-2117.
47. O'Fallon BD, Seger J, Adler FR, (2010) A continuous-state coalescent and the impact of weak selection on the structure of genealogies. Mol Biol Evol 27: 1162-1172.
48. Hallatschek O, Nelson DR, (2008) Gene surfing in expanding populations. Theor Popul Biol 73: 158-170.
49. Hallatschek O, (2011) The noisy edge of traveling waves. Proc Natl Acad Sci USA 108: 1783-1787.
50. Neher R, Shraiman BI, (2012) Fluctuations of fitness distributions and the rate of muller's ratchet. Genetics 191: 1283-1293.
51. Fisher DS, (2013) Asexual evolution waves: uctuations and universality. J Stat Mech 2013: P01011.
52. Good BH, Desai MM, (2013) Fluctuations in fitness distributions and the effects of weak linked selection on sequence evolution. Theor Pop Biol 85: 86-102.
53. Goyal S, Balick DJ, Jerison ER, Neher RA, Shraiman BI, et al. (2012) Dynamic mutation-selection balance as an evolutionary attractor. Genetics 191: 1309-1319.
54. Tsimring L, Levine H, Kessler D, (1996) Rna virus evolution via a fitness-space model. Phys Rev Lett 90: 088103.
55. Cohen E, Kessler DA, Levine H, (2005) Front propagation up a reaction rate gradient. Phys Rev E 72: 066126.
56. Rouzine IM, Wakeley J, Coffin JM, (2003) The solitary wave of asexual evolution. Proc Natl Acad Sci USA 100: 587-592.
57. Rouzine I, Brunet E, Wilke C, (2008) The traveling-wave approach to asexual evolution: Muller's ratchet and the speed of adaptation. Theor Pop Bio 73: 24-46.
58. Bolthausen E, Sznitman AS, (1998) On ruelle's probability cascades and an abstract cavity method. Communications in Mathematical Physics 197: 247-276.
59. Bender CM, Orszag SA (1978) Advanced Mathematical Methods for Scientists and Engineers. New York: McGraw-Hill.
60. Eyre-Walker A, Keightley PD, (2007) The distribution of fitness effects of new mutations. Nat Rev Gen 8: 610-618.
61. Zeng K, (2012) A coalescent model of background selection with recombination, demography and variation in selection coefficients. Heredity 110: 363-371.
62. Desai MM, Fisher DS, (2007) Beneficial mutation selection balance and the effect of genetic linkage on positive selection. Genetics 176: 1759-1798.
63. Schifiels S, Szöllösi G, Mustonen V, Lässig M, (2011) Emergent neutrality in adaptive asexual evolution. Genetics 189: 1361-1375.
64. Good BH, Rouzine IM, Balick DJ, Hallatschek O, Desai MM, (2012) Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations. Proc Natl Acad Sci 109: 4950-4955.
65. Desai MM, Walczak AM, Fisher DS, (2013) Genetic diversity and the structure of genealogies in rapidly adapting populations. Genetics 193: 565-585.
66. Kosheleva K, Desai MM, (2013) The dynamics of genetic draft in rapidly adapting populations. Genetics 195: 1007-1025.
67. Weissman DB, Barton NH, (2012) Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics 8: e1002740.
68. Franklin I, Lewontin RC, (1970) Is the gene the unit of selection? Genetics 65: 707-734.
69. Slatkin M, (1972) On treating the chromosome as the unit of selection. Genetics 72: 157-168.
70. Hudson RR, Kaplan NL, (1988) The coalescent process in models with selection and recombination. Genetics 120: 831-840.
71. Robertson A, (1961) Inbreeding in artificial selection programmes. Genet Res 2: 189-194.
72. Neher RA, Shraiman BI, (2011) Statistical genetics and evolution of quantitative traits. Rev Mod Phys 83: 1283-1300.
73. Neher RA, Kessinger TA, Shraiman BI, (2013) Coalescence and genetic diversity in sexual populations under selection. Proc Nat Acad Sci 110: 15836-15841.
74. Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, et al. (2010) Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467: 1099-1103.
75. Cutter AD, Payseur BA, (2003) Selection at linked sites in the partial selfer Caenorhabditis elegans. Mol Biol Evol 20: 665-673.
76. de Visser JAGM, Zeyl CW, Gerrish PJ, Blanchard JL, Lenski RE, (1999) Diminishing returns from mutation supply rate in asexual populations. Science 283: 404-406.
77. Miralles R, Gerrish PJ, Moya A, Elena SF, (1999) Clonal interference and the evolution of rna viruses. Science 285: 1745-1747.
78. Kao KC, Sherlock G, (2008) Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nature Genetics 40: 1499-1504.
79. Strelkowa N, Lässig M, (2012) Clonal interference in the evolution of inuenza. Genetics 192: 671-682.
80. Loewe L, Charlesworth B, (2006) Inferring the distribution of mutational effects on fitness in drosophila. Biol Lett 2: 426-430.
81. Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, et al. (2007) Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol 3: e189.
82. Hudson RR, (2002) Generating samples under a wright-fisher neutral model. Bioinformatics 18: 337-338.
83. Wang W, Thornton K, Berry A, Long M, (2002) Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295: 134-137.
84. Sheldahl LA, Weinreich DM, Rand DM, (2003) Recombination, dominance and selection on amino acid polymorphism in the drosophila genome: Contrasting patterns on the x and fourth chromosomes. Genetics 165: 1195-1208.
85. Kong A, Frigge ML, Masson G, Besenbacher S, et al. (2012) Rate of de novo mutations and the importance of father's age to disease risk. Nature 488: 471-475.
86. Consortium TGP, (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.