Comparison of FST outlier tests for SNP loci under selection

Molecular Ecology Resources

Volumn 11, Issue SUPPL. 1, 2011, Pages 184-194

  Narum, Shawn R ^a   Hess, Jon E ^a  

^a Hagerman Fish Culture Experiment Station ^*  (United States)

Author keywords

Balancing selection; Candidate markers; Divergent selection; FST outlier tests

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; COMPUTER PROGRAM; COMPUTER SIMULATION; EVALUATION; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC SELECTION; GENOME; SINGLE NUCLEOTIDE POLYMORPHISM;

COMPUTER SIMULATION; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETIC MARKERS; GENOME; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC; SOFTWARE;

EID: 79951750950     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2011.02987.x     Document Type: Article

References (29)

1. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Research, 12, 1805-1814.
2. Akey JM (2009) Constructing genomic maps of positive selection in humans: where do we go from here? Genome Research, 19, 711-722.
3. Antao T, Lopes A, Lopes RJ et al. (2008) LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics, 9, 323.
4. Antoniazza S, Burri R, Fumagalli L, Goudet J, Roulin A (2010) Local adaptation maintains clinal variation in melanin-based coloration of European barn owls (Tyto alba). Evolution, 64, 1944-1954.
5. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969-980.
6. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society London Series B, 263, 1619-1626.
7. Canino MF, O'Reilly PT, Hauser L, Bentzen P (2005) Genetic differentiation in walleye pollock (Theragra chalcogramma) in response to selection at the pantophysin (PanI) locus. Canadian Journal of Fisheries and Aquatic Sciences, 62, 2519-2529.
8. Chase K, Jones P, Martin A, Ostrander EA, Lark KG (2009) Genetic mapping of fixed phenotypes: disease frequency as a breed characteristic. Journal of Heredity, 100, S37-S41.
9. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
10. Excoffier L, Hofer T, Foll M (2009) Detecting loci under selection in a hierarchically structured population. Heredity, 103, 285-298.
11. Foll M, Gaggiotti OE (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics, 180, 977-993.
12. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution, 59, 1633-1638.
13. Hermisson J (2009) Who believes in whole-genome scans for selection? Heredity, 103, 283-284.
14. Joost S, Bonin A, Bruford MW et al. (2007) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genetics approach to adaptation. Molecular Ecology, 16, 3955-3969.
15. Joost S, Kalbermatten M, Bonin A (2008) Spatial Analysis Method (SAM): a software tool combining molecular and environmental data to identify candidate loci for selection Molecular Ecology Resources, 8, 957-960.
16. Kelley JL, Madeoy J, Calhoun JC, Swanson W, Akey JM (2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Research, 16, 980-989.
17. 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.
18. Nachman MW, Hoekstra HE, D'Agostino SL (2003) The genetic basis of adaptive melanism in pocket mice. Proceedings of the National Academy of Sciences, 100, 5268-5273.
19. Narum SR, Campbell NR, Kozfkay CC, Meyer KA (2010) Adaptation of redband trout in desert and montane environments. Molecular Ecology, 19, 4622-4637, doi: .
20. Neuenschwander S, Hospital F, Guillaume F, Goudet J (2008) quantiNEMO: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. Bioinformatics, 24, 1552-1553.
21. Nosil P, Egan SP, Funk DJ (2008) Heterogeneous genomic differentiation between walking-stick ecotypes: 'isolation by adaptation' and multiple roles for divergent selection. Evolution, 62, 316-336.
22. Park MY, Hastie T (2008) Penalized logistic regression for detecting gene interactions. Biostatistics, 9, 30-50.
23. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics, 38, 904-909.
24. Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association studies. American Journal of Human Genetics, 65, 220-228.
25. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248-249.
26. Vitalis R, Dawson K, Boursot P (2001) Interpretation of variation across marker loci as evidence of selection. Genetics, 158, 1811-1823.
27. Wachowiak W, Balk PA, Savolainen O (2009) Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.). Tree Genetics and Genomes, 5, 117-132.
28. Xue Y, Zhang H, Huang N et al. (2009) Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation. Genetics, 183, 1065-1077.
29. Zhang F, Wang Y, Deng H (2008) Comparison of population-based association study methods correcting for population stratification. PLoS ONE, 3, e3392, doi: .