Comparing three different methods to detect selective loci using dominant markers

Journal of Evolutionary Biology

Volumn 23, Issue 10, 2010, Pages 2267-2276

  Perez Figueroa A ^a   Garcia Pereira M J ^a   Saura, M ^a   Rolan Alvarez E ^a   Caballero, A ^a  

^a UNIVERSITY OF VIGO   (Spain)

Author keywords

Amplified fragment length polymorphisms; Candidate loci; FST; Genome scan; Neutral model; Outliers

Indexed keywords

COMPARATIVE STUDY; DETECTION METHOD; GENE EXPRESSION; GENETIC MARKER; GENETIC STRUCTURE; GENOME; NATURAL SELECTION; OUTLIER; POLYMORPHISM;

ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; COMPUTER SIMULATION; DOMINANT GENE; GENE LOCUS; GENETIC SELECTION; GENOME; GENOMICS; METHODOLOGY;

COMPUTER SIMULATION; GENES, DOMINANT; GENETIC LOCI; GENOME; GENOMICS; SELECTION, GENETIC; SOFTWARE;

EID: 77956579317     PISSN: 1010061X     EISSN: 14209101     Source Type: Journal    
DOI: 10.1111/j.1420-9101.2010.02093.x     Document Type: Article

References (67)

1. Acheré V, Favre JM, Besnard G, Jeandroz S. Genomic organization of molecular differentiation in Norway spruce (Picea abies). Mol. Ecol. 2005, 14:3191-3201.
2. Beaumont MA, Balding DJ. Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol. 2004, 13:969-980.
3. Beaumont MA, Nichols RA. Evaluating loci for use in the genetic analysis of population structure. Proc. Biol. Sci. 1996, 263:1619-1626.
4. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 1995, 57:289-300.
5. Bensch S, Akesson M. Ten years of AFLP in ecology and evolution: why so few animals? Mol. Ecol. 2005, 14:2899-2914.
6. Bitocchi E, Nanni L, Rossi M, Bellucci E, Giardini E, Buonamici A, Vendramin GG, Papa R. Introgression from modern hybrid varieties into landrace populations of maize (Zea mays ssp. mays L.) in central Italy. Mol. Ecol. 2009, 18:603-621.
7. Blel H, Panfili J, Guinand B, Berrebi P, Said K, Durand J-D. Selection footprint at the first intron of the Prl gene in natural populations of the flathead mullet (Mugil cephalus, L. 1758). J. Exp. Mar. Biol. Ecol. 2010, 387:60-67.
8. Bonhomme M, Blancher A, Jalil MF, Crouau-Roy B. Factors shaping genetic variation in the MHC of natural non-human primate populations. Tissue Antigens 2007, 70:398-411.
9. Bonin A, Taberlet P, Miaud C, Pompanon F. Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria). Mol. Biol. Evol. 2006, 23:773-783.
10. Bonin A, Nicole F, Pompanon F, Miaud C, Taberlet P. Population adaptive index: a new method to help measure intraspecific genetic diversity and prioritize populations for conservation. Conserv. Biol. 2007, 21:697-708.
11. Bryja J, Charbonnel N, Berthier K, Galan M, Cosson J-F. Density-related changes in selection pattern for major histocompatibility complex genes in fluctuating populations of voles. Mol. Ecol. 2007, 16:5084-5097.
12. Caballero A, Quesada H, Rolán-Álvarez E. Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics 2008, 179:539-554.
13. Carvajal-Rodriguez A, de Uña-Alvarez J, Rolan-Alvarez E. A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests. BMC Bioinformatics 2009, 10. http://webs.uvigo.es/acraaj/SGoF.htm, See
14. Chen L, Yang G. A genomic scanning using AFLP to detect candidate loci under selection in the finless porpoise (Neophocaena phocaenoides). Genes Genet. Syst. 2009, 84:307-313.
15. Egan SP, Nosil P, Funk D. Selection and genomic differentiation during ecological speciation: isolating the contributions of host association via comparative genome scan of Neochlamisus bebbianae leaf beetles. Evolution 2008, 62:1162-1181.
16. Eveno E, Collada C, Guevara MA, Leger V, Soto A, Diaz L, Leger P, Gonzalez-Martinez SC, Cervera MT, Plomion C, Garnier-Gere PH. Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses. Mol. Biol. Evol. 2008, 25:417-437.
17. Excoffier L, Hofer T, Foll M. Detecting loci under selection in a hierarchically structured population. Heredity 2009, 103:285-298.
18. Flint J, Bond J, Rees DC, Boyce AJ, Roberts-Thomson JM, Excoffier L, Clegg MA, Beaumont MA, Nichols RA, Harding RM. Minisatellite mutational processes reduce Fst estimates. Hum. Genet. 1999, 105:567-576.
19. Foll M, Gaggiotti O. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 2008, 180:977-995.
20. Freeland JR, Biss P, Conrad KF, Silvertown J. Selection pressures have caused genome-wide population differentiation of Anthoxanthum odoratum despite the potential for high gene flow. J. Evol. Biol. 2010, 23:776.
21. Gaggiotti O, Bekkevold D, Jorgensen HBH, Foll M, Carvalho GR, Andre C, Ruzzante DE. Disentangling the effects of evolutionary, demographic, and environmental factors influencing genetic structure of natural populations: Atlantic herring as a case study. Evolution 2009, 63:2939-2951.
22. Gagnaire PA, Albert V, Jónsson B, Bernatchez L. Natural selection influences AFLP intraspecific genetic variability and introgression patterns in Atlantic eels. Mol. Ecol. 2009, 18:1678-1691.
23. Galindo J, Morán P, Rolán-Álvarez E. Comparing geographical genetic differentiation between candidate and noncandidate loci for adaptation strengthens support for parallel ecological divergence in the marine snail Littorina saxatilis. Mol. Ecol. 2009, 18:919-930.
24. Holderegger R, Herrmann D, Poncet B, Gugerli F, Thuiller W, Taberlet P, Gielly L, Rioux D, Brodbeck S, Aubert S, Manel S. Land ahead: using genome scans to identify molecular markers of adaptive relevance. Plant Ecol. Divers 2008, 1:273-283.
25. Joost S, Bonin A, Bruford MW, Després SL, Conord C, Erhardt G, Taberlet P. A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Mol. Ecol. 2007, 16:3955-3969.
26. Joost S, Kalbermatten M, Bonin A. Spatial analysis method (SAM): a software tool combining molecular and environmental data to identify candidate loci for selection. Mol. Ecol. Resour. 2008, 8:957-960.
27. Jump AS, Hunt JM, Martínez-Izquierdo JA, Peñuelas J. Natural selection and climate change: temperature-linked spatial and temporal trends in gene frequency in Fagus sylvatica. Mol. Ecol. 2006, 15:3469-3480.
28. Kane NC, Rieseberg L. Selective sweeps reveal candidate genes for adaptation to drought and salt tolerance in common sunflower, Helianthus annuus. Genetics 2007, 175:1823-1834.
29. Knapen D, De Wolf H, Knaepkens G, Bervoets L, Eens M, Blust R, Verheyen E. Historical metal pollution in natural gudgeon populations: inferences from allozyme, microsatellite and condition factor analysis. Aquat. Toxicol. 2009, 95:17-26.
30. Lewontin R, Krakauer J. Distribution of gene frequency as a test of theory of selective neutrality of polymorphisms. Genetics 1973, 74:175-195.
31. Manel S, Conord C, Després L. Genome scan to assess the respective role of host-plant and environmental constraints on the adaptation of a widespread insect. BMC Evol. Biol. 2009, 9:288-297.
32. Marden JI. Hypothesis testing: from p values to Bayes factors. J. Am. Stat. Assoc. 2000, 95:1316-1320.
33. Mealor BA, Hild A. Potential selection in native grass populations by exotic invasion. Mol. Ecol. 2006, 15:2291-2300.
34. Medugorac I, Medugorac A, Russ I, Veit-Kensch CE, Taberlet P, Luntz B, Mix HM, Förster M. Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size. Mol. Ecol. 2009, 18:3394-3410.
35. Meudt HM, Clarke AC. Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci. 2007, 12:106-117.
36. Meyer C-L, Vitalis R, Saumitou-Laprade P, Castric C. Genomic pattern of adaptive divergence in Arabidopsis halleri, a model species for tolerance to heavy metal. Mol. Ecol. 2009, 18:2050-2062.
37. Michalski S, Durka W, Jentsch A, Kreyling J, Pompe S, Schweiger O, Willner E, Beierkuhnlein C. Evidence for genetic differentiation and divergent selection in an autotetraploid forage grass (Arrhenatherum elatius). Theor. Appl. Genet. 2010, 120:1151-1162.
38. Miller NJ, Ciosi M, Sappington TW, Ratcliffe ST, Spencer JL, Giuillemaud T. Genome scan of Diabrotica virgifera virgifera for genetic variation associated with crop rotation tolerance. J. Appl. Entomol. 2007, 131:378-385.
39. Mueller UG, Wolfenbarger L. AFLP genotyping and fingerprinting. Trends Ecol. Evol. 1999, 14:389-394.
40. Murray MC, Hare MP. A genomic scan for divergent selection in a secondary contact zone between Atlantic and Gulf of Mexico oysters, Crassostrea virginica. Mol. Ecol. 2006, 15:4229-4242.
41. Nei M, Chakravarti A. Drift variances of Fst and Gst statistics obtained from a finite number of isolated populations. Theor. Popul. Biol. 1977, 11:307-325.
42. Nielsen R. Molecular signatures of natural selection. Annu. Rev. Genet. 2005, 39:197-218.
43. Nielsen EE, Hemmer-Hansen J, Poulsen NA, Loeschcke V, Moen T, Johansen T, Mittelholzer C, Taranger G-L, Ogden R, Carvalho GR. Genomic signatures of local directional selection in a high gene flow marine organism: the Atlantic cod (Gadus morhua). BMC Evol. Biol. 2009, 9:276-286.
44. Nosil P, Egan SP, Funk D. Heterogeneous genomic differentiation between walking-stick ecotypes: "isolation by adaptation" and multiple roles for divergent selection. Evolution 2008, 62:316-336.
45. O'Malley KG, Camara MD, Banks M. Candidate loci reveal genetic differentiation between temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha). Mol. Ecol. 2007, 16:4930-4941.
46. Oetjen K, Reusch TBH. Genome scans detect consistent divergent selection among subtidal vs. intertidal populations of the marine angiosperm Zostera marina. Mol. Ecol. 2007, 16:5156-5157.
47. Oetjen K, Ferber S, Dankert I, Reusch TBH. New evidence for habitat-specific selection in Wadden Sea Zostera marina populations revealed by genome scanning using SNP and microsatellite markers. Mar. Biol. 2010, 157:81-89.
48. Papa R, Bellucci E, Rossi M, Leonardi S, Rau D, Gepts P, Nanni L, Attene G. Tagging the signatures of domestication in common bean (Phaseolus vulgaris) by means of pooled DNA samples. Ann. Bot. London 2007, 100:1039-1051.
49. Paris M, Boyer S, Bonin A, Collado A, David J, Despres L. Genome scan in the mosquito Aedes rusticus: population structure and detection of positive selection after insecticide treatment. Mol. Ecol. 2010, 19:325-337.
50. Parisod C, Joost S. Divergent selection in trailing-versus leading-edge populations of Biscutella laevigata. Ann. Bot. London 2010, 105:655-660.
51. Raeymaekers JAM, Houdt JKJV, Larmuseau MHD, Geldof S, Volckaert FAM. Divergent selection as revealed by PST and QTL-based FST in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient. Mol. Ecol. 2007, 16:891-905.
52. Ridgway T, Riginos C, Davis J, HoeghGuldberg O. Genetic connectivity patterns of Pocillopora verrucosa in southern African Marine Protected Areas. Mar. Ecol. Prog. Ser. 2008, 354:161-168.
53. Robertson A. Gene frequency distributions as a test of selective neutrality. Genetics 1975, 81:775-785.
54. Santalla M, Ron AM, La Fuente M. Integration of genome and phenotypic scanning gives evidence of genetic structure in Mesoamerican common bean (Phaseolus vulgaris L.) landraces from the southwest of Europe. Theor. Appl. Genet. 2010, 120:1635-1651.
55. Savolainen V, Anstett M-C, Lexer C, Hutton I, Clarkson JJ, Norup MV, Powell MP, Springate D, Salamin N, Baker W. Sympatric speciation in palms on an oceanic island. Nat. Lett. 2006, 411:210-213.
56. Scotti-Saintagne C, Mariette S, Porth I, Goicoechea PG, Barreneche T, Bodènés C, Burg K, Kremer A. Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.]. Genetics 2004, 168:1615-1626.
57. Smith TB, Milá B, Grether GF, Slabbekoorn H, Sepil I, Buermann W, Saatchi S, Pollinger JP. Evolutionary consequences of human disturbance in a rainforest bird species from Central Africa. Mol. Ecol. 2008, 17:58-71.
58. Sokal RR, Rohlf FJ. Biometry 1995, Freeman & Co., New York
59. Tiranti B, Negri V. Selective microenvironmental effects play a role in shaping genetic diversity and structure in a Phaseolus vulgaris L. landrace: implications for on-farm conservation. Mol. Ecol. 2007, 16:4942-4955.
60. Tsumura Y, Kado T, Takahashi T, Tani N, Ujino-Ihara T, Iwata H. Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics 2007, 176:2393-2403.
61. Vasemägi A, Nilsson J, Primmer CR. Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Mol. Biol. Evol. 2005, 22:1067-1076.
62. Vitalis R, Dawson K, Boursot P. Interpretation of variation across marker loci as evidence of selection. Genetics 2001, 158:1811-1823.
63. Vitalis R, Dawson K, Boursot P, Belkhir K. DetSel 1.0: a computer program to detect markers responding to selection. J. Hered. 2003, 94:429-431.
64. Volis S. Detection of signatures of positive selection in naturally occurring genetic variation. Population Genetics Research Progress 2008, 279-310. Koven VT. In, ed, pp, Nova Science Publishers, Hauppauge, NY, USA
65. Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution 1984, 38:1358-1370.
66. Wilding CS, Butlin RK, Grahame J. Differential gene exchange between parapatric morphs of Littorina saxatilis detected using AFLP markers. J. Evol. Biol. 2001, 14:611-619.
67. Zhivotovsky LA. Estimating population structure in diploids with multilocus dominant DNA markers. Mol. Ecol. 1999, 8:907-913.