Measuring natural selection on genotypes and phenotypes in the wild

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 74, Issue , 2009, Pages 155-168

  Linnen, C R ^a   Hoekstra, H E ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ADAPTATION; CONFERENCE PAPER; DNA SEQUENCE; ECOLOGY; GENE FREQUENCY; GENETIC TRAIT; GENOTYPE; MOLECULAR EVOLUTION; MUTATION; NATURAL SELECTION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; WILD ANIMAL; ARTICLE; DNA INTEGRATION; EVOLUTIONARY ADAPTATION; GENE MUTATION; GENETIC IDENTIFICATION; MORPHOLOGICAL TRAIT; SPATIAL ANALYSIS; ALLELE; ANIMAL; BIOLOGICAL MODEL; EVOLUTION; GENETIC SELECTION; GENETICS; PEROMYSCUS; REVIEW; SMEGMAMORPHA;

ALLELES; ANIMALS; DNA; EVOLUTION; GENE FREQUENCY; GENOTYPE; MODELS, GENETIC; PEROMYSCUS; PHENOTYPE; SELECTION, GENETIC; SMEGMAMORPHA;

EID: 77957745688     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2009.74.045     Document Type: Conference Paper

References (171)

1. Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152. (Pubitemid 41509351)
2. Andolfatto P. 2007. Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res 17: 1755-1762.
3. Arnold SJ, Wade MJ. 1984a. On the measurement of natural and sexual selection: Applications. Evolution 38: 720-734.
4. Arnold SJ, Wade MJ. 1984b. On the measurement of natural and sexual selection: Theory. Evolution 38: 709-719. (Pubitemid 16277744)
5. Barrett RDH, Rogers SM, Schluter D. 2008. Natural selection on a major armor gene in threespine stickleback. Science 322: 255-257.
6. Barrett RDH, Rogers SM, Schluter D, Peichel C. 2009. Environment specific pleiotropy facilitates divergence at the Ectodysplasin locus in threespine stickleback. Evolution 63: 2831-2837.
7. Barton NH. 1979a. Gene flow past a cline. Heredity 43: 333-339.
8. Barton NH. 1979b. The dynamics of hybrid zones. Heredity 43: 341-359.
9. Barton NH. 1983. Multilocus clines. Evolution 37: 454-471.
10. Barton NH, Gale KS. 1993. Genetic analysis of hybrid zones. In Hybrid zones and the evolutionary process (ed. RG Harrison), pp. 13-45. Oxford University Press, New York.
11. Barton NH, Hewitt GM. 1985. Analysis of hybrid zones. Annu Rev Ecol Syst 16: 113-148.
12. Bell MA, Foster SA. 1994. The evolutionary biology of the threespine stickleback. Oxford University Press, Oxford.
13. Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA, Rhodes M, Reich DE, Hirschhorn JN. 2004. Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 74: 1111-1120.
14. Bishop JA. 1972. An experimental study of the cline of industrial melanism in Biston betularia (L.) (Lepidoptera) between urban Liverpool and rural north Wales. J Anim Ecol 41: 209-243.
15. Biswas S, Akey JM. 2006. Genomic insights into positive selection. Trends Genet 22: 437-446.
16. Boag PT, Grant PR. 1981. Intense natural selection in a population of Darwin's finches (Geospizinae) in the Galapagos. Science 214: 82-85.
17. es from temporal allele frequency data. Genetics 179: 497-502.
18. Braverman JM, Hudson RR, Kaplan NL, Langley CH, Stephan W. 1995. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140: 783-796.
19. Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL. 2002. The cost of inbreeding in Arabidopsis. Nature 416: 531-534.
20. Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez RD, et al. 2005. Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.
21. Colosimo PF, Peichel CL, Nereng K, Blackman BK, Shapiro MD, Schluter D, Kingsley DM. 2004. The genetic architecture of parallel armor plate reduction in threespine sticklebacks. PLoS Biol 2: e109.
22. Colosimo PF, Hosemann KE, Balabhadra S, Villarreal G, Dickson M, Grimwood J, Schmutz J, Myers RM, Schluter D, Kingsley DM. 2005. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307: 1928-1933.
23. Conner JK. 1996. Understanding natural selection: An approach integrating selection gradients, multiplicative fitness components, and path analysis. Ethol Ecol Evol 8: 387-397.
24. Conner JK, Hartl DL. 2004. A primer of ecological genetics. Sinauer, Sunderland, MA.
25. Cook LM. 2003. The rise and fall of the carbonaria form of the peppered moth. Q Rev Biol 78: 399-417.
26. Cook LM, Mani GS. 1980. A migration-selection model for the morph frequency variation in the peppered moth over England and Wales. Biol J Linn Soc 13: 179-198.
27. Darwin C. 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. John Murray, London.
28. De Jong G. 1994. The fitness of fitness concepts and the description of natural selection. Q Rev Biol 69: 3-29. (Pubitemid 2080246)
29. Dice LR. 1947. Effectiveness of selection by owls of deer-mice (Pero mys cus maniculatus) which contrast in color with their background. Contrib Lab Vertebrate Biol Univ Michigan 34: 1-20.
30. Dice LR. 1949. The selection index and its test of significance. Evolution 3: 262-265.
31. Duhl DM, Vrieling H, Miller KA, Wolff GL, Barsh GS. 1994. Neomorphic agouti mutations in obese yellow mice. Nat Genet 8: 59-65. (Pubitemid 24274061)
32. Eanes WF. 1999. Analysis of selection on enzyme polymorphisms. Annu Rev Ecol Syst 30: 301-326.
33. Ehrenreich IM, Purugganan MD. 2006. The molecular genetic basis of plant adaptation. Am J Bot 93: 953-962. (Pubitemid 44065649)
34. Ellegren H, Sheldon BC. 2008. Genetic basis of fitness differences in natural populations. Nature 452: 169-175.
35. Endler JA. 1977. Geographic variation, speciation, and clines. Princeton University Press, Princeton, NJ.
36. Endler JA. 1986. Natural selection in the wild (Monographs in Population Biology). Princeton University Press, Princeton, NJ.
37. Erickson DL, Fenster CB, Stenoien HK, Price D. 2004. Quantitative trait locus analyses and the study of evolutionary process. Mol Ecol 13: 2505-2522.
38. Ewens WJ. 2004. Mathematical population genetics. Springer, New York.
39. Eyre-Walker A. 2002. Changing effective population size and the McDonald-Kreitman test. Genetics 162: 2017-2024.
40. Eyre-Walker A. 2006. The genomic rate of adaptive evolution. Trends Ecol Evol 21: 569.
41. Falconer DS, Mackay TFC. 1996. Introduction to quantitative genetics. Longman, Essex, England.
42. Fay JC, Wu C-I. 2000. Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
43. Feder ME, Mitchell-Olds T. 2003. Evolutionary and ecological functional genomics. Nat Rev Genet 4: 651-657.
44. Fitch WM, Bush RM, Bender CA, Cox NJ. 1997. Long term trends in the evolution of H(3) HA1 human influenza type A. Proc Natl Acad Sci 94: 7712-7718.
45. Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
46. Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics 133: 693-709.
47. Garrigan D, Lewontin R, Wakeley J. 2010. Measuring the sensitivity of single-locus "neutrality tests" using a direct perturbation approach. Mol Biol Evol 27: 73-89.
48. Gibbs HL, Grant PR. 1987. Oscillating selection on Darwin's finches. Nature 327: 511-513.
49. Grant PR. 1981. The feeding of Darwin's finches on Tribulus cistoides (L.) seeds. Anim Behav 29: 785-793.
50. Grant BR. 2003. Evolution in Darwin's finches: A review of a study on Isla Daphne Major in the Galapagos archipelago. Zoology 106: 255-259.
51. Grant PR, Grant BR. 1995. Predicting microevolutionary responses to directional selection on heritable variation. Evolution 49: 241-251.
52. Grant PR, Grant BR. 2002. Unpredictable evolution in a 30-year study of Darwin's finches. Science 296: 707-711.
53. Grant PR, Grant BR. 2008. How and why species multiply: The radiation of Darwin's finches. Princeton University Press, Princeton, NJ.
54. Grossman SR, Shylakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, et al. 2010. A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327: 883-886.
55. Hahn M. 2007. Detecting natural selection on cis-regulatory DNA. Genetica 129: 7-18. (Pubitemid 44949612)
56. Haldane JBS. 1924. A mathematical theory of natural and artificial selection. Trans Camb Philos Soc 23: 19-41.
57. Haldane JBS. 1930. A mathematical theory of natural and artificial selection. Part VI. Isolation. Proc Camb Philos Soc 26: 220-230.
58. Haldane JBS. 1932. The causes of evolution. Longmans, London.
59. Haldane JBS. 1948. The theory of a cline. J Genet 48: 277-284.
60. Hartl DL, Clark AG. 2007. Principles of population genetics. Sinauer, Sunderland, MA.
61. Hermisson J, Pennings PS. 2005. Soft sweeps: Molecular population genetics of adaptation from standing genetic variation. Genetics 169: 2335-2352.
62. Hoekstra HE. 2006. Genetics, development and evolution of adaptive pigmentation in vertebrates. Heredity 97: 222-234.
63. Hoekstra HE, Hoekstra JM, Berrigan D, Vignieri SN, Hoang A, Hill CE, Beerli P, Kingsolver JG. 2001. Strength and tempo of directional selection in the wild. Proc Natl Acad Sci 98: 9157-9160.
64. Hoekstra HE, Drumm KE, Nachman MW. 2004. Ecological genetics of adaptive color polymorphism in pocket mice: Geographic variation in selected and neutral genes. Evolution 58: 1329-1341.
65. Hoekstra HE, Hirschmann RJ, Bundey RA, Insel PA, Crossland JP. 2006. A single amino acid mutation contributes to adaptive beach mouse color pattern. Science 313: 101-104.
66. Hoffmann AA, Willi Y. 2008. Detecting genetic responses to environmental change. Nat Rev Genet 9: 421-432.
67. Hudson RR, Kreitman M, Aguade M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
68. Hummel S, Schmidt D, Kremeyer B, Herrmann B, Oppermann M. 2005. Detection of the CCR5-Δ32 HIV resistance gene in Bronze Age skeletons. Genes Immun 6: 371-374. (Pubitemid 40903412)
69. Ingvarsson P. 2004. Population subdivision and the Hudson-Kreitman-Aguade test: Testing for deviations from the neutral model in organelle genomes. Genet Res 83: 31-39.
70. Jensen JD, Kim Y, DuMont VB, Aquadro CF, Bustamante CD. 2005. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170: 1401-1410.
71. Jensen JD, Thornton KR, Bustamante CD, Aquadro CF. 2007a. On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. Genetics 176: 2371-2379.
72. Jensen JD, Wong A, Aquadro CF. 2007b. Approaches for identifying targets of positive selection. Trends Genet 23: 568-577.
73. Jensen JD, Thornton KR, Andolfatto P. 2008. An approximate Bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLoS Genet 4: e1000198.
74. Kaplan NL, Hudson RR, Langley CH. 1989. The "hitchhiking effect" revisited. Genetics 123: 887-899.
75. Kim Y. 2006. Allele frequency distribution under recurrent selective sweeps. Genetics 172: 1967-1978.
76. Kim Y, Nielsen R. 2004. Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513-1524. (Pubitemid 39045653)
77. Kim Y, Stephan W. 2002. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777. (Pubitemid 34194545)
78. Kimura M. 1977. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267: 275-276. (Pubitemid 8095610)
79. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge.
80. Kimura M, Crow JF. 1978. Effect of overall phenotypic selection on genetic change at individual loci. Proc Natl Acad Sci 75: 6168-6171. (Pubitemid 9100968)
81. Kingsley EP, Manceau M, Wiley CD, Hoekstra HE. 2009. Melanism in Peromyscus is caused by independent mutations in Agouti. PLoS ONE 4: e6435.
82. Kingsolver JG, Hoekstra HE, Hoekstra JM, Berrigan D, Vignieri SN, Hill CE, Hoang A, Gibert P, Beerli P. 2001. The strength of phenotypic selection in natural populations. Am Nat 157: 245-261. (Pubitemid 32214660)
83. Kruuk LEB, Slate J, Wilson AJ. 2008. New answers for old questions: The evolutionary quantitative genetics of wild animal populations. Annu Rev Ecol Evol Syst 39: 525-548.
84. Lande R. 1979. Quantitative genetic analysis of multivariate evolution, applied to brain: Body size allometry. Evolution 33: 402-416.
85. Lande R, Arnold SJ. 1983. The measurement of selection on correlated characters. Evolution 37: 1210-1226.
86. Lenormand T. 2002. Gene flow and the limits to natural selection. Trends Ecol Evol 17: 183-189.
87. Lexer C, Welch ME, Durphy JL, Rieseberg LH. 2003a. Natural selection for salt tolerance quantitative trait loci (QTLs) in wild sunflower hybrids: Implications for the origin of Helianthus paradoxus, a diploid hybrid species. Mol Ecol 12: 1225-1235. (Pubitemid 36573124)
88. Lexer C, Welch ME, Raymond O, Rieseberg LH, Nason J. 2003b. The origin of ecological divergence in Helianthus paradoxus (Asteraceae): Selection on transgressive characters in a novel hybrid habitat. Evolution 57: 1989-2000.
89. Lexer C, Rosenthal DM, Raymond O, Donovan LA, Rieseberg LH. 2005. Genetics of species differences in the wild annual sunflowers, Helianthus annuus and H. petiolaris. Genetics 169: 2225-2239.
90. Linnen CR, Kingsley EP, Jensen JD, Hoekstra HE. 2009. On the origin and spread of an adaptive allele in deer mice. Science 325: 1095-1098.
91. Ludwig A, Pruvost M, Reissmann M, Benecke N, Brockmann G A, Castanos P, Cieslak M, Lippold S, Llorente L, Malaspinas AS, et al. 2009. Coat color variation at the beginning of horse domestication. Science 324: 485.
92. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P. 2003. The power and promise of population genomics: From genotyping to genome typing. Nat Rev Genet 4: 981-994.
93. Mackay TFC. 2001. Quantitative trait loci in Drosophila. Nat Rev Genet 2: 11-20.
94. Mackay TFC, Stone EA, Ayroles JF. 2009. The genetics of quantitative traits: Challenges and prospects. Nat Rev Genet 10: 565-577.
95. Mallet J, Barton N, Gerardo LM, Jose SC, Manuel MM, Eeley H. 1990. Estimates of selection and gene flow from measures of cline width and linkage disequilibrium in Heliconius hybrid zones. Genetics 124: 921-936.
96. Mani GS. 1982. A theoretical analysis of the morph frequency variation in the peppered moth over England and Wales. Biol J Linn Soc 17: 259-267.
97. Marchinko KB. 2009. Predation's role in repeated phenotypic and genetic divergence of armor in threespine stickleback. Evolution 63: 127-138.
98. Marchinko KB, Schluter D. 2007. Parallel evolution by correlated response: Lateral plate reduction in threespine stickleback. Evolution 61: 1084-1090. (Pubitemid 46699442)
99. Maynard Smith J, Haigh J. 1974. The hitch-hiking effect of a favourable gene. Genet Res 23: 23-35.
100. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
101. McGraw JB, Caswell H. 1996. Estimation of individual fitness from life-history data. Am Nat 147: 47-64. (Pubitemid 126514444)
102. Meiklejohn C, Kim Y, Hartl D, Parsch J. 2004. Identification of a locus under complex positive selection in Drosophila simulans by haplotype mapping and composite-likelihood estimation. Genetics 168: 265-279.
103. Milkman R. 1978. Selection differentials and selection coefficients. Genetics 88: 391-403.
104. Miltenberger RJ, Wakamatsu K, Ito S, Woychik RP, Russell LB, Michaud EJ. 2002. Molecular and phenotypic analysis of 25 recessive, homozygous-viable alleles at the mouse Agouti locus. Genetics 160: 659-674.
105. Mullen LM, Hoekstra HE. 2008. Natural selection along an environmental gradient: A classic cline in mouse pigmentation. Evolution 62: 1555-1569.
106. Mundy NI, Kelly J. 2006. Investigation of the role of the agouti signaling protein gene (ASIP) in coat color evolution in primates. Mamm Genome 17: 1205-1213. (Pubitemid 44915822)
107. Naish KA, Hard JJ. 2008. Bridging the gap between the genotype and the phenotype: Linking genetic variation, selection and adaptation in fishes. Fish Fisheries 9: 396-422.
108. Nielsen R. 2005. Molecular signatures of natural selection. Annu Rev Genet 39: 197-218.
109. Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
110. Nielsen R, Yang Z. 2003. Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol 20: 1231-1239.
111. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3: e170.
112. Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andrés AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, et al. 2009. Darwinian and demographic forces affecting human protein coding genes. Genome Res 19: 838-849.
113. Novembre J, Galvani AP, Slatkin M. 2005. The geographic spread of the CCR5 Δ32 HIV-resistance allele. PLoS Biol 3: e339.
114. Nurnberger B, Barton N, MacCallum C, Jason G, Appleby M. 1995. Natural selection on quantitative traits in the Bombina hybrid zone. Evolution 49: 1224-1238. (Pubitemid 3025838)
115. Olsen K, Sutherland B, Small L. 2007. Molecular evolution of the Li/li chemical defence polymorphism in white clover (Trifolium repens L.). Mol Ecol 16: 4180-4193.
116. Orr HA. 2005. The genetic theory of adaptation: A brief history. Nat Rev Genet 6: 119-127.
117. Orr HA. 2009. Fitness and its role in evolutionary genetics. Nat Rev Genet 10: 531-539.
118. Outram AK, Stear NA, Bendrey R, Olsen S, Kasparov A, Zaibert V, Thorpe N, Evershed RP. 2009. The earliest horse harnessing and milking. Science 323: 1332-1335.
119. Pavlidis P, Hutter S, Stephan W. 2008. A population genomic approach to map recent positive selection in model species. Mol Ecol 17: 3585-3598.
120. Pennings PS, Hermisson J. 2006a. Soft sweeps II: Molecular population genetics of adaptation from recurrent mutation or migration. Mol Biol Evol 23: 1076-1084.
121. Pennings PS, Hermisson J. 2006b. Soft sweeps III: The signature of positive selection from recurrent mutation. PLoS Genet 2: e186.
122. Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, et al. 2006. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443: 167-172.
123. Pool JE, Aquadro CF. 2007. The genetic basis of adaptive pigmentation variation in Drosophila melanogaster. Mol Ecol 16: 2844-2851. (Pubitemid 47035464)
124. Price GR. 1970. Selection and covariance. Nature 227: 520-521.
125. Price TD, Grant PR, Gibbs HL, Boag PT. 1984. Recurrent patterns of natural selection in a population of Darwin's finches. Nature 309: 787-789.
126. Przeworski M. 2002. The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.
127. Przeworski M, Coop G, Wall J. 2005. The signature of positive selection on standing genetic variation. Evolution 59: 2312-2323.
128. Reznick D. 1982. The impact of predation on life history evolution in Trinidadian guppies: Genetic basis of observed life history patterns. Evolution 36: 1236-1250.
129. Reznick D, Endler JA. 1982. The impact of predation on life history evolution in Trinidadian guppies (Poecilia reticulata). Evolution 36: 160-177.
130. Reznick DN, Shaw FH, Rodd FH, Shaw RG. 1997. Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata). Science 275: 1934-1937. (Pubitemid 27336073)
131. Rieseberg LH. 1991. Homoploid reticulate evolution in Helianthus (Asteraceae): Evidence from ribosomal genes. Am J Bot 78: 1218-1237.
132. Rieseberg LH, Burke JM. 2001. The biological reality of species: Gene flow, selection, and collective evolution. Taxon 50: 47-67.
133. Rieseberg LH, Carter R, Zona S. 1990. Molecular tests of the hypothesized hybrid origin of two diploid Helianthus species (Asteraceae). Evolution 44: 1498-1511.
134. Rieseberg LH, Archer MA, Wayne RK. 1999. Transgressive segregation, adaptation and speciation. Heredity 83: 363-372.
135. Rieseberg LH, Raymond O, Rosenthal DM, Lai Z, Livingstone K, Nakazato T, Durphy JL, Schwarzbach AE, Donovan LA, Lexer C. 2003. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301: 1211-1216.
136. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, et al. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
137. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES. 2006. Positive natural selection in the human lineage. Science 312: 1614-1620.
138. Saccheri IJ, Rousset F, Watts PC, Brakefield PM, Cook LM. 2008. Selection and gene flow on a diminishing cline of melanic peppered moths. Proc Natl Acad Sci 105: 16212-16217.
139. Sawyer SA, Hartl DL. 1992. Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
140. Sawyer S, Kulathinal R, Bustamante C, Hartl D. 2003. Bayesian analysis suggests that most amino acid replacements in Drosoph ila are driven by positive selection. J Mol Evol 57: S154-S164.
141. Sawyer SA, Parsch J, Zhang Z, Hartl DL. 2007. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proc Natl Acad Sci 104: 6504-6510.
142. Schemske DW, Bierzychudek P. 2001. Evolution of flower color in the desert annual Linanthus parryae: Wright revisited. Evolution 55: 1269-1282. (Pubitemid 32774047)
143. Schemske DW, Bradshaw HD. 1999. Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus). Proc Natl Acad Sci 96: 11910-11915.
144. Schemske DW, Horvitz CC. 1989. Temporal variation in selection on a floral character. Evolution 43: 461-465.
145. Sella G, Petrov DA, Przeworski M, Andolfatto P. 2009. Pervasive natural selection in the Drosophila genome? PLoS Genet 5: e1000495.
146. Siepielski AM, DiBattista JD, Carlson SM. 2009. It's about time: The temporal dynamics of phenotypic selection in the wild. Ecol Lett 12: 1261-1276.
147. Siracusa LD. 1994. The agouti gene: Turned on to yellow. Trends Genet 10: 423-428.
148. Slate J, Gratten J, Beraldi D, Stapley J, Hale M, Pemberton JM. 2009. Gene mapping in the wild with SNPs: Guidelines and future directions. Genetica 136: 97-107.
149. Slatkin M. 1973. Gene flow and selection in a cline. Genetics 75: 733-756.
150. Slatkin M. 1975. Gene flow and selection in a two-locus system. Genetics 81: 787-802.
151. Slatkin M. 1978. Spatial patterns in the distributions of polygenic characters. J Theor Biol 70: 213-228.
152. Slatkin M. 2003. Gene flow in natural populations. Annu Rev Ecol Syst 16: 393-430.
153. Steiner CC, Weber JN, Hoekstra HE. 2007. Adaptive variation in beach mice produced by two interacting pigmentation genes. PLoS Biol 5: e219.
154. Stephan W, Song Y, Langley C. 2006. The hitchhiking effect on linkage disequilibrium between linked neutral loci. Genetics 172: 2647-2663.
155. Stinchcombe JR, Hoekstra HE. 2008. Combining population genomics and quantitative genetics: Finding the genes underlying ecologically important traits. Heredity 100: 158-170.
156. Sumner FB. 1929a. The analysis of a concrete case of intergradation between two subspecies. Proc Natl Acad Sci 15: 110-120.
157. Sumner FB. 1929b. The analysis of a concrete case of intergradation between two subspecies. II Additional data and interpretations. Proc Natl Acad Sci 15: 481-493.
158. Suzuki Y, Gojobori T. 1999. A method for detecting positive selection at single amino acid sites. Mol Biol Evol 16: 1315-1328.
159. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595. (Pubitemid 19274682)
160. Thompson R. 2008. Estimation of quantitative genetic parameters. Proc R Soc Lond B Biol Sci 275: 679-686.
161. Thornton K, Andolfatto P. 2006. Approximate bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
162. Thornton KR, Jensen JD. 2007. Controlling the false-positive rate in multilocus genome scans for selection. Genetics 175: 737-750.
163. Thornton KR, Jensen JD, Becquet C, Andolfatto P. 2007. Progress and prospects in mapping recent selection in the genome. Heredity 98: 340-348.
164. Vasemagi A, Primmer CR. 2005. Challenges for identifying functionally important genetic variation: The promise of combining complementary research strategies. Mol Ecol 14: 3623-3642. (Pubitemid 43919918)
165. Vignieri SN, Larson JG, Hoekstra HE. 2010. The selective advantage of crypsis in mice. Evolution (in press).
166. Wakeley J, Aliacar N. 2001. Gene genealogies in a metapopulation. Genetics 159: 893-905.
167. Wallace AR. 1858. On the tendency of varieties to depart indefinitely from the original type. J Proc Linn Soc 3: 53-62.
168. Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, Nielsen R. 2007. Localizing recent adaptive evolution in the human genome. PLoS Genet. 3: e90.
169. Wright SJ. 1931. Evolution in Mendelian populations. Genetics 16: 97-159.
170. Wright SI, Charlesworth B. 2004. The HKA test revisited: A maximum-likelihood-ratio test of the standard neutral model. Genetics 168: 1071-1076. (Pubitemid 39491480)
171. Yang Z, Bielawski JP. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15: 496-503.