Distortions in genealogies due to purifying selection and recombination

Genetics

Volumn 195, Issue 1, 2013, Pages 221-230

  Nicolaisen, Lauren E ^a   Desai, Michael M ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; EFFECTIVE POPULATION SIZE; GENEALOGY; GENETIC LINKAGE; GENETIC RECOMBINATION; GENOME ANALYSIS; HUMAN; MATHEMATICAL PARAMETERS; PRIORITY JOURNAL; PURIFYING SELECTION; QUANTITATIVE ANALYSIS;

COALESCENT; GENEALOGIES; LINKAGE; PURIFYING SELECTION; RECOMBINATION;

GENETIC FITNESS; HAPLOIDY; MODELS, GENETIC; PEDIGREE; POPULATION; RECOMBINATION, GENETIC; SELECTION, GENETIC;

EID: 84883767655     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.152983     Document Type: Article

References (37)

1. Austerlitz, F., B. Jung-Muller, B. Godelle, and P.-H. Gouyon, 1997 Evolution of coalescence times, genetic diversity and structure during colonization. Theor. Popul. Biol. 51(2): 148-164.
2. Barton, N. H., and A. M. Etheridge, 2004 The effect of selection on genealogies. Genetics 166: 1115-1131.
3. Charlesworth, B., 1994 The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. 63: 213-227.
4. Charlesworth, B., 1996 Background selection and patterns of genetic diversity in Drosophila melanogaster. Genet. Res. 68(2): 131-150.
5. Charlesworth, B., 2012 The effects of deleterious mutations on evolution at linked sites. Genetics 190: 5-22.
6. Charlesworth, B., 2013 Background selection 20 years on: The Wilhelmine E. Key 2012 invitational lecture. J. Hered. 104: 161-171.
7. Charlesworth, B., M. Morgan, and D. Charlesworth, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289.
8. Charlesworth, D., B. Charlesworth, and M. T. Morgan, 1995 The pattern of neutral molecular variation under the background selection model. Genetics 141: 1619-1632.
9. Eriksson, A., B. Mehlig, M. Rafajlovic, and S. Sagitov, 2010 The total branch length of sample genealogies in populations of variable size. Genetics 186: 601-611.
10. Good, B. H., A. M. Walczak, R. A. Neher, and M. M. Desai, 2013 Interference limits resolution of selection pressures from linked neutral diversity. arXiv:1306.1215. Available at: http:// arxiv.org/abs/1306.1215.
11. Haddrill, P., L. Loewe, and B. Charlesworth, 2010 Estimating the parameters of selection on nonsynonymous mutations in Drosophila pseudoobscura and D. miranda. Genetics 185: 1381-1396.
12. Haigh, J., 1978 The accumulation of deleterious genes in a population-Muller's ratchet. Theor. Popul. Biol. 14: 251-267.
13. Haldane, J., 1919 The combination of linkage values and the calculation of distances between the loci of linked factors. J. Genet. 8(29): 309-320.
14. Hudson, R., and N. Kaplan, 1994 Gene trees with background selection, pp. 140-153 Non-Neutral Evolution: Theories and Molecular Data, edited by B. Golding. Chapman & Hall, New York.
15. Hudson, R., and N. Kaplan, 1995a The coalescent process and background selection. Philos. Trans. R. Soc. Lond. B Biol. Sci. 349(1327): 19-23.
16. Hudson, R., and N. Kaplan, 1995b Deleterious background selection with recombination. Genetics 141: 1605-1617.
17. Keightley, P., and A. Eyre-Walker, 2007 Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177: 2251-2261.
18. Kimura, M., and T. Maruyama, 1966 The mutational load with epistatic gene interactions in fitness. Genetics 54: 1337.
19. Loewe, L., and B. Charlesworth, 2007 Background selection in single genes may explain patterns of codon bias. Genetics 175: 1381-1393.
20. Lohmueller, K., A. Albrechtsen, Y. Li, S. Kim, T. Korneliussen et al., 2011 Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet. 7(10): e1002326.
21. McVicker, G., D. Gordon, C. Davis, and P. Green, 2009 Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet. 5(5): e1000471.
22. Nicolaisen, L., and M. Desai, 2012 Distortions in genealogies due to purifying selection. Mol. Biol. Evol. 29: 3589-3600.
23. Nordborg, M., B. Charlesworth, and D. Charlesworth, 1996 The effect of recombination on background selection. Genet. Res. 67: 159-174.
24. O'Fallon, B., 2011 A method for accurate inference of population size from serially sampled genealogies distorted by selection. Mol. Biol. Evol. 28(11): 3171-3181.
25. O'Fallon, B., J. Seger, and F. Adler, 2010 A continuous-state coalescent and the impact of weak selection on the structure of gene genealogies. Mol. Biol. Evol. 27(5): 1162.
26. Polanski, A., and M. Kimmel, 2003 New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. Genetics 165: 427-436.
27. Seger, J., W. A. Smith, J. J. Perry, J. Hunn, Z. A. Kaliszewska et al., 2010 Gene genealogies strongly distorted by weakly interfering mutations in constant environments. Genetics 184: 529-545.
28. Walczak, A. M., L. E. Nicolaisen, J. B. Plotkin, and M. M. Desai, 2012 The structure of genealogies in the presence of purifying selection: A "fitness-class coalescent". Genetics 190: 753-779.
29. Williamson, S., and M. Orive, 2002 The genealogy of a sequence subject to purifying selection at multiple sites. Mol. Biol. Evol. 19(8): 1376.
30. Zeng, K., 2012 A coalescent model of background selection with recombination, demography and variation in selection coefficients. Heredity 110: 363-371.
31. Zeng, K., and B. Charlesworth, 2011 The joint effects of background selection and genetic recombination on local gene genealogies. Genetics 189: 251-266.
32. Barton, N. H. and A. M. Etheridge, 2004 The effect of selection on genealogies. Genetics 166: 1115-1131.
33. Charlesworth, B., 2012 The effects of deleterious mutations on evolution at linked sites. Genetics 190: 5-22.
34. Charlesworth, B., M. Morgan, and D. Charlesworth, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134(4): 1289.
35. Hudson, R. and N. Kaplan, 1995 Deleterious background selection with recombination. Genetics 141: 1605-1617.
36. O'Fallon, B., J. Seger, and F. Adler, 2010 A continuous-state coalescent and the impact of weak selection on the structure of gene genealogies. Mol. Biol. Evol. 27(5): 1162.
37. Zeng, K. and B. Charlesworth, 2011 The joint effects of background selection and genetic recombination on local gene genealogies. Genetics 189(1): 251-266.