A coalescent model of background selection with recombination, demography and variation in selection coefficients

Heredity

Volumn 110, Issue 4, 2013, Pages 363-371

  Zeng, K ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

background selection; population demography; recombination; structured coalescent; the distribution of fitness effects

Indexed keywords

ACCURACY ASSESSMENT; COALESCENCE; DATA INTERPRETATION; DEMOGRAPHY; FITNESS; FORWARD MODELING; GENETIC VARIATION; MUTATION; NATURAL SELECTION; POLYMORPHISM; POPULATION SIZE; RECOMBINATION;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; DEMOGRAPHY; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; MUTATION; POPULATION DENSITY; REPRODUCTIVE FITNESS; THEORETICAL MODEL;

ANIMALS; DEMOGRAPHY; GENETIC FITNESS; GENETIC VARIATION; MODELS, GENETIC; MODELS, THEORETICAL; MUTATION; POPULATION DENSITY; RECOMBINATION, GENETIC; SELECTION, GENETIC;

EID: 84875759191     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2012.102     Document Type: Article

References (40)

1. Begun DJ, Aquadro CF (1992). Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356: 519-520.
2. Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE et al. (2008). Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 4: E1000083.
3. Cai JJ, Macpherson JM, Sella G, Petrov DA (2009). Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet 5: E1000336.
4. Charlesworth B (1990). Mutation-selection balance and the evolutionary advantage of sex and recombination. Genet Res 55: 199-221.
5. Charlesworth B (2012a). The effects of deleterious mutations on evolution at linked sites. Genetics 190: 5-22.
6. Charlesworth B (2012b). The role of background selection in shaping patterns of molecular evolution and variation: Evidence from variability on the Drosophila x chromosome. Genetics 191: 233-246.
7. Charlesworth B, Charlesworth D (2010). Elements of Evolutionary Genetics. . Roberts and Company Publishers: Greenwood Village.
8. Charlesworth B, Morgan MT, Charlesworth D (1993). The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
9. Charlesworth D, Charlesworth B, Morgan MT (1995). The pattern of neutral molecular variation under the background selection model. Genetics 141: 1619-1632.
10. Comeron JM, Guthrie TB (2005). Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila. Mol Biol Evol 22: 2519-2530.
11. Cutter AD, Choi JY (2010). Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae. Genome Res 20: 1103-1111.
12. Ewens WJ (2004). Mathematical Population Genetics, 2nd edn. Springer-Verlag: Berlin
13. Eyre-Walker A, Keightley PD (2007). The distribution of fitness effects of new mutations. Nat Rev Genet 8: 610-618.
14. Eyre-Walker A, Keightley PD (2009). Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol Biol Evol 26: 2097-2108.
15. Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD (2012). Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice. Mol Biol Evol 29: 675-687.
16. Fu YX, Li WH (1993). Statistical tests of neutrality of mutations. Genetics 133: 693-709.
17. Gordo I, Navarro A, Charlesworth B (2002). Muller's ratchet and the pattern of variation at a neutral locus. Genetics 161: 835-848.
18. Haddrill PR, Zeng K, Charlesworth B (2011). Determinants of synonymous and nonsynonymous variability in three species of Drosophila. Mol Biol Evol 28: 1731-1743.
19. Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G et al. (2011). Classic selective sweeps were rare in recent human evolution. Science 331: 920-924.
20. Hill WG, Robertson A (1966). The effect of linkage on limits to artificial selection. Genet Res 8: 269-294.
21. Hudson RR (1990). Gene genealogies and the coalescent process. Oxford Surv Evol Biol 7: 1-44.
22. Hudson RR, Kaplan NL (1995). Deleterious background selection with recombination. Genetics 141: 1605-1617.
23. Johnson T (1999). The approach to mutation-selection balance in an infinite asexual population, and the evolution of mutation rates. Proc Biol Sci 266: 2389-2397.
24. 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.
25. Kimura M (1969). The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61: 893-903.
26. Kimura M, Maruyama T (1966). The mutational load with epistatic gene interactions in fitness. Genetics 54: 1337-1351.
27. Loewe L, Charlesworth B (2007). Background selection in single genes may explain patterns of codon bias. Genetics 175: 1381-1393.
28. Lohmueller KE, Albrechtsen A, Li Y, Kim SY, Korneliussen T, Vinckenbosch N et al. (2011). Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet 7: E1002326.
29. Maynard Smith J, Haigh J (1974). The hitch-hiking effect of a favourable gene. Genet Res 23: 23-35.
30. McVicker G, Gordon D, Davis C, Green P (2009). Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet 5: E1000471.
31. Nordborg M, Charlesworth B, Charlesworth D (1996). The effect of recombination on background selection. Genet Res 67: 159-174.
32. Sella G, Petrov DA, Przeworski M, Andolfatto P (2009). Pervasive natural selection in the Drosophila genome? PLoS Genet 5: E1000495.
33. Shapiro JA, Huang W, Zhang C, Hubisz MJ, Lu J, Turissini DA et al. (2007). Adaptive genic evolution in the Drosophila genomes. Proc Natl Acad Sci USA 104: 2271-2276.
34. Slatkin M, Hudson RR (1991). Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
35. Stephan W (2010). Genetic hitchhiking versus background selection: The controversy and its implications. Phil Trans R Soc B 366: 1245-1253.
36. Tajima F (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
37. Wakeley J (2008). Conditional gene genealogies under strong purifying selection. Mol Biol Evol 25: 2615-2626.
38. 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.
39. Watterson GA (1975). On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256-276.
40. Zeng K, Charlesworth B (2011). The joint effects of background selection and genetic recombination on local gene genealogies. Genetics 189: 251-266.