Balancing selection and its effects on sequences in nearby genome regions

PLoS Genetics

Volumn 2, Issue 4, 2006, Pages 379-384

  Charlesworth, Deborah ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; DNA POLYMORPHISM; GENE FUNCTION; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HAPLOTYPE; HUMAN; LOCAL ADAPTATION; MARKER GENE; MEDICAL INFORMATION; MOLECULAR EVOLUTION; REVIEW; ANIMAL; CHROMOSOME MAP; FEMALE; GENE FREQUENCY; GENETIC POLYMORPHISM; GENETIC SELECTION; GENOME; NUCLEOTIDE SEQUENCE; TIME;

ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; EVOLUTION, MOLECULAR; FEMALE; GENE FREQUENCY; GENOME; POLYMORPHISM, GENETIC; SELECTION (GENETICS); TIME; VARIATION (GENETICS);

EID: 33646484211     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020064     Document Type: Review

References (82)

1. Levene H (1953) Genetic equilibrium when more than one niche is available. Am Nat 87: 331-333.
2. Gillespie JH (1978) A general model to account for enzyme variation in natural populations. V. The SAS/CFF model. Theor Popul Biol 14: 1-45.
3. Gouyon PH, Vichot F, Damme Jv (1991) Nuclear-cytoplasmic male sterility: Single point equilibria versus limit cycles. Am Nat 137: 498-514.
4. Seger J (1988) Dynamics of some simple host-parasite models with more than two genotypes in each species. Philos Trans R Soc Lond B Biol Sci 319: 541-555.
5. Frank SA (1993) Coevolutionary genetics of plants and pathogens. Evol Ecol 7: 45-75.
6. Takahata N (1990) A simple genealogical structure of strongly balanced allelic lines and trans-species polymorphism. Proc Natl Acad Sci U S A 87: 2419-2423.
7. Vekemans X, Slatkin M (1994) Gene and allelic genealogies at a gametophytic self-incompatibility locus. Genetics 137: 1157-1165.
8. Wu J, Saupe SJ, Glass NL (1998) Evidence for balancing selection operating at the het-c heterokaryon incompatibility locus in filamentous fungi. Proc Natl Acad Sci U S A 95: 12398-12402.
9. May G, Shaw F, Badrane H, Vekemans X (1999) The signature of balancing selection: Fungal mating compatibility gene evolution. Proc Natl Acad Sci U S A 96: 9172-9177.
10. Hudson RR, Kaplan NL (1988) The coalescent process in models with selection and recombination. Genetics 120: 831-840.
11. Charlesworth B, Nordborg M, Charlesworth D (1997) The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided inbreeding and outcrossing populations. Genet Res 70: 155-174.
12. Takahata N, Satta Y (1998) Footprints of intragenic recombination at HLA loci. Immunogenetics 47: 430-441.
13. Bull JJ (1983) Evolution of sex determining mechanisms. Menlo Park (California): Benjamin/Cummings. 316 p.
14. Lahn BT, Page DC (1999) Four evolutionary strata on the human X chromosome. Science 286: 964-967.
15. Lawson-Handley LJ, Ceplitis H, Ellegren H (2004) Evolutionary strata on the chicken Z chromosome: Implications for sex chromosome evolution. Genetics 167: 367-376.
16. Nicolas M, Marais G, Hykelova V, Janousek B, Laporte V, et al. (2005) A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants. PLoS Biology 3: e4. DOI: 10.1371/journal.pbio.0030004
17. Charlesworth B, Charlesworth D, Barton NH (2003) The effects of genetic and geographic structure on neutral variation. Annu Rev Ecol Evol S 34: 99-125.
18. Wiuf C, Zhao K, Innan H, Nordborg M (2004) The probability and chromosomal extent of trans-specific polymorphism. Genetics 168: 2363-2372.
19. Frank SA (1989) The evolutionary dynamics of cytoplasmic male sterility. Am Nat 133: 345-576.
20. Charlesworth D (1981) A further study of the problem of the maintenance of females in gynodioecious species. Heredity 46: 27-39.
21. Städler T, Delph LF (2002) Ancient mitochondrial haplotypes and evidence for intragenic recombination in a gynodioecious plant. Proc Natl Acad Sci U S A 99: 11730-11735.
22. Hasselmann M, Beye M (2004) Signatures of selection among sex-determining alleles of the honey bee. Proc Natl Acad Sci U S A 101: 4888-4893.
23. Richman AD, Uyenoyama MK, Kohn JR (1996) Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae. Science 273: 1212-1216.
24. Lu Y (2002) Molecular evolution at the self-incompatibility locus of Physalis longifolia (Solanaceae). J Mol Evol 54: 784-793.
25. Lu Y (2001) Roles of lineage sorting and phylogenetic relationship in the genetic diversity at the self-incompatibility locus of Solanaceae. Heredity 86: 195-205.
26. Sato T, Nishio T, Kimura R, Kusaba M, Suzuki G, et al. (2002) Coevolution of the S-locus genes SRK, SLG and SP11/SCR in Brassica oleracea and B. rapa. Genetics 162: 931-940.
27. Charlesworth D, Bartolomé C, Schierup MH, Mable BK (2003) Haplotype structure of the stigmatic self-incompatibility gene in natural populations of Arabidopsis lyrata. Mol Biol Evol 20: 1741-1753.
28. Rose LE, Bittner-Eddy PD, Langley CH, Holub EB, Michelmore RW, et al. (2004) The maintenance of extreme amino acid diversity at the disease resistance gene, RPP13, in Arabidopsis thaliana. Genetics 166: 1517-1527.
29. Nordborg M, Hu TT, Ishino Y, Jhaveri Y, Toomajian C, et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3:
30. Navarro A, Barton NH (2002) The effects of multilocus balancing selection on neutral variability. Genetics 161: 849-863.
31. Cork JM, Purugganan MD (2005) High-diversity genes in the Arabidopsis genome. Genetics 170: 1897-1911.
32. Carrington M (1999) Recombination within the human MHC. Immunol Rev 167: 245-256.
33. Raymond CK, Kas A, Qiu R, Zhou Y, Subramanian Sa, et al. (2005) Ancient haplotypes of the HLA Class II region. Genome Res 15: 1250-1257.
34. Traherne JA, Horton R, Roberts AN, Miretti MM, Hurles ME, et al. (2006) Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. PLoS Genetics 2: 81-92. DOI: 10.1371/journal.pgen.0020009
35. Boer RJD, Borghans JAM, Boven MV, Kesmir C, Weissing FJ (2004) Heterozygote advantage fails to explain the high degree of polymorphism of the MHC. Immunogenetics 55: 725-731.
36. Muirhead CA, Glass NL, Slatkin M (2002) Multilocus self-recognition systems in fungi as a cause of trans-species polymorphism. Genetics 161: 633-641.
37. Sato T, Fujimoto R, Toriyama K, Nishio T (2003) Commonality of self-recognition specificity of S haplotypes between Brassica oleracea and Brassica rapa. Plant Mol Biol 52: 617-626.
38. Adams EJ, Cooper S, Thomson G, Parham P (2000) Common chimpanzees have greater diversity than humans at two of the three highly polymorphic MHC class I genes. Immunogenetics 51: 410-424.
39. Klein J, Takahata N, O'hUigin C (1993) Trans-specific Mhc polymorphism and the origin of species in primates. J Med Primatol 22: 57-64.
40. Ioerger TR, Clark AG, Kao T-H (1990) Polymorphism at the self-incompatibility locus in Solanaceae predates speciation. Proc Natl Acad Sci U S A 87: 9732-9735.
41. Schierup MH, Mikkelsen AM, Hein J (2001) Recombination, balancing selection and phylogenies in MHC and self-incompatibility genes. Genetics 159: 1833-1844.
42. Garrigan D, Hedrick PW (2003) Perspective: Detecting adaptive molecular polymorphism: Lessons from the MHC. Evolution 57: 1707-1722.
43. Clark AG (1997) Neutral behavior of shared polymorphism. Proc Natl Acad Sci U S A 94: 7730-7734.
44. Geluk A, Elferink DG, Slierendregt BL, Meijgaarden KEv, Vries RRd, et al. (1993) Evolutionary conservation of major histocompatibility complex-DR/peptide/T cell interactions in primates. J Exp Med 177: 979-987.
45. Stajich JE, Hahn MW (2005) Disentangling the effects of demography and selection in human history. Mol Biol Evol 22: 63-73.
46. O'hUigin C, Sato A, Klein J (1997) Evidence for convergent evolution of A and B blood group antigens in primates. Hum Genetics 101: 141-148.
47. Asthana S, Schmidt S, Sunyaev S (2005) A limited role for balancing selection. Trends Genet 21: 30-32.
48. Hughes A, Nei M (1988) Pattern of nucleotide substitution at MHC class I loci reveals overdominant selection. Nature 335: 167-170.
49. Bergelson J, Kreitman M, Stahl EA, Tian D (2001) Evolutionary dynamics of plant R-genes. Science 292: 2281-2285.
50. Shen J, Araki H, Chen L, Chen Q, Tian D (2006) Unique evolutionary mechanism in R-Genes under the presence/absence polymorphism in Arabidopsis thaliana. Genetics 172: 1243-1250.
51. Teshima KM, Przeworski M (2006) Directional positive selection on an allele of arbitrary dominance. Genetics 172: 713-718.
52. Kim Y, Stephan W (2003) Selective sweeps in the presence of interference among partially linked loci. Genetics 164: 389-398.
53. Wang ET, Kodama G, Baldi P, Moyzis RK (2006) Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci U S A 103: 135-140.
54. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, et al. (2005) Genomic scans for selective sweeps using SNP data. Genome Res 15: 1566-1575.
55. Nair S, Williams JT, Brockman A, Paiphun L, Mayxay M, et al. (2003) A selective sweep driven by pyrimethamine treatment in Southeast Asian malaria parasites. Mol Biol Evol 20: 1526-1536.
56. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
57. Currat M, Trabuchet G, Rees D, Perrin P, Harding RM, et al. (2002) Molecular analysis of the beta-globin gene cluster in the Niokholo Mandenka population reveals a recent origin of the beta(S) Senegal mutation. Am J Hum Genet 70: 207-223.
58. Kohn MH, Pelz H-J, Wayne RK (2000) Natural selection mapping of the warfarin-resistance gene. Proc Natl Acad Sci U S A 97: 7911-7915.
59. Wooding S, Kim UK, Bamshad MJ, Larsen J, Jorde LB, et al. (2004) Natural selection and molecular evolution in PTC, a bitter-taste receptor gene. Am J Hum Genet 74: 637-646.
60. Verrelli BC, McDonald JH, Argyropoulos G, Destro-Bisol G, Froment A, et al. (2002) Evidence for balancing selection from nucleotide sequence analyses of human. Am J Hum Genet 71: 455-462.
61. Ohashi J, Naka I, Patarapotikul J, Hananantachai H, Brittenham G, et al. (2004) Extended linkage disequilibrium surrounding the hemoglobin e variant due to malarial selection. Am J Hum Genet 74: 1198-1208.
62. Dobzhansky T (1943) Genetics of natural populations IX. Temporal changes in the composition of populations of Drosophila pseudoobscura. Genetics 28: 162-186.
63. Eanes WF (1999) Analysis of selection on enzyme polymorphisms. Annu Rev Ecol Syst 30: 301-326.
64. Sezgin E, Duvernell DD, Matzkin LM, Duan Y, Zhu C-T, et al. (2004) Single-locus latitudinal clines and their relationship to temperate adaptation in metabolic genes and derived alleles in Drosophila melanogaster. Genetics 168: 923-931.
65. Andolfatto P, Depaulis F, Navarro A (2001) Inversion polymorphisms and nucleotide variability in Drosophila. Genet Res 77: 1-8.
66. Li H, Stephan W (2005) Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome. Genetics 171: 377-378.
67. Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, et al. (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Res 15: 1576-1583.
68. Novembre JA, Galvani AP, Slatkin M (2005) The geographic spread of the CCR5 Δ32 HIV-resistance allele. PLoS Biology 3: DOI: 10.1371/journal.pbio. 0030339
69. Galtier N, Depaulis F, Barton NH (2000) Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 155: 981-987.
70. Kreitman M, Akashi H (1995) Molecular evidence for natural selection. Annu Rev Ecol Syst 26: 403-422.
71. Eyre-Walker A (2003) Changing effective population size and the McDonald-Kreitman test. Genetics 162: 2017-2024.
72. Ingvarsson PK (2004) Population subdivision and the Hudson-Kreitman- Aguade test: Testing for deviations from the neutral model in organelle genomes. Genet Res 83: 31-39.
73. Schierup MH, Vekemans X, Charlesworth D (2000) The effect of subdivision on variation at multi-allelic loci under balancing selection. Genet Res 76: 51-62.
74. Williamson S, Fledel-Alon A, Bustamante CD (2004) Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance. Genetics 168: 463-475.
75. Linhart YB, Grant MC (1996) Evolutionary significance of local genetic differentiation in plants. Ann Rev Ecol Syst 27: 237-277.
76. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12: 1805-1814.
77. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol 13: 969-980.
78. Kaltz O, Gandon S, Michalakis Y, Shykoff JA (1999) Local maladaptation in the anther-smut fungus Microbotryum violaceum to its host plant Silene latifolia: Evidence from a cross-inoculation experiment. Evolution 53: 39-407.
79. Schierup MH, Vekemans X, Charlesworth D (2000) The effect of hitch-hiking on genes linked to a balanced polymorphism in a subdivided population. Genet Res 76: 63-73.
80. Muirhead CA (2001) Consequences of population structure on genes under balancing selection. Evolution 55: 1532-1541.
81. Richman AD, Herrera LG, Nash D, Schierup MH (2003) Relative roles of mutation and recombination in generating allelic polymorphism at an MHC class II locus in Peromyscus maniculatus. Genet Res 82: 89-99.
82. Lewontin RC, Ginzburg LR, Tuljapurkar SD (1978) Heterosis as an explanation for large amounts of genic polymorphism. Genetics 88: 149-169.