Statistical analysis of amplified fragment length polymorphism data: A toolbox for molecular ecologists and evolutionists

Molecular Ecology

Volumn 16, Issue 18, 2007, Pages 3737-3758

  Bonin, A ^a,b   Ehrich, D ^c   Manel, S ^b  

^a Diversity Arrays Technology P/L   (Australia)

^b UNIVERSITÉ JOSEPH FOURIER   (France)

^c UNIVERSITY OF OSLO   (Norway)

Author keywords

AFLP; Genetic diversity; Hybridization; Loci under selection; Population structure; Statistical

Indexed keywords

BIOLOGY; COMPUTER PROGRAM; COMPUTER SIMULATION; ECOLOGY; EVOLUTION; GENE FREQUENCY; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC PROCEDURES; HYBRIDIZATION; METHODOLOGY; PHENOTYPE; REVIEW;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ECOLOGY; EVOLUTION; GENE FREQUENCY; GENETIC MARKERS; GENETIC TECHNIQUES; HYBRIDIZATION, GENETIC; PHENOTYPE; POLYMORPHISM, GENETIC; SOFTWARE;

EID: 34548570134     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03435.x     Document Type: Review

References (162)

1. Ajmone-Marsan P, Negrini R, Milanesi E et al 2002) Genetic distances within and across cattle breeds as indicated by biallelic AFLP markers. Animal Genetics, 33, 280 286.
2. 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.
3. Albert V, Jonsson B, Bernatchez L (2006) Natural hybrids in Atlantic eels (Anguilla anguilla, A. rostrata): evidence for successful reproduction and fluctuating abundance in space and time. Molecular Ecology, 15, 1903 1916.
4. Anderson M (2003) pco: A Fortran Computer Program for Principal Coordinate Analysis. Distributed by the Author. University of Auckland, New Zealand.
5. Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics, 160, 1217 1229.
6. Assunção AG, Pieper B, Vromans J et al 2006) Construction of a genetic linkage map of Thlaspi caerulescens and quantitative trait loci analysis of zinc accumulation. New Phytologist, 170, 21 32.
7. Barbujani G, Oden NL, Sokal R (1989) Detecting regions of abrupt change in maps of biological variables. Systematic Zoology, 38, 376 389.
8. Barluenga M, Stolting KN, Salzburger W, Muschick M, Meyer A (2006) Sympatric speciation in Nicaraguan crater lake cichlid fish. Nature, 439, 719 723.
9. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London. Series B, Biological Sciences, 263, 1619 1626.
10. Bensch S, Akesson M (2005) Ten years of AFLP in ecology and evolution: why so few animals? Molecular Ecology, 14, 2899 2914.
11. Bensch S, Akesson S, Irwin DE (2002a) The use of AFLP to find an informative SNP: genetic differences across a migratory divide in willow warblers. Molecular Ecology, 11, 2359 2366.
12. Bensch S, Helbig AJ, Salomon M, Seibold I (2002b) Amplified fragment length polymorphism analysis identifies hybrids between two subspecies of warblers. Molecular Ecology, 11, 473 481.
13. Black WC, Baer CF, Antolin MF, DuTeau NM (2001) Population genomics: genome-wide sampling of insect populations. Annual Review of Entomology, 46, 441 469.
14. Blears MJ, de Grandis SA, Lee H, Trevors JT (1998) Amplified fragment length polymorphism (AFLP): a review of the procedure and its applications. Journal of Industrial Microbiology and Biotechnology, 21, 99 114.
15. Bonin A, Bellemain E, Bronken Eidesen P et al 2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology, 13, 3261 3273.
16. Bonin A, Miaud C, Taberlet P, 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.
17. Borowsky RL (2001) Estimating nucleotide diversity from random amplified polymorphic DNA and amplified fragment length polymorphism data. Molecular Phylogenetics and Evolution, 18, 143 148.
18. Buerkle CA (2005) Maximum-likelihood estimation of a hybrid index based on molecular markers. Molecular Ecology Notes, 5, 684 687.
19. 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.
20. Campbell D, Duchesne P, Bernatchez L (2003) AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites. Molecular Ecology, 12, 1979 1991.
21. de Casas RR, Besnard G, Schonswetter P, Balaguer L, Vargas P (2006) Extensive gene flow blurs phylogeographic but not phylogenetic signal in Olea europaea L. Theoretical and Applied Genetics, 113, 575 583.
22. Cavers S, Degen B, Caron H et al 2005) Optimal sampling strategy for estimation of spatial genetic structure in tree populations. Heredity, 95, 281 289.
23. Charlesworth B (1998) Measure of divergence between populations and the effect of forces that reduce variability. Molecular Biology and Evolution, 15, 538 543.
24. Clark AG, Lanigan CM (1993) Prospects for estimating nucleotide divergence with RAPDs. Molecular Biology and Evolution, 10, 1096 1111.
25. Congiu L, Dupanloup I, Patarnello T et al 2001) Identification of interspecific hybrids by amplified fragment length polymorphism: the case of sturgeon. Molecular Ecology, 10, 2355 2359.
26. Conord C, Lempérière G, Taberlet P, Després L (2006) Genetic structure of the forest pest Hylobius abietis on conifer plantations at different spatial scales in Europe. Heredity, 97, 46 55.
27. Corander J, Waldmann P, Silanpää J (2003) Bayesian analysis of genetic differentiation between populations. Genetics, 163, 367 374.
28. Corander J, Waldmann P, Marttinen P, Sillanpää M (2004) baps2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics, 20, 2363 2369.
29. Corander J, Siren J, Arjas E) Bayesian spatial modelling of genetic population structure. Computational Statistics.
30. Crida A, Manel S (in press) wombsoft: a r package that implements the Wombling method to identify genetic boundary. Molecular Ecology Notes.
31. Degen B, Petit R, Kremer A (2001) sgs-Spatial genetic software: a computer program for analysis of spatial genetic and phenotypic structures of individuals and populations. Journal of Heredity, 92, 447 448.
32. Després L, Loriot S, Gaudeul M (2002) Geographic pattern of genetic variation in the European globeflower Trollius europaeus L. (Ranunculaceae) inferred from amplified fragment length polymorphism markers. Molecular Ecology, 11, 2237 2347.
33. Dice LR (1945) Measures of the amount of ecologic association between species. Ecology, 26, 297 302.
34. Duarte JM, dos Santos JB, Melo LC (1999) Comparison of similarity coefficients based on RAPD markers in the common bean. Genetics and Molecular Biology, 22, 427 432.
35. Duchesne P, Bernatchez L (2002) aflpop: a computer program for simulated and real populations allocation, based on AFLP data. Molecular Ecology Notes, 2, 380 383.
36. 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 of London. Series B, Biological Sciences, 271, 97 105.
37. Epperson B (2003) Geographical Genetics. Princeton University Press, Princeton, New Jersey.
38. Erickson DL, Fenster CB, Stenoien HK, Price D (2004) Quantitative trait locus analyses and the study of evolutionary process. Molecular Ecology, 13, 2505 2522.
39. Excoffier L, Heckel G (2006) Computer programs for population genetics data analysis: a survival guide. Nature Reviews Genetics, 7, 745 758.
40. Excoffier L, Smouse P, Quattro J (1992) Analysis of molecular variance inferred for metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479 491.
41. Falush D, Stephens M, Pritchard J (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567 1587.
42. Falush D, Stephens M, Pritchard J) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes.
43. Felsenstein J (2004) phylip (Phylogeny Inference Package). Distributed by the Author. Department of Genome Sciences, University of Washington, Seattle.
44. Foulley JL, van Schriek MGM, Alderson L et al 2006) Genetic diversity analysis using lowly polymorphic dominant markers: the example of AFLP in pigs. Journal of Heredity, 97, 244 252.
45. François O, Ancelet S, Guillot G (2006) Bayesian clustering using hidden Markov random fields in spatial population genetics. Genetics, 174, 805 816.
46. Gardner KM, Latta RG (2006) Identifying loci under selection across contrasting environments in Avena barbata using quantitative trait locus mapping. Molecular Ecology, 15, 1321 1333.
47. Gaudeul M, Till-Bottraud I, Barjon F, Manel S (2004) Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): comparison of AFLP and microsatellite markers. Heredity, 92, 508 518.
48. Guillot G, Estoup A, Mortier F, Cosson J (2005) A spatial statistical model for landscape genetics. Genetics, 170, 1261 1280.
49. Guo YP, Saukel J, Mittermayr R, Ehrendorfer F (2005) AFLP analyses demonstrate genetic divergence, hybridization, and multiple polyploidization in the evolution of Achillea (Asteraceae-Anthemideae). New Phytologist, 166, 273 289.
50. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Molecular Biology, 57, 461 485.
51. van Haeringen WA, Den Bieman MG, Lankhorst AE, van Lith HA, van Zutphen LF (2002) Application of AFLP markers for QTL mapping in the rabbit. Genome, 45, 914 921.
52. Hansen M, Kraft T, Christiansson M, Nilsson NO (1999) Evaluation of AFLP in Beta. Theoretical and Applied Genetics, 98, 845 852.
53. Hardy OJ (2003) Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers. Molecular Ecology, 12, 1577 1588.
54. Hardy OJ, Vekemans X (2002) spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes, 2, 618 620.
55. Hardy OJ, Maggia L, Bandou E et al 2006) Fine-scale genetic structure and gene dispersal inferences in 10 Neotropical tree species. Molecular Ecology, 15, 559 571.
56. Hawthorne DJ (2001) AFLP-based genetic linkage map of the Colorado potato beetle Leptinotarsa decemlineata: sex chromosomes and a pyrethroid-resistance candidate gene. Genetics, 158, 695 700.
57. Helbig AJ, Seibold I, Kocum A et al 2005) Genetic differentiation and hybridization between greater and lesser spotted eagles (Accipitriformes: Aquila clanga, A. pomarina). Journal of Ornithology, 146, 226 234.
58. Hill WG, Weir BS (2004) Moment estimation of population diversity and genetic distance from data on recessive markers. Molecular Ecology, 13, 895 908.
59. Hollingsworth PM, Ennos RA (2004) Neighbour-joining trees, dominant markers and population genetic structure. Heredity, 92, 490 498.
60. Holsinger K (1999) Analysis of genetic diversity in geographically structured populations: a Bayesian perspective. Hereditas, 130, 245 255.
61. Holsinger KE, Lewis PO, Dey DK (2002) A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology, 11, 1157 1164.
62. Hosmer DW, Lemeshow S (2000) Applied Logistic Regression. John Wiley, New York.
63. Innan H, Terauchi R, Kahl G, Tajima F (1999) A method for estimating nucleotide diversity from AFLP data. Genetics, 151, 1157 1164.
64. Irwin D, Bensch S, Irwin J, Price T (2005) Speciation by distance in a ring species. Science, 307, 414 415.
65. Isabel N, Beaulieu J, Thériault P, Bousquet J (1999) Direct evidence for biased gene diversity estimates from dominant random amplified polymorphic DNA (RAPD) fingerprints. Molecular Ecology, 8, 477 483.
66. Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bulletin de la Société Vaudoise Des Sciences Naturelles, 44, 223 270.
67. Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Research, 29, E25.
68. Joost S, Bonin A (in press) Spatial analysis to detect signatures of selection along a gradient of altitude in the common frog (Rana temporaria). Proceedings of the 5th European Colloquium on Theoretical and Quantitative Geography.
69. Joost S, Bonin A, Bruford MW, Després L, Conord C, Erhardt G, Taberlet P (in press) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach of adaptation. Molecular Ecology.
70. Jump AS, Hunt JM, Martinez-Izquierdo JA, Penuelas J (2006) Natural selection and climate change: temperature-linked spatial and temporal trends in gene frequency in Fagus sylvatica. Molecular Ecology, 15, 3469 3480.
71. Kis-Papo T, Kirzhner V, Wasser SP, Nevo E (2003) Evolution of genomic diversity and sex at extreme environments: fungal life under hypersaline Dead Sea stress. Proceedings of the National Academy of Sciences, USA, 100, 14970 14975.
72. Knowles LL (2004) The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology, 17, 1 10.
73. Kolliker R, Kraehenbuehl R, Boller B, Widmer F (2006) Genetic diversity and pathogenicity of the grass pathogen Xanthomonas translucens pv. graminis. Systematic and Applied Microbiology, 29, 109 119.
74. Koopman WJM (2005) Phylogenetic signal in AFLP data sets. Systematic Biology, 54, 197 217.
75. Koopman WJM, Gort G (2004) Significance tests and weighted values for AFLP similarities, based on Arabidopsis in silico AFLP fragment length distributions. Genetics, 167, 1915 1928.
76. Kosman E (2003) Nei's gene diversity and the index of average differences are identical measures of diversity within populations. Plant Pathology, 52, 533 535.
77. Kosman E, Leonard KJ (2005) Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species. Molecular Ecology, 14, 415 424.
78. Krauss SL (2000) Accurate gene diversity estimates from amplified fragment length polymorphism (AFLP) markers. Molecular Ecology, 9, 1241 1245.
79. Kremer A, Caron H, Cavers S et al 2005) Monitoring genetic diversity in tropical trees with multilocus dominant markers. Heredity, 95, 274 280.
80. 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.
81. Lynch M, Milligan BG (1994) Analysis of population genetic structure with RAPD markers. Molecular Ecology, 3, 91 99.
82. Mackay TF (2001) The genetic architecture of quantitative traits. Annual Review of Genetics, 303 339.
83. Mallet J (2005) Hybridization as an invasion of the genome. Trends in Ecology & Evolution, 20, 229 237.
84. Manel S, Dias J, Ormerod S (1999) Alternative methods for predicting species distribution: an illustration with Himalayan river birds. Journal of Applied Ecology, 36, 734 747.
85. Manel S, Gaggiotti OE, Waples RS (2005) Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology & Evolution.
86. Manni F, Guerard E, Heyer E (2004) Geographic patterns of genetic, morphologic and linguistic variation: how barriers can be detected by using Monmonier's algorithm. Human Biology, 76, 173 190.
87. Mariac C, Robert T, Allinne C et al 2006) Genetic diversity and gene flow among pearl millet crop/weed complex: a case study. Theoretical and Applied Genetics, 113, 1003 1014.
88. Mariette S, Chagne D, Lezier C et al 2001) Genetic diversity within and among Pinus pinaster populations: comparison between AFLP and microsatellite markers. Heredity, 86, 469 479.
89. Mariette S, Le Corre V, Austerlitz F, Kremer A (2002) Sampling within the genome for measuring within-population diversity: trade-offs between markers. Molecular Ecology, 11, 1145 1156.
90. Mba C, Tohme J (2005) Use of AFLP markers in surveys of plant diversity. In: Molecular Evolution: Producing the Biochemical Data, Part B (eds Zimmer EA, Roalson EH pp. 177 201. Academic Press, San Diego, California.
91. McCullagh P, Nelder J (1989) Generalized Linear Models, 2nd edn. Chapman & Hall, London.
92. McMillan AM, Bagley MJ, Jackson SA, Nacci DE (2006) Genetic diversity and structure of an estuarine fish (Fundulus heteroclitus) indigenous to sites associated with a highly contaminated urban harbor. Ecotoxicology, 15, 539 548.
93. Mealor BA, Hild AL (2006) Potential selection in native grass populations by exotic invasion. Molecular Ecology, 15, 2291 2300.
94. Mechanda SM, Baum BR, Johnson DA, Arnason JT (2004) Sequence assessment of comigrating AFLP™ bands in Echinacea - implications for comparative biological studies. Genome, 47, 15 25.
95. Mendelson TC, Shaw KL (2005) Use of AFLP markers in surveys of arthropod diversity. In: Molecular Evolution: Producing the Biochemical Data, Part B (eds Zimmer EA, Roalson EH pp. 161 177. Academic Press, San Diego, California.
96. Meudt HM, Clarke AC (2007) Almost forgotten or latest practice? AFLP applications, analyses, and advances. Trends in Plant Science, 12, 106 117.
97. Miller MP (2005) Allele in space (ais): computer software for the joint analysis of interindividual spatial and genetic information. Journal of Heredity, 96, 722 724.
98. Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants - salient statistical tools and considerations. Crop Science, 43, 1235 1248.
99. Monmonier M (1973) Maximum-difference barriers: an alternative numerical regionalization method. Geographical Analysis, 3, 245 261.
100. Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends in Ecology & Evolution, 14, 389 394.
101. Narum SR (2006) Beyond Bonferroni: less conservative analyses for conservation genetics. Conservation Genetics, 7, 783 787.
102. Nei M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, USA, 70, 3321 3323.
103. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583 590.
104. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
105. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, USA, 76, 5269 5273.
106. Nielsen R (2005) Molecular signatures of natural selection. Annual Review of Genetics, 39, 197 218.
107. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology, 13, 1143 1155.
108. O'Hanlon PC, Peakall R (2000) A simple method for the detection of size homoplasy among amplified fragment length polymorphism fragments. Molecular Ecology, 9, 815 816.
109. Paetkau D, Slades R, Burdens M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Molecular Ecology, 13, 55 65.
110. Paun O, Stuessy TF, Horandl E (2006) The role of hybridization, polyploidization and glaciation in the origin and evolution of the apomictic Ranunculus cassubicus complex. New Phytologist, 171, 223 236.
111. Peakall R, Smouse PE (2006) genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288 295.
112. Polyakov A, Beharav A, Avivi A, Nevo E (2004) Mammalian microevolution in action: adaptive edaphic genomic divergence in blind subterranean mole-rats. Proceedings of the Royal Society of London. Series B, Biological Sciences, 271, S156 S159.
113. Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nature Reviews Genetics, 6, 847 859.
114. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959.
115. Prochazka M, Walder K, Xia J (2001) AFLP fingerprinting of the human genome. Human Genetics, 108, 59 65.
116. R Development Core Team (2004) A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria.
117. Raffl C, Schonswetter P, Erschbamer B (2006) 'Sax-sess' - genetics of primary succession in a pioneer species on two parallel glacier forelands. Molecular Ecology, 15, 2433 2440.
118. Reif JC, Melchinger AE, Frisch M (2005) Genetical and mathematical properties of similarity and dissimilarity coefficients applied in plant breeding and seed bank management. Crop Science, 45, 1 7.
119. Rieseberg LH, Whitton J, Gardner K (1999) Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics, 152, 713 727.
120. Ritland K (2005) Multilocus estimation of pairwise relatedness with dominant markers. Molecular Ecology, 14, 3157 3165.
121. Rivera-Ocasio E, Aide T, McMillan W (2006) The influence of spatial scale on the genetic structure of widespread tropical wetland tree, Pterocarpus officinalis (Fabaceae). Conservation Genetics, 7, 251 266.
122. 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.
123. Rogers SM, Campbell D, Baird SJE, Danzmann RG, Bernatchez L (2001) Combining the analyses of introgressive hybridisation and linkage mapping to investigate the genetic architecture of population divergence in the lake whitefish (Coregonus clupeaformis, Mitchill). Genetica, 111, 25 41.
124. Rogers SM, Isabel N, Bernatchez L (2007) Linkage maps of the dwarf and normal lake whitefish (Coregonus clupeaformis) species complex and their hybrid reveal the genetic architecture of population divergence. Genetics, 175, 375 398.
125. Rombauts S (2003) AFLPinSilico, simulating AFLP fingerprints. Bioinformatics, 19, 776 777.
126. Rouppe van der Voort JNAM, Van Zandvoort O, Van Eck HJ et al 1997) Use of allele specificity of comigrating AFLP markers to align genetic maps from different potato genotypes. Molecular Genomics and Genetics, 255, 438 447.
127. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219 1228.
128. SanCristobal M, Chevalet C, Peleman J et al 2006) Genetic diversity in European pigs utilizing amplified fragment length polymorphism markers. Animal Genetics, 37, 232 238.
129. Savolainen V, Anstett MC, Lexer C et al 2006) Sympatric speciation in palms on an oceanic island. Nature, 441, 210 213.
130. Schonswetter P, Tribsch A (2005) Vicariance and dispersal in the alpine perennial Bupleurum stellatum L. (Apiaceae). Taxon, 54, 725 732.
131. Schonswetter P, Tribsch A, Stehlik I, Niklfeld H (2004) Glacial history of high alpine Ranunculus glacialis (Ranunculaceae) in the European Alps in a comparative phylogeographical context. Biological Journal of the Linnean Society, 81, 183 195.
132. Scotti-Saintagne C, Mariette S, Porth I et al 2004) Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.]. Genetics, 168, 1615 1626.
133. Shan F, Clarke HC, Plummer JA, Yan G, Siddique KHM (2005) Geographical patterns of genetic variation in the world collections of wild annual Cicer characterized by amplified fragment length polymorphisms. Theoretical and Applied Genetics, 110, 381 391.
134. Shannon CE (1948) A mathematical theory of communication. Bell System Technical Journal, 27, 379 423 and 623 656.
135. Simmons MP, Zhang LB, Webb CT, Müller K (2007) A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference. Molecular Phylogenetics and Evolution, 42, 528 542.
136. Singh M, Chabane K, Valkoun J, Blake T (2006) Optimum sample size for estimating gene diversity in wild wheat using AFLP markers. Genetic Resources and Crop Evolution, 53, 23 33.
137. Skrede I, Eidesen PB, Portela RP, Brochmann C (2006) Refugia, differentiation and postglacial migration in arctic-alpine Eurasia, exemplified by the mountain avens (Dryas octopetala L.). Molecular Ecology, 15, 1827 1840.
138. Slate J (2005) Quantitative trait locus mapping in natural populations: progress, caveats and future directions. Molecular Ecology.
139. Sokal RR, Michener CD (1958) A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin, 38, 1409 1438.
140. Sørensen T (1948) A method of establishing groups of equal amplitude in plant sociology based on similarity of species content and its application to analyses of the vegetation on Danish commons. Kongelige Danske Videnskabernes Selskabs Biologiske Skrifter, 5, 1 34.
141. Sork VL, Nason J, Campbell DR, Fernandez JF (1999) Landscape approaches to historical and contemporary gene flow in plants. Trends in Ecology & Evolution, 14, 129 224.
142. Stewart CN, Excoffier L (1996) Assessing population genetic structure and variability with RADP data: application to Vaccinium macrocarpon (American Cranberry). Journal of Evolutionary Biology, 9, 153 171.
143. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences, USA, 100, 9440 9445.
144. Storz JF (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology, 14, 671 688.
145. Tero N, Aspi J, Siikamäki P, Jäkäläniemi A (2005) Local genetic population structure in an endangered plant species, Silene tatarica (Caryophyllaceae). Heredity, 94, 478 487.
146. Van de Peer Y, De Wachter R (1994) treecon for windows: a software package for the construction and drawing of evolutionary trees for the Microsoft windows environment. Computational and Applied Biosciences, 10, 569 570.
147. 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.
148. Verhoeven KJ, Vanhala TK, Biere A, Nevo E, van Damme JM (2004) The genetic basis of adaptive population differentiation: a quantitative trait locus analysis of fitness traits in two wild barley populations from contrasting habitats. Evolution, 58, 270 283.
149. Vos P, Hagers R, Bleeker M et al 1995) AFLP: new technique for DNA fingerprinting. Nucleic Acids Research, 23, 4407 4414.
150. Wang J (2004) Estimating pairwise relatedness from dominant genetic markers. Molecular Ecology, 13, 3169 3178.
151. Wang ZS, Baker AJ, Hill GE, Edwards SV (2003) Reconciling actual and inferred population histories in the house finch (Carpodacus mexicanus) by AFLP analysis. Evolution, 57, 2852 2864.
152. Weir B (1996) Genetic Data Analysis II. Sinauer & Associates, Massachusetts.
153. Weir B, Cockerham C (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358 1370.
154. Whitlock MC, McCauley DE (1999) Indirect measure of gene flow and migration. Heredity, 82, 117 125.
155. 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.
156. Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18, 6531 6535.
157. Wolfe AD, Xiang QY, Kephart SR (1998) Assessing hybridization in natural populations of Penstemon (Scrophulariaceae) using hypervariable intersimple sequence repeat (ISSR) bands. Molecular Ecology, 7, 1107 1125.
158. Womble W (1951) Differential systematics. Science, 28, 315 322.
159. Wu B, Liu N, Zhao H (2006) psmix: an r package for population structure inference via maximum likelihood method. BMC Bioinformatics, 7, 317 326.
160. Yeh F, Boyle T (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belgian Journal of Botany, 129, 157.
161. Zhivotovsky L (1999) Estimating population structure in diploids with multilocus dominant DNA markers. Molecular Ecology, 8, 907 913.
162. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20, 176 183.