Applications and implications of neutral versus non-neutral markers in molecular ecology

International Journal of Molecular Sciences

Volumn 12, Issue 6, 2011, Pages 3966-3988

  Kirk, Heather ^a   Freeland, Joanna R ^a  

^a TRENT UNIVERSITY   (Canada)

Author keywords

Gene expression; Genetic differentiation; Genetic diversity; Genetic drift; Molecular markers; Natural selection; Next generation sequencing

Indexed keywords

MOLECULAR MARKER; BIOLOGICAL MARKER;

EVOLUTIONARY ADAPTATION; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC DRIFT; GENETIC VARIABILITY; INBREEDING; MOLECULAR ECOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NATURAL SELECTION; NONHUMAN; PHENOTYPE; POPULATION SIZE; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; ENVIRONMENTAL ASPECTS AND RELATED PHENOMENA; EVOLUTION; GENETIC LINKAGE; GENETIC SELECTION; GENOMICS; METABOLISM;

ANIMALS; BIOLOGICAL EVOLUTION; BIOLOGICAL MARKERS; ECOLOGICAL AND ENVIRONMENTAL PHENOMENA; GENETIC LINKAGE; GENETIC VARIATION; GENOMICS; SELECTION, GENETIC;

EID: 79959711643     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms12063966     Document Type: Review

References (132)

1. Freeland, J.R.; Kirk, H.; Petersen, S. Molecular Ecology, 2nd ed.; Wiley & Sons: Chichester, UK, 2011.
2. Freeland, J.R.; Gillespie, J.; Ciotir, C.; Dorken, M.E. Conservation genetics of Hill's thistle (Cirsium hillii). Botany 2010, 88, 1073-1080.
3. Silvertown, J.; Biss, P.M.; Freeland, J. Community genetics: Resource addition has opposing effects on genetic and species diversity in a 150-year experiment. Ecol. Lett. 2009, 12, 165-170.
4. Storfer, A.; Murphy, M.A.; Spear, S.F.; Holderegger, R.; Waits, L.P. Landscape genetics: Where are we now? Mol. Ecol. 2010, 19, 3496-3514.
5. Waser, P.M.; Hadfield, J.D. How much can parentage analyses tell us about precapture dispersal? Mol. Ecol. 2011, 20, 1277-1288.
6. Ferriol, M.; Pichot, C.; Lefevre, F. Variation of selfing rate and inbreeding depression among individuals and across generations within an admixed Cedrus population. Heredity 2011, 106, 146-157.
7. Freeland, J.R.; Lodge, R.J.; Okamura, B. Sex and outcrossing in a sessile freshwater invertebrate. Freshwater Biol. 2003, 48, 301-305.
8. Raye, G.; Miquel, C.; Coissac, E.; Redjadj, C.; Loison, A.; Taberlet, P. New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: Chamois diet in autumn as a case study. Ecol. Res. 2011, 26, 265-276.
9. Zeale, M.R.K.; Butlin, R.K.; Barker, G.L.A.; Lees, D.C.; Jones, G. Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Mol. Ecol. Res. 2011, 11, 236-244.
10. Bottger-Schnack, R.; Machida, R.J. Comparison of morphological and molecular traits for species identification and taxonomic grouping of oncaeid copepods. Hydrobiologia 2011, 666, 111-125.
11. Hawlitschek, O.; Porch, N.; Hendrich, L.; Balke, M. Ecological niche modelling and nDNA sequencing support a new, morphologically cryptic beetle species unveiled by DNA barcoding. PLoS One 2011, 6, e16662. doi:10.1371/journal.pone.0016662.
12. Freeland, J.R.; Rimmer, V.K.; Okamura, B. Evidence for a residual post-glacial founder effect in a highly dispersive freshwater invertebrate. Limnol. Oceanog. 2004, 49, 879-883.
13. Pepper, M.; Fujita, M.K.; Moritz, C.; Keogh, J.S. Palaeoclimate change drove diversification among isolated mountain refugia in the Australian arid zone. Mol. Ecol. 2011, 20, 1529-1545.
14. Ballentine, B.; Greenberg, R. Common garden experiment reveals genetic control of phenotypic divergence between swamp sparrow subspecies that lack divergence in neutral genotypes. PLoS One 2010, 5, e10229. doi:10.1371/journal.pone.0010229.
15. Kawakami, T.; Morgan, T.J.; Nippert, J.B.; Ocheltree, T.W.; Keith, R.; Dhakal, P.; Ungerer, M.C. Natural selection drives clinal life history patterns in the perennial sunflower species, Helianthus maximiliani. Mol. Ecol. 2011, 20, 2318-2328.
16. Richter-Boix, A.; Quintela, M.; Segelbacher, G.; Laurila, A. Genetic analysis of differentiation among breeding ponds reveals a candidate gene for local adaptation in Rana arvalis. Mol. Ecol. 2011, 20, 1582-1600.
17. Cassel-Lundhagen, A.; Tammaru, T.; Windig, J.J.; Ryrholm, N.; Nylin, S. Are peripheral populations special? Congruent patterns in two butterfly species. Ecography 2009, 32, 591-600.
18. Pampoulie, C.; Danielsdottir, A.K.; Storr-Paulsen, M.; Hovgard, H.; Hjorleifsson, E.; Steinarsson, B.A. Neutral and Nonneutral Genetic Markers Revealed the Presence of Inshore and Offshore Stock Components of Atlantic Cod in Greenland Waters. Trans. Am. Fish. Soc. 2011, 140, 307-319.
19. Jump, A.S.; Marchant, R.; Penuelas, J. Environmental change and the option value of genetic diversity. Trends Plant Sci. 2009, 14, 51-58.
20. Jump, A.S.; Penuelas, J. Running to stand still: Adaptation and the response of plants to rapid climate change. Ecol. Lett. 2005, 8, 1010-1020.
21. Eckert, C.G.; Samis, K.E.; Lougheed, S.C. Genetic variation across species' geographical ranges: The central-marginal hypothesis and beyond. Mol. Ecol. 2008, 17, 1170-1188.
22. Gebremedhin, B.; Ficetola, G.F.; Naderi, S.; Rezaei, H.R.; Maudet, C.; Rioux, D.; Luikart, G.; Flagstad, O.; Thuiller, W.; Taberlet, P. Frontiers in identifying conservation units: From neutral markers to adaptive genetic variation. Anim. Conserv. 2009, 12, 107-109.
23. Piertney, S.B.; Webster, L.M.I. Characterising functionally important and ecologically meaningful genetic diversity using a candidate gene approach. Genetica 2010, 138, 419-432.
24. Abzhanov, A.; Kuo, W.P.; Hartmann, C.; Grant, B.R.; Grant, P.R.; Tabin, C.J. The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches. Nature 2006, 442, 563-567.
25. Ben-Shahar, Y. The foraging gene, behavioral plasticity, and honeybee division of labor. J. Compar. Phys. 2005, 191, 987-994.
26. Case, R.A.J.; Hutchinson, W.F.; Hauser, L.; Buehler, V.; Clemmesen, C.; Dahle, G.; Kjesbu, O.S.; Moksness, E.; Ottera, H.; Paulsen, H.; Svasand, T.; Thorsen, A.; Carvalho, G.R. Association between growth and Pan I genotype within Atlantic cod full-sibling families. Trans. Am. Fish. Soc. 2006, 135, 241-250.
27. Haag, C.R.; Saastamoinen, M.; Marden, J.H.; Hanski, I. A candidate locus for variation in dispersal rate in a butterfly metapopulation. Proc. Biol. Sci. 2005, 272, 2449-2456.
28. Baudry, E.; Desmadril, M.; Werren, H. Rapid adaptive evolution of the tumor suppressor gene Pten in an insect lineage. J. Mol. Evol. 2006, 62, 738-744.
29. Voss, S.R.; Prudic, K.L.; Oliver, J.C.; Shaffer, H.B. Candidate gene analysis of metamorphic timing in ambystomatid salamanders. Mol. Ecol. 2003, 12, 1217-1223.
30. Kronforst, M.R.; Young, L.G.; Kapan, D.D.; McNeely, C.; O'Neill, R.J.; Gilbert, L.E. Linkage of butterfly mate preference and wing color preference cue at the genomic location of wingless. Proc. Natl. Acad. Sci. USA 2006, 103, 6575-6580.
31. Gratten, J.; Beraldi, D.; Lowder, B.V.; McRae, A.F.; Visscher, P.M.; Pemberton, J.M.; Slate, J. Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep. Proc. R. Soc. B 2007, 274, 619-626.
32. Gotzek, D.; Ross, K.G. Genetic regulation of colony social organization in fire ants: An integrative overview. Q. Rev. Biol. 2007, 82, 201-226.
33. Ficetola, G.F.; Garner, T.W.J.; Wang, J.L.; de Bernardi, F. Rapid selection against inbreeding in a wild population of a rare frog. Evol. Appl. 2010, 4, 30-38.
34. Kupper, C.; Kosztolanyi, A.; Augustin, J.; Dawson, D.A.; Burke, T.; Szekely, T. Heterozygosity-fitness correlations of conserved microsatellite markers in Kentish plovers Charadrius alexandrinus. Mol. Ecol. 2010, 19, 5172-5185.
35. Szulkin, M.; Bierne, N.; David, P. Heterozygosity-fitness correlations: A time for reappraisal. Evolution 2010, 64, 1202-1217.
36. Chapman, J.R.; Nakagawa, S.; Coltman, D.W.; Slate, J.; Sheldon, B.C. A quantitative review of heterozygosity-fitness correlations in animal populations. Mol. Ecol. 2009, 18, 2746-2765.
37. Grueber, C.E.; Waters, J.M.; Jamieson, I.G. The imprecision of heterozygosity-fitness correlations hinders the detection of inbreeding and inbreeding depression in a threatened species. Mol. Ecol. 2010, 20, 67-79.
38. Thoss, M.; Ilmonen, P.; Musolf, K.; Penn, D.J. Major histocompatibility complex heterozygosity enhances reproductive success. Mol. Ecol. 2011, 20, 1546-1557.
39. Paige, K.N. The Functional Genomics of Inbreeding Depression: A New Approach to an Old Problem. Bioscience 2010, 60, 267-277.
40. Kristensen, T.N.; Sorensen, P.; Kruhoffer, M.; Pedersen, K.S.; Loeschcke, V. Genome-wide analysis on inbreeding effects on gene expression in Drosophila melanogaster. Genetics 2005, 171, 157-167.
41. Kristensen, T.N.; Sorensen, P.; Pedersen, K.S.; Kruhoffer, M.; Loeschcke, V. Inbreeding by environmental interactions affect gene expression in Drosophila melanogaster. Genetics 2006, 173, 1329-1336.
42. Crnokrak, P.; Roff, D.A. Inbreeding depression in the wild. Heredity 1999, 83, 260-270.
43. Demontis, D.; Pertoldi, C.; Loeschcke, V.; Mikkelsen, K.; Axelsson, T.; Kristensen, T.N. Efficiency of selection, as measured by single nucleotide polymorphism variation, is dependent on inbreeding rate in Drosophila melanogaster. Mol. Ecol. 2009, 18, 4551-4563.
44. Kristensen, T.N.; Pedersen, K.S.; Vermeulen, C.J.; Loeschcke, V. Research on inbreeding in the "omic" era. Trends Ecol. Evol. 2009, 25, 44-52.
45. Pujol, B.; Pannell, J.R. Reduced responses to selection after species range expansion. Science 2008, 321, 96.
46. Markert, J.A.; Champlin, D.M.; Gutjahr-Gobell, R.; Grear, J.S.; Kuhn, A.; McGreevy, T.J.; Roth, A.; Bagley, M.J.; Nacci, D.E. Population genetic diversity and fitness in multiple environments. BMC Evol. Biol. 2010, 10, 205. doi:10.1186/1471-2148-10-205.
47. Wright, S. Evolution in mendelian populations. Genetics 1931, 16, 97-159.
48. Wright, S. Size of population and breeding structure in relation to evolution. Science 1938, 87, 430-431.
49. Karasov, T.; Messer, P.W.; Petrov, D.A. Evidence that adaptation in Drosophila is not limited by mutation at single sites. PLoS Genet. 2010, 6, e1000924. doi:10.1371/journal.pgen.1000924.
50. Spurgin, L.G.; Richardson, D.S. How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proc. R. Soc. B 2010, 277, 979-988.
51. Charlesworth, D.; Bartolome, C.; Schierup, M.H.; Mable, B.K. Haplotype structure of the stigmatic self-incompatibility gene in natural populations of Arabidopsis lyrata. Mol. Biol. Evol. 2003, 20, 1741-1753.
52. Cho, S.C.; Huang, Z.Y.; Green, D.R.; Smith, D.R.; Zhang, J.Z. Evolution of the complementary sex-determination gene of honey bees: Balancing selection and trans-species polymorphisms. Genome Res. 2006, 16, 1366-1375.
53. Radwan, J.; Biedrzycka, A.; Babik, W. Does reduced MHC diversity decrease viability of vertebrate populations? Biol. Conserv. 2010, 143, 537-544.
54. Hohenlohe, P.A.; Bassham, S.; Etter, P.D.; Stiffler, N.; Johnson, E.A.; Cresko, W.A. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet. 2010, 6, e1000862. doi:10.1371/journal.pgen.1000862.
55. Martinez-Fernandez, M.; Bernatchez, L.; Rolan-Alvarez, E.; Quesada, H. Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis. BMC Evol. Biol. 2010, 10, 356.
56. Merila, J.; Crnokrak, P. Comparison of genetic differentiation at marker loci and quantitative traits. J. Evol. Biol. 2001, 14, 892-903.
57. Takahata, N.; Nei, M. Fst and Gst Statistics in the Finite Island Model. Genetics 1984, 107, 501-504.
58. Kohn, M.H.; Shapiro, J.; Wu, C.I. Decoupled differentiation of gene expression and coding sequence among Drosophila populations. Genes Genet. Syst. 2008, 83, 265-273.
59. Luikart, G.; England, P.R.; Tallmon, D.; Jordan, S.; Taberlet, P. The power and promise of population genomics: From genotyping to genome typing. Nat. Rev. Genet. 2003, 4, 981-994.
60. Storz, J.F.; Nachman, M.W. Natural selection on protein polymorphism in the rodent genus Peromyscus: Evidence from interlocus contrasts. Evolution 2003, 57, 2628-2635.
61. Slate, J.; David, P.; Dodds, K.G.; Veenvliet, B.A.; Glass, B.C.; Broad, T.E.; McEwan, J.C. Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data. Heredity 2004, 93, 255-265.
62. Vali, U.; Einarsson, A.; Waits, L.; Ellegren, H. To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations? Mol. Ecol. 2008, 17, 3808-3817.
63. Ouborg, N.J.; Pertoldi, C.; Loeschcke, V.; Bijlsma, R.; Hedrick, P.W. Conservation genetics in transition to conservation genomics. Trends Genet. 2010, 26, 177-187.
64. Hudson, M.E. Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol. Ecol. Res. 2008, 8, 3-17.
65. Shendure, J.; Ji, H.L. Next-generation DNA sequencing. Nat. Biotechnol. 2008, 26, 1135-1145.
66. Stapley, J.; Reger, J.; Feulner, P.G.D.; Smadja, C.; Galindo, J.; Ekblom, R.; Bennison, C.; Ball, A.D.; Beckerman, A.P.; Slate, J. Adaptation genomics: the next generation. Trends Ecol. Evol. 2010, 25, 705-712.
67. McCarthy, A. Third generation DNA sequencing: Pacific Biosciences' single molecule real time technology. Chem. Biol. 2010, 17, 675-676.
68. Ragoussis, J. Genotyping technologies for genetic research. Ann. Rev. Genomics Hum. Genet. 2009, 10, 117-133.
69. Fan, J.B.; Chee, M.S.; Gunderson, K.L. Highly parallel genomic assays. Nat. Rev. Genet. 2006, 7, 632-644.
70. Pertoldi, C.; Bijlsma, R.; Loeschcke, V. Conservation genetics in a globally changing environment: Present problems, paradoxes and future challenges. Biodivers. Conserv. 2007, 16, 4147-4163.
71. Squirrell, J.; Hollingsworth, P.M.; Woodhead, M.; Russell, J.; Lowe, A.J.; Gibby, M.; Powell, W. How much effort is required to isolate nuclear microsatellites from plants? Mol. Ecol. 2003, 12, 1339-1348.
72. Zane, L.; Bargelloni, L.; Patarnello, T. Strategies for microsatellite isolation: A review. Mol. Ecol. 2002, 11, 1-16.
73. Molodstova, D.; Crowe, E.; Olson, A.; Yee, J.; Freeland, J.R. Conserved flanking microsatellite sequences (ReFS) differentiate between Lepidoptera species, and provide insight into microsatellite evolution. Syst. Entomol. 2011, 36, 371-376.
74. Boguski, M.S.; Lowe, T.M.J.; Tolstoshev, C.M. DbEST-Database for Expressed Sequence Tags. Nat. Genet. 1993, 4, 332-333.
75. Ellis, J.R.; Burke, J.M. EST-SSRs as a resource for population genetic analyses. Heredity 2007, 99, 125-132.
76. Chagne, D.; Chaumeil, P.; Ramboer, A.; Collada, C.; Guevara, A.; Cervera, M.T.; Vendramin, G.G.; Garcia, V.; Frigerio, J.M.M.; Echt, C.; Richardson, T.; Plomion, C. Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theor. Appl. Genet. 2004, 109, 1204-1214.
77. Gutierrez, M.V.; Patto, M.C.V.; Huguet, T.; Cubero, J.I.; Moreno, M.T.; Torres, A.M. Cross-species amplification of Medicago truncatula microsatellites across three major pulse crops. Theor. Appl. Genet. 2005, 110, 1210-1217.
78. Pashley, C.H.; Ellis, J.R.; McCauley, D.E.; Burke, J.M. EST databases as a source for molecular markers: Lessons from Helianthus. J. Heredity 2006, 97, 381-388.
79. Kalia, R.K.; Rai, M.K.; Kalia, S.; Singh, R.; Dhawan, A.K. Microsatellite markers: An overview of the recent progress in plants. Euphytica 2011, 177, 309-334.
80. North, A.; Pennanen, J.; Ovaskainen, O.; Laine, A.L. Local adaptation in a changing world: The roles of gene-flow, mutation, and sexual reproduction. Evolution 2010, 65, 79-89.
81. Hansen, M.M.; Meier, K.; Mensberg, K.L.D. Identifying footprints of selection in stocked brown trout populations: A spatio-temporal approach. Mol. Ecol. 2010, 19, 1787-1800.
82. Williams, L.M.; Oleksiak, M.F. Signatures of selection in natural populations adapted to chronic pollution. BMC Evol. Biol. 2008, 8, 282. doi:10.1186/1471-2148-8-282.
83. Narum, S.R.; Hess, J.E. Comparison of FST outlier tests for SNP loci under selection. Mol. Ecol. Resour. 2011, 11, 184-194.
84. Prunier, J.; Laroche, J.; Beaulieu, J.; Bousquet, J. Scanning the genome for gene SNPs related to climate adaptation and estimating selection at the molecular level in boreal black spruce. Mol. Ecol. 2011, 20, 1702-1716.
85. 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.
86. Excoffier, L.; Hofer, T.; Foll, M. Detecting loci under selection in a hierarchically structured population. Heredity 2009, 103, 285-298.
87. Perez-Figueroa, A.; Garcia-Pereira, M.J.; Saura, M.; Rolan-Alvarez, E.; Caballero, A. Comparing three different methods to detect selective loci using dominant markers. J. Evol. Biol. 2010, 23, 2267-2276.
88. Apple, J.L.; Grace, T.; Joern, A.; Amand, P.S.; Wisely, S.M. Comparative genome scan detects host-related divergent selection in the grasshopper Hesperotettix viridis. Mol. Ecol. 2010, 19, 4012-4028.
89. Freeland, J.R.; Biss, P.; Conrad, K.F.; 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, 776-782.
90. Nunes, V.L.; Beaumont, M.A.; Butlin, R.K.; Paulo, O.S. Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient. Mol. Ecol. 2011, 20, 193-205.
91. Gomez-Uchida, D.; Seeb, J.E.; Smith, M.J.; Habicht, C.; Quinn, T.P.; Seeb, L.W. Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations. BMC Evol. Biol. 2011, 11, 48.
92. Renaut, S.; Nolte, A.W.; Rogers, S.M.; Derome, N.; Bernatchez, L. SNP signatures of selection on standing genetic variation and their association with adaptive phenotypes along gradients of ecological speciation in lake whitefish species pairs (Coregonus spp.). Mol. Ecol. 2011, 20, 545-559.
93. Helyar, S.J.; Hemmer-Hansen, J.; Bekkevold, D.; Taylor, M.I.; Ogden, R.; Limborg, M.T.; Cariani, A.; Maes, G.E.; Diopere, E.; Carvalho, G.R.; Nielsen, E.E. Application of SNPs for population genetics of nonmodel organisms: New opportunities and challenges. Mol. Ecol. Res. 2011, 11, 123-136.
94. O'Malley, K.G.; Ford, M.J.; Hard, J.J. Clock polymorphism in Pacific salmon: Evidence for variable selection along a latitudinal gradient. Proc. R. Soc. B 2010, 277, 3703-3714.
95. Eckert, A.J.; Bower, A.D.; Gonzalez-Martinez, S.C.; Wegrzyn, J.L.; Coop, G.; Neale, D.B. Back to nature: Ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Mol. Ecol. 2010, 19, 3789-3805.
96. Gilchrist, A.S.; Meats, A.W. The genetic structure of populations of an invading pest fruit fly, Bactrocera tryoni, at the species climatic range limit. Heredity 2010, 105, 165-172.
97. Paaby, A.B.; Blacket, M.J.; Hoffmann, A.A.; Schmidt, P.S. Identification of a candidate adaptive polymorphism for Drosophila life history by parallel independent clines on two continents. Mol. Ecol. 2010, 19, 760-774.
98. Bradbury, I.R.; Hubert, S.; Higgins, B.; Borza, T.; Bowman, S.; Paterson, I.G.; Snelgrove, P.V.R.; Morris, C.J.; Gregory, R.S.; Hardie, D.C.; Hutchings, J.A.; Ruzzante, D.E.; Taggart, C.T.; Bentzen, P. Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature. Proc. R. Soc. B 2010, 277, 3725-3734.
99. Yang, Z.H.; Bielawski, J.P. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 2000, 15, 496-503.
100. McDonald, J.H.; Kreitman, M. Adaptive Protein Evolution at the Adh Locus in Drosophila. Nature 1991, 351, 652-654.
101. Bustamante, C.D.; Fledel-Alon, A.; Williamson, S.; Nielsen, R.; Hubisz, M.T.; Glanowski, S.; Tanenbaum, D.M.; White, T.J.; Sninsky, J.J.; Hernandez, R.D.; Civello, D.; Adams, M.D.; Cargill, M.; Clark, A.G. Natural selection on protein-coding genes in the human genome. Nature 2005, 437, 1153-1157.
102. Petersen, L.; Bollback, J.P.; Dimmic, M.; Hubisz, M.; Nielsen, R. Genes under positive selection in Escherichia coli. Genome Res. 2007, 17, 1336-1343.
103. Yang, Z.H.; Wong, W.S.W.; Nielsen, R. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 2005, 22, 1107-1118.
104. Goldman, N.; Yang, Z.H. Codon-Based Model of Nucleotide Substitution for Protein-Coding DNA-Sequences. Mol. Biol. Evol. 1994, 11, 725-736.
105. Nam, K.; Mugal, C.; Nabholz, B.; Schielzeth, H.; Wolf, J.B.W.; Backstrom, N.; Kunstner, A.; Balakrishnan, C.N.; Heger, A.; Ponting, C.P.; Clayton, D.F.; Ellegren, H. Molecular evolution of genes in avian genomes. Genome Biol. 2010, 11, R68. doi:10.1186/gb-2010-11-6-r68.
106. Ersoz, E.S.; Wright, M.H.; Gonzalez-Martinez, S.C.; Langley, C.H.; Neale, D.B. Evolution of Disease Response Genes in Loblolly Pine: Insights from Candidate Genes. PLoS One 2010, 5, e14234. doi:10.1371/journal.pone.0014234.
107. Oleksyk, T.K.; Zhao, K.; de la Vega, F.M.; Gilbert, D.A.; O'Brien, S.J.; Smith, M.W. Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations. PLoS One 2008, 3, e1712. doi:10.1371/journal.pone.0001712.
108. Eyre-Walker, A. Changing effective population size and the McDonald-Kreitman test. Genetics 2002, 162, 2017-2024.
109. Eyre-Walker, A.; Keightley, P.D. Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change. Mol. Biol. Evol. 2009, 26, 2097-2108.
110. Maynard Smith, J.; Haigh, J. The hitch-hiking effect of a favourable gene. Genet. Res. 1974, 23, 23-35.
111. Kim, Y.; Stephan, W. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 2002, 160, 765-777.
112. McVean, G. The structure of linkage disequilibrium around a selective sweep. Genetics 2007, 175, 1395-1406.
113. Sabeti, P.C.; Reich, D.E.; Higgins, J.M.; Levine, H.Z.P.; Richter, D.J.; Schaffner, S.F.; Gabriel, S.B.; Platko, J.V.; Patterson, N.J.; McDonald, G.J.; Ackerman, H.C.; Campbell, S.J.; Altshuler, D.; Cooper, R.; Kwiatkowski, D.; Ward, R.; Lander, E.S. Detecting recent positive selection in the human genome from haplotype structure. Nature 2002, 419, 832-837.
114. Beaumont, M.A.; Balding, D.J. Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol. 2004, 13, 969-980.
115. 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, 977-993.
116. Excoffier, L.; Foll, M.; Petit, R.J. Genetic Consequences of Range Expansions. Ann. Rev. Ecol. Evol. Syst. 2009, 40, 481-501.
117. Kuhner, M.K. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 2006, 22, 768-770.
118. 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. Res. 2008, 8, 957-960.
119. Siol, M.; Wright, S.I.; Barrett, S.C.H. The population genomics of plant adaptation. New Phytol. 2010, 188, 313-332.
120. Galindo, J.; Moran, P.; Rolan-Alvarez, 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.
121. Charlesworth, B.; Nordborg, M.; Charlesworth, D. The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genet. Res. 1997, 70, 155-174.
122. Nosil, P.; Funk, D.J.; Ortiz-Barrientos, D. Divergent selection and heterogeneous genomic divergence. Mol. Ecol. 2009, 18, 375-402.
123. Thibert-Plante, X.; Hendry, A.P. Five questions on ecological speciation addressed with individual-based simulations. J. Evol. Biol. 2009, 22, 109-123.
124. Mackay, T.F.C.; Langley, C.H. Molecular and Phenotypic Variation in the Achaete-Scute Region of Drosophila melanogaster. Nature 1990, 348, 64-66.
125. Latta, R.G.; Gardner, K.M.; Staples, D.A. Quantitative trait locus mapping of genes under selection across multiple years and sites in Avena barbata: Epistasis, pleiotropy, and genotype-by-environment interactions. Genetics 2010, 185, 375-385.
126. Stranger, B.E.; Stahl, E.A.; Raj, T. Progress and promise of genome-wide association studies for human complex trait genetics. Genetics 2011, 187, 367-383.
127. Aranzana, M.J.; Kim, S.; Zhao, K.Y.; Bakker, E.; Horton, M.; Jakob, K.; Lister, C.; Molitor, J.; Shindo, C.; Tang, C.L.; Toomajian, C.; Traw, B.; Zheng, H.G.; Bergelson, J.; Dean, C.; Marjoram, P.; Nordborg, M. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet. 2005, 1, 531-539.
128. Li, Y.; Huang, Y.; Bergelson, J.; Nordborg, M.; Borevitz, J.O. Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 2010, 107, 21199-21204.
129. Akey, J.M.; Ruhe, A.L.; Akey, D.T.; Wong, A.K.; Connelly, C.F.; Madeoy, J.; Nicholas, T.J.; Neff, M.W. Tracking footprints of artificial selection in the dog genome. Proc. Natl. Acad. Sci. USA 2010, 107, 1160-1165.
130. Cockram, J.; White, J.; Zuluaga, D.L.; Smith, D.; Comadran, J.; Macaulay, M.; Luo, Z.W.; Kearsey, M.J.; Werner, P.; Harrap, D.; Tapsell, C.; Liu, H.; Hedley, P.E.; Stein, N.; Schulte, D.; Steuernagel, B.; Marshall, D.F.; Thomas, W.T.B.; Ramsay, L.; Mackay, I.; Balding, D.J.; Waugh, R.; O'Sullivan, D.M. Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc. Natl. Acad. Sci. USA 2010, 107, 21611-21616.
131. Oleksyk, T.K.; Smith, M.W.; O'Brien, S.J. Genome-wide scans for footprints of natural selection. Phil. Trans. R. Soc. B 2010, 365, 185-205.
132. Storz, J.F.; Wheat, C.W. Integrating evolutionary and functional approaches to infer adaptation at specific loci. Evolution 2010, 64, 2489-2509.