Uninformative polymorphisms bias genome scans for signatures of selection

BMC Evolutionary Biology

Volumn 12, Issue 1, 2012, Pages

  Roesti, Marius ^a   Salzburger, Walter ^a   Berner, Daniel ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

Allele frequency distribution; F ST; Gasterosteus aculeatus; Genetic marker; Hitchhiking; Population differentiation; Singleton

Indexed keywords

ALLELE; GENETIC DIFFERENTIATION; GENETIC DRIFT; GENETIC MARKER; GENOME; POLYMERASE CHAIN REACTION; POLYMORPHISM; STREAM; TELEOST;

GASTEROSTEUS ACULEATUS;

ANIMAL; ARTICLE; GENE FREQUENCY; GENETIC MARKER; GENETIC SELECTION; GENETICS; GENOMICS; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; SMEGMAMORPHA;

ANIMALS; GENE FREQUENCY; GENETIC MARKERS; GENOMICS; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC; SMEGMAMORPHA;

EID: 84862564389     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-12-94     Document Type: Article

References (45)

1. The genic view of the process of speciation. Wu CI, J Evol Biol 2001 14 851 865 10.1046/j.1420-9101.2001.00335.x (Pubitemid 34029787)
2. Which evolutionary processes influence natural genetic variation for phenotypic traits? Mitchell-Olds T, Willis JH, Goldstein DB, Nat Rev Genet 2007 8 845 856 17943192 (Pubitemid 47609091)
3. Divergent selection and heterogeneous genomic divergence. Nosil P, Funk DJ, Ortiz-Barrientos D, Mol Ecol 2009 18 375 402 10.1111/j.1365-294X.2008.03946. x 19143936
4. Evidence for ecological speciation and its alternative. Schluter D, Science 2009 323 737 741 10.1126/science.1160006 19197053
5. Genetics in geographically structured populations: defining, estimating and interpreting FST. Holsinger KE, Weir BS, Nat Rev Genet 2009 10 639 650 10.1038/nrg2611 19687804
6. Distribution of gene frequency as a test of theory of selective neutrality of polymorphisms. Lewontin RC, Krakauer J, Genetics 1973 74 175 195 4711903
7. Hitch-hiking effect of a favorable gene. Maynard Smith J, Haigh J, Genet Res 1974 23 23 35 10.1017/S0016672300014634 4407212
8. Adaptation and speciation: what can Fst tell us? Beaumont MA, Trends Ecol Evol 2005 20 435 440 10.1016/j.tree.2005.05.017 16701414 (Pubitemid 41026729)
9. Using genome scans of DNA polymorphism to infer adaptive population divergence. Storz JF, Mol Ecol 2005 14 671 688 10.1111/j.1365-294X.2005.02437.x 15723660 (Pubitemid 40346460)
10. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Stinchcombe JR, Hoekstra HE, Heredity 2008 100 158 170 17314923 (Pubitemid 351156869)
11. Evaluating loci for use in the genetic analysis of population structure. Beaumont MA, Nichols RA, Proc R Soc Lond B 1996 263 1619 1626 10.1098/rspb.1996.0237 (Pubitemid 27055553)
12. Identifying adaptive genetic divergence among populations from genome scans. Beaumont MA, Balding DJ, Mol Ecol 2004 13 969 980 10.1111/j.1365-294X. 2004.02125.x 15012769 (Pubitemid 38390600)
13. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Foll M, Gaggiotti O, Genetics 2008 180 977 993 10.1534/genetics.108.092221 18780740
14. Detecting loci under selection in a hierarchically structured population. Excoffier L, Hofer T, Foll M, Heredity 2009 103 285 298 10.1038/hdy.2009.74 19623208
15. Interrogating a high-density SNP map for signatures of natural selection. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD, Genome Res 2002 12 1805 1814 10.1101/gr.631202 12466284 (Pubitemid 35469929)
16. Genomic islands of speciation in Anopheles gambiae. Turner TL, Hahn MW, Nuzhdin SV, PLoS Biol 2005 3 285 10.1371/journal.pbio.0030285 16076241 (Pubitemid 41306440)
17. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA, PLoS Genet 2010 6 1000862 10.1371/journal.pgen.1000862 20195501
18. Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Lawniczak MKN, Emrich SJ, Holloway AK, Regier AP, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, et al. Science 2010 330 512 514 10.1126/science.1195755 20966253
19. Estimating F-statistics for the analysis of population-structure. Weir BS, Cockerham CC, Evolution 1984 38 1358 1370 10.2307/2408641
20. Ewens W, Mathematical population genetics Springer, New York 1979
21. Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Hermisson J, Pennings PS, Genetics 2005 169 2335 2352 10.1534/genetics.104.036947 15716498 (Pubitemid 40695640)
22. DNA polymorphism detectable by restriction endonucleases. Nei M, Tajima F, Genetics 1981 97 145 163 6266912
23. Genotype and SNP calling from next-generation sequencing data. Nielsen R, Paul JS, Albrechtsen A, Song YS, Nat Rev Genet 2011 12 443 451 10.1038/nrg2986 21587300
24. The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Marth GT, Czabarka E, Murvai J, Sherry ST, Genetics 2004 166 351 372 10.1534/genetics.166.1.351 15020430 (Pubitemid 38364726)
25. Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Keightley PD, Eyre-Walker A, Genetics 2007 177 2251 2261 10.1534/genetics.107.080663 18073430 (Pubitemid 350277004)
26. Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations. Oleksyk TK, Zhao K, De La Vega FM, Gilbert DA, O'Brien SJ, Smith MW, PLoS One 2008 3 1712 10.1371/journal.pone.0001712 18320033 (Pubitemid 351903001)
27. Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature. Bradbury IR, Hubert S, Higgins B, Borza T, Bowman S, Paterson IG, Snelgrove PVR, Morris CJ, Gregory RS, Hardie DC, et al. Proc R Soc B 2010 277 3725 3734 10.1098/rspb.2010.0985 20591865
28. The impact of next-generation sequencing technology on genetics. Mardis ER, Trends Genet 2008 24 133 141 10.1016/j.tig.2007.12.007 18262675
29. Rapid SNP discovery and genetic mapping using sequenced RAD markers. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA, PLoS One 2008 3 3376 10.1371/journal.pone.0003376 18852878
30. Constraints on speciation suggested by comparing lake-stream stickleback divergence across two continents. Berner D, Roesti M, Hendry AP, Salzburger W, Mol Ecol 2010 19 4963 4978 10.1111/j.1365-294X.2010.04858.x 20964754
31. Variable progress toward ecological speciation in parapatry: stickleback across eight lake-stream transitions. Berner D, Grandchamp A-C, Hendry AP, Evolution 2009 63 1740 1753 10.1111/j.1558-5646.2009.00665.x 19228184
32. Natural selection drives patterns of lake-stream divergence in stickleback foraging morphology. Berner D, Adams DC, Grandchamp A-C, Hendry AP, J Evol Biol 2008 21 1653 1665 10.1111/j.1420-9101.2008.01583.x 18691241
33. Genome Project Data P: The Sequence Alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Bioinformatics 2009 25 2078 2079 10.1093/bioinformatics/btp352 19505943
34. R Development Team, R: A language and environment for statistical computing R Foundation for Statistical Computing, Vienna, Austria 2010
35. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R, Bioinformatics 2009 25 2607 2608 10.1093/bioinformatics/btp450 19654119
36. Genetic traces of ancient demography. Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, Sherry ST, Proc Nat Acad Sci USA 1998 95 1961 1967 10.1073/pnas.95.4.1961 9465125 (Pubitemid 28103502)
37. Natural selection has driven population differentiation in modern humans. Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L, Nat Genet 2008 40 340 345 10.1038/ng.78 18246066 (Pubitemid 351311765)
38. A 11 desaturase gene genealogy reveals two divergent allelic classes within the European corn borer (Ostrinia nubilalis). Geiler KA, Harrison RG, BMC Evol Biol 2010 10 112 10.1186/1471-2148-10-112 20423501
39. Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans. Keightley PD, Halligan DL, Genetics 2011 188 931 940 10.1534/genetics.111.128355 21596896
40. The transient distribution of allele frequencies under mutation pressure. Nei M, Li W-H, Genet Res 1976 28 205 214 10.1017/S0016672300016906 1026567 (Pubitemid 8033647)
41. Maintenance of genetic variability under joint effect of mutation, selection and random drift. Li WH, Genetics 1978 90 349 382 17248867 (Pubitemid 9049486)
42. Statistical properties of segregating sites. Fu YX, Theor Pop Biol 1995 48 172 197 10.1006/tpbi.1995.1025
43. An analysis of strategies for discovery of single-nucleotide polymorphisms. Eberle MA, Kruglyak L, Genet Epidemiol 2000 19 29 35 10.1002/1098-2272(2000)19:1+<::AID-GEPI5>3.0.CO;2-P
44. Non-equilibrium theory of the allele frequency spectrum. Evans SN, Shvets Y, Slatkin M, Theor Pop Biol 2007 71 109 119 10.1016/j.tpb.2006.06.005 (Pubitemid 44751057)
45. Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs. Roesti M, Hendry AP, Salzburger W, Berner D, Mol Ecol 2012 21 2852 2862 10.1111/j.1365-294X.2012. 05509.x 22384978