Sequence differentiation in regions identified by a genome scan for local adaptation

Molecular Ecology

Volumn 17, Issue 13, 2008, Pages 3123-3135

  Wood, Henry M ^a   Grahame, John W ^a   Humphray, Sean ^b   Rogers, Jane ^b   Butlin, Roger K ^c  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

AFLP; Littorina; Population genomics; Transposable element

Indexed keywords

ADAPTATION; ANIMAL; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CLASSIFICATION; DNA SEQUENCE; GASTROPOD; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENETICS; GENOME; GROWTH, DEVELOPMENT AND AGING; MALE; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; UNITED KINGDOM;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLONING, MOLECULAR; ENGLAND; GASTROPODA; GENE EXPRESSION REGULATION; GENETICS, POPULATION; GENOME; MALE; MOLECULAR SEQUENCE DATA; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); GASTROPODA; LITTORINA; LITTORINA SAXATILIS;

EID: 45549108208     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03755.x     Document Type: Article

References (51)

1. Akey JM, Eberle MA, Rieder MJ et al 2004) Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biology, 2, 1591 1599.
2. Batzer MA, Deininger PL (2002) Alu repeats and human genomic diversity. Nature Reviews Genetics, 3, 370 379.
3. ST tell us? Trends in Ecology & Evolution, 20, 435 440.
4. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969 980.
5. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society B: Biological Sciences, 263, 1619 1626.
6. Bonin A, Taberlet P, Miaud C, Pompanon F (2006) Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria). Molecular Biology and Evolution, 23, 773 783.
7. Brookfield JFY (2003) Mobile DNAs: the poacher turned gamekeeper. Current Biology, 13, R846 R847.
8. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology, 268, 78 94.
9. Cambridge PG, Kitching JA (1982) Shell shape in living and fossil (Norwich Crag) Nucella lapillus (L.) in relation to habitat. Journal of Conchology, 31, 31 38.
10. Campbell D, Bernatchez L (2004) Generic scan using AFLP markers as a means to assess the role of directional selection in the divergence of sympatric whitefish ecotypes. Molecular Biology and Evolution, 21, 945 956.
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 populations. Genetical Research, 70, 155 174.
12. Christiansen FB (1974) Sufficient conditions for protected polymorphism in a subdivided population. American Naturalist, 108, 157 166.
13. Chung H, Bogwitz MR, McCart C et al 2007) Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics, 175, 1071 1077.
14. ffrench-Constant R, Daborn P, Feyereisen R (2006) Resistance and the jumping gene. Bioessays, 28, 6 8.
15. De Kovel CGF (2006) The power of allele frequency comparisons to detect the footprint of selection in natural and experimental situations. Genetics Selection Evolution, 38, 3 23.
16. Emelianov I, Marec F, Mallet J (2004) Genomic evidence for divergence with gene flow in host races of the larch budmoth. Proceedings of the Royal Society B: Biological Sciences, 271, 97 105.
17. Excoffier L, Laval G, Schneider S (2005) arlequin ver. 3.0: an integrated software for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
18. Grahame JW, Wilding CS, Butlin RK (2006) Adaptation to a steep environmental gradient and an associated barrier to gene exchange in Littorina saxatilis. Evolution, 60, 268 278.
19. Greenspan G, Geiger D (2004) Model-based inference of haplotype block variation. Journal of Computational Biology, 11, 495 506.
20. Hall TA (1999) bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95 98.
21. Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA-sequences. Genetics, 111, 147 164.
22. Hull SL, Grahame J, Mill PJ (1996) Morphological divergence and evidence for reproductive isolation in Littorina saxatilis (Olivi) in northeast England. Journal of Molluscan Studies, 62, 89 99.
23. Jordan IK, Rogozin IB, Glazko GV, Koonin EV (2003) Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends in Genetics, 19, 68 72.
24. Kayser M, Brauer S, Stoneking M (2003) A genome scan to detect candidate regions influenced by local natural selection in human populations. Molecular Biology and Evolution, 20, 893 900.
25. Kazazian HH (2004) Mobile elements: drivers of genome evolution. Science, 303, 1626 1632.
26. Kelly JL, Madeoy J, Calhoun JC et al 2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Research, 16, 980 989.
27. Kim Y, Stephan W (2003) Selective sweeps in the presence of interference among partially linked loci. Genetics, 164, 389 398.
28. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics, 4, 981 994.
29. Murray MC, Hare MP (2006) A genomic scan for divergent selection in a secondary contact zone between Atlantic and Gulf of Mexico oysters, Crassostrea virginica. Molecular Ecology, 15, 4229 4242.
30. Nielsen R (2001) Statistical tests of selective neutrality in the age of genomics. Heredity, 86, 641 647.
31. Nielsen R (2005) Molecular signatures of natural selection. Annual Review of Genetics, 39, 197 218.
32. Nielsen R, Bustamante C, Clark AG et al 2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology, 3, 976 985.
33. Orr HA (2001) The genetics of species differences. Trends in Ecology & Evolution, 16, 343 350.
34. Pannell JR (2003) Coalescence in a metapopulation with recurrent local extinction and recolonization. Evolution, 57, 949 961.
35. Panova M, Hollander J, Johannesson K (2006) Site-specific genetic divergence in parallel hybrid zones suggests nonallopatric evolution of reproductive barriers. Molecular Ecology, 15, 4021 4031.
36. Poinar HN, Schwarz C, Qi J et al 2006) Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science, 311, 392 394.
37. Quesada H, Posada D, Caballero A, Moran P, Rolan-Alvarez E (2007) Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail. Evolution, 61, 1600 1612.
38. Rogers SM, Bernatchez L (2005) Integrating QTL mapping and genome scans towards the characterization of candidate loci under parallel selection in the lake whitefish (Coregonus clupeaformis). Molecular Ecology, 14, 351 361.
39. Rogers SM, Bernatchez L (2007) The genetic architecture of ecological speciation and the association with signatures of selection in natural lake whitefish (Coregonas sp., Salmonidae) species pairs. Molecular Biology and Evolution, 24, 1423 1438.
40. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) dnasp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
41. Rozen S, Skaletsky HJ (2000) primer 3 on the WWW for general users and for biologist programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (eds Krawetz S, Msiener S pp. 365 386. Humana Press, Totowa, New Jersey.
42. Savolainen V, Anstett MC, Lexer C et al 2006) Sympatric speciation in palms on an oceanic island. Nature, 441, 210 213.
43. ST-based methods at detecting the signature of selection in microsatellite markers linked to a selection-targeted locus. PhD Thesis. University of Reading, Berkshire, UK.
44. Storz JF (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology, 14, 671 688.
45. Teshima KM, Coop G, Przeworski M (2006) How reliable and empirical genomic scans for selective sweeps? Genome Research, 16, 702 712.
46. Vasemagi A, Nilsson J, Primmer CR (2005) Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Molecular Biology and Evolution, 22, 1067 1076.
47. Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology, 11, 139 151.
48. Vitalis R, Dawson K, Boursot P, Belkhir K (2003) detsel 1.0: a computer program to detect markers responding to selection. Journal of Heredity, 94, 429 431.
49. Wilding CS, Butlin RK, Grahame J (2001) Differential gene exchange between parapatric morphs of Littorina saxatilis detected using AFLP markers. Journal of Evolutionary Biology, 14, 611 619.
50. Wu DY, Ugozzoli L, Pal BK, Qian J, Wallace RB (1991) The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction. DNA and Cell Biology, 10, 233 238.
51. Yatabe Y, Kane NC, Scotti-Saintagne C, Rieseberg LH (2007) Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, Helianthus annuus and H. petiolaris. Genetics, 175, 1883 1893.