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Volumn 109, Issue 6, 2012, Pages 340-348

Challenges and pitfalls in the characterization of anonymous outlier AFLP markers in non-model species: Lessons from an ocellated lizard genome scan

Author keywords

AFLP sequence; capillary electrophoresis; dominant markers; outlier's validation; selection

Indexed keywords

MICROSATELLITE DNA;

EID: 84869221631     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2012.48     Document Type: Article
Times cited : (12)

References (44)
  • 1
    • 77956599988 scopus 로고    scopus 로고
    • Comparative genome scan detects host-related divergent selection in the grasshopper Hesperotettix viridis
    • Apple JL, Grace T, Joern A, Amand PS, Wisely SM (2010). Comparative genome scan detects host-related divergent selection in the grasshopper Hesperotettix viridis. Mol Ecol 19:4012-4028.
    • (2010) Mol Ecol , vol.19 , pp. 4012-4028
    • Apple, J.L.1    Grace, T.2    Joern, A.3    Amand, P.S.4    Wisely, S.M.5
  • 2
    • 0032900678 scopus 로고    scopus 로고
    • Median-joining networks for inferring intraspecific phylogenies
    • Bandelt H-J, Forster P, Röhl A (1999). Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48. (Pubitemid 29024937)
    • (1999) Molecular Biology and Evolution , vol.16 , Issue.1 , pp. 37-48
    • Bandelt, H.-J.1    Forster, P.2    Rohl, A.3
  • 4
    • 26944462056 scopus 로고    scopus 로고
    • Ten years of AFLPs in ecology and evolution: Why so few animals?
    • Bensch S, Akesson M (2005). Ten years of AFLPs in ecology and evolution: why so few animals? Mol Ecol 14:2899-2914.
    • (2005) Mol Ecol , vol.14 , pp. 2899-2914
    • Bensch, S.1    Akesson, M.2
  • 5
    • 34548570134 scopus 로고    scopus 로고
    • Statistical analysis of amplified fragment length polymorphism data: A toolbox for molecular ecologists and evolutionists
    • DOI 10.1111/j.1365-294X.2007.03435.x
    • Bonin A, Ehrich D, Manel S (2007). Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Mol Ecol 16:3737-3758. (Pubitemid 47397323)
    • (2007) Molecular Ecology , vol.16 , Issue.18 , pp. 3737-3758
    • Bonin, A.1    Ehrich, D.2    Manel, S.3
  • 6
    • 33644901809 scopus 로고    scopus 로고
    • Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria)
    • Bonin A, Taberlet P, Miaud C, Pompanon F (2006). Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria). Mol Biol Evol 23:773-783.
    • (2006) Mol Biol Evol , vol.23 , pp. 773-783
    • Bonin, A.1    Taberlet, P.2    Miaud, C.3    Pompanon, F.4
  • 8
    • 77949281433 scopus 로고    scopus 로고
    • Population genomics and speciation
    • Butlin RK (2010). Population genomics and speciation. Genetica 138:409-418.
    • (2010) Genetica , vol.138 , pp. 409-418
    • Butlin, R.K.1
  • 9
    • 52049095988 scopus 로고    scopus 로고
    • Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci
    • Caballero A, Quesada H, Rolan-Alvarez E (2008). Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics 179:539-554.
    • (2008) Genetics , vol.179 , pp. 539-554
    • Caballero, A.1    Quesada, H.2    Rolan-Alvarez, E.3
  • 10
    • 70349506039 scopus 로고    scopus 로고
    • Detecting loci under selection in a hierarchically structured population
    • Excoffier L, Hofer T, Foll M (2009). Detecting loci under selection in a hierarchically structured population. Heredity 103:285-298.
    • (2009) Heredity , vol.103 , pp. 285-298
    • Excoffier, L.1    Hofer, T.2    Foll, M.3
  • 11
    • 85007110786 scopus 로고    scopus 로고
    • Arlequin (version 3.0): An integrated software package for population genetics data analysis
    • Excoffier L, Laval G, Schneider S (2005). Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47-50.
    • (2005) Evol Bioinform Online , vol.1 , pp. 47-50
    • Excoffier, L.1    Laval, G.2    Schneider, S.3
  • 12
    • 33747401249 scopus 로고    scopus 로고
    • Phase determination from direct sequencing of length-variable DNA regions
    • DOI 10.1111/j.1471-8286.2006.01355.x
    • Flot JF, Tillier A, Samadi S, Tillier S (2006). Phase determination from direct sequencing of length-variable DNA regions. Mol Ecol Notes 6:627-630. (Pubitemid 44252559)
    • (2006) Molecular Ecology Notes , vol.6 , Issue.3 , pp. 627-630
    • Flot, J.-F.1    Tillier, A.2    Samadi, S.3    Tillier, S.4
  • 13
    • 78149427025 scopus 로고    scopus 로고
    • Estimating population structure from AFLP amplification intensity
    • Foll M, Fischer MC, Heckel G, Excoffier L (2010). Estimating population structure from AFLP amplification intensity. Mol Ecol 19:4638-4647.
    • (2010) Mol Ecol , vol.19 , pp. 4638-4647
    • Foll, M.1    Fischer, M.C.2    Heckel, G.3    Excoffier, L.4
  • 14
    • 58149347836 scopus 로고    scopus 로고
    • A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective
    • Foll M, Gaggiotti O (2008). A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180:977-993.
    • (2008) Genetics , vol.180 , pp. 977-993
    • Foll, M.1    Gaggiotti, O.2
  • 15
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall TA (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98.
    • (1999) Nucleic Acids Symp ser , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 16
    • 50849103300 scopus 로고    scopus 로고
    • Spatial analysis method (SAM): A software tool combining molecular and environmental data to identify candidate loci for selection
    • 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. Mol Ecol Resour 8:957-960.
    • (2008) Mol Ecol Resour , vol.8 , pp. 957-960
    • Joost, S.1    Kalbermatten, M.2    Bonin, A.3
  • 17
    • 0028161068 scopus 로고
    • Reproductive strategies in three Spanish populations of the ocellated lizard, Lacerta lepida (Sauria, Lacertidae)
    • Mateo JA, Castanet J (1994). Reproductive strategies in 3 Spanish populations of the ocellated lizard, Lacerta lepida (Sauria, Lacertidae). Acta Oecol 15:215-229. (Pubitemid 2142445)
    • (1994) Acta Oecologica , vol.15 , Issue.2 , pp. 215-229
    • Mateo, J.A.1    Castanet, J.2
  • 18
    • 18144424743 scopus 로고
    • Variation morphologique et révision taxonomique de l'espèce Lacerta lepida Daudin, 1802 (Sauria, Lacertidae)
    • Mateo JA, Castroviejo J (1990). Variation morphologique et révision taxonomique de l'espèce Lacerta lepida Daudin, 1802 (Sauria, Lacertidae). Bull Mus Natl Hist Nat, Paris 12:691-706.
    • (1990) Bull Mus Natl Hist Nat, Paris , vol.12 , pp. 691-706
    • Mateo, J.A.1    Castroviejo, J.2
  • 20
    • 79953034159 scopus 로고    scopus 로고
    • Scanning the European corn borer (Ostrinia spp.) genome for adaptive divergence between host-affiliated sibling species
    • Midamegbe A, Vitalis R, Malausa T, Delava E, Cros-Arteil S, Streiff R (2011). Scanning the European corn borer (Ostrinia spp.) genome for adaptive divergence between host-affiliated sibling species. Mol Ecol 20:1414-1430.
    • (2011) Mol Ecol , vol.20 , pp. 1414-1430
    • Midamegbe, A.1    Vitalis, R.2    Malausa, T.3    Delava, E.4    Cros-Arteil, S.5    Streiff, R.6
  • 21
    • 40449084290 scopus 로고    scopus 로고
    • A population genomic analysis of species boundaries: Neutral processes, adaptive divergence and introgression between two hybridizing plant species
    • DOI 10.1111/j.1365-294X.2008.03709.x
    • Minder AM, Widmer A (2008). A population genomic analysis of species boundaries: neutral processes, adaptive divergence and introgression between two hybridizing plant species. Mol Ecol 17:1552-1563. (Pubitemid 351347655)
    • (2008) Molecular Ecology , vol.17 , Issue.6 , pp. 1552-1563
    • Minder, A.M.1    Widmer, A.2
  • 22
    • 79958780974 scopus 로고    scopus 로고
    • Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: Multiple refugia, range expansions and secondary contact zones
    • Miraldo A, Hewitt GM, Paulo OS, Emerson BC (2011). Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones. BMC Evol Biol 11:170.
    • (2011) BMC Evol Biol , vol.11 , pp. 170
    • Miraldo, A.1    Hewitt, G.M.2    Paulo, O.S.3    Emerson, B.C.4
  • 23
    • 33750219667 scopus 로고    scopus 로고
    • A genomic scan for divergent selection in a secondary contact zone between Atlantic and Gulf of Mexico oysters, Crassostrea virginica
    • DOI 10.1111/j.1365-294X.2006.03060.x
    • Murray MC, Hare MP (2006). A genomic scan for divergent selection in a secondary contact zone between Atlantic and Gulf of Mexico oysters, Crassostrea virginica. Mol Ecol 15:4229-4242. (Pubitemid 44607164)
    • (2006) Molecular Ecology , vol.15 , Issue.13 , pp. 4229-4242
    • Murray, M.C.1    Hare, M.P.2
  • 24
    • 78651270029 scopus 로고    scopus 로고
    • Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient
    • Nunes VL, Beaumont MA, Butlin RK, Paulo OS (2011a). Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient. Mol Ecol 20:193-205.
    • (2011) Mol Ecol , vol.20 , pp. 193-205
    • Nunes, V.L.1    Beaumont, M.A.2    Butlin, R.K.3    Paulo, O.S.4
  • 25
    • 80052641110 scopus 로고    scopus 로고
    • Association of Mc1r variants with ecologically relevant phenotypes in the European ocellated lizard, Lacerta lepida
    • Nunes VL, Miraldo A, Beaumont MA, Butlin RK, Paulo OS (2011b). Association of Mc1r variants with ecologically relevant phenotypes in the European ocellated lizard, Lacerta lepida. J Evol Biol 24:2289-2298.
    • (2011) J Evol Biol , vol.24 , pp. 2289-2298
    • Nunes, V.L.1    Miraldo, A.2    Beaumont, M.A.3    Butlin, R.K.4    Paulo, O.S.5
  • 26
    • 73949133488 scopus 로고    scopus 로고
    • Genome scan in the mosquito Aedes rusticus: Population structure and detection of positive selection after insecticide treatment
    • Paris M, Boyer S, Bonin A, Collado A, Jean-Philippe D, Despres L (2010). Genome scan in the mosquito Aedes rusticus: population structure and detection of positive selection after insecticide treatment. Mol Ecol 19:325-337.
    • (2010) Mol Ecol , vol.19 , pp. 325-337
    • Paris, M.1    Boyer, S.2    Bonin, A.3    Collado, A.4    Jean-Philippe, D.5    Despres, L.6
  • 27
    • 84859110693 scopus 로고    scopus 로고
    • Identifying insecticide resistance genes in mosquito by combining AFLP genome scans and 454 pyrosequencing
    • Paris M, Despres L (2012). Identifying insecticide resistance genes in mosquito by combining AFLP genome scans and 454 pyrosequencing. Mol Ecol 21:1672-1686.
    • (2012) Mol Ecol , vol.21 , pp. 1672-1686
    • Paris, M.1    Despres, L.2
  • 28
    • 40449088093 scopus 로고    scopus 로고
    • The role of vicariance vs. dispersal in shaping genetic patterns in ocellated lizard species in the western Mediterranean
    • DOI 10.1111/j.1365-294X.2008.03706.x
    • Paulo OS, Pinheiro J, Miraldo A, Bruford MW, Jordan WC, Nichols RA (2008). The role of vicariance vs. dispersal in shaping genetic patterns in ocellated lizard species in the western Mediterranean. Mol Ecol 17:1535-1551. (Pubitemid 351347654)
    • (2008) Molecular Ecology , vol.17 , Issue.6 , pp. 1535-1551
    • Paulo, O.S.1    Pinheiro, J.2    Miraldo, A.3    Bruford, M.W.4    Jordan, W.C.5    Nichols, R.A.6
  • 30
    • 55149125146 scopus 로고    scopus 로고
    • Concatenator: Sequence data matrices handling made easy
    • Pina-Martins F, Paulo OS (2008). Concatenator: sequence data matrices handling made easy. Mol Ecol Resour 8:1254-1255.
    • (2008) Mol Ecol Resour , vol.8 , pp. 1254-1255
    • Pina-Martins, F.1    Paulo, O.S.2
  • 32
    • 77954554418 scopus 로고    scopus 로고
    • Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina
    • Poncet BN, Herrmann D, Gugerli F, Taberlet P, Holderegger R, Gielly L et al. (2010). Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Mol Ecol 19:2896-2907.
    • (2010) Mol Ecol , vol.19 , pp. 2896-2907
    • Poncet, B.N.1    Herrmann, D.2    Gugerli, F.3    Taberlet, P.4    Holderegger, R.5    Gielly, L.6
  • 33
    • 50049089040 scopus 로고    scopus 로고
    • A high-throughput genome-walking method and its use for cloning unknown flanking sequences
    • Reddy PS, Mahanty S, Kaul T, Nair S, Sopory SK, Reddy MK (2008). A high-throughput genome-walking method and its use for cloning unknown flanking sequences. Anal Biochem 381:248-253.
    • (2008) Anal Biochem , vol.381 , pp. 248-253
    • Reddy, P.S.1    Mahanty, S.2    Kaul, T.3    Nair, S.4    Sopory, S.K.5    Reddy, M.K.6
  • 34
    • 80052100827 scopus 로고    scopus 로고
    • RAD in the realm of next-generation sequencing technologies
    • Rowe HC, Renaut S, Guggisberg A (2011). RAD in the realm of next-generation sequencing technologies. Mol Ecol 20:3499-3502.
    • (2011) Mol Ecol , vol.20 , pp. 3499-3502
    • Rowe, H.C.1    Renaut, S.2    Guggisberg, A.3
  • 35
    • 0033990048 scopus 로고    scopus 로고
    • Primer 3 on the WWW for general users and for biologist programmers
    • Krawetz S, Misener S (eds) Humana Press: Totowa, New Jersey
    • Rozen S, Skaletsky HJ (2000). Primer 3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds). Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press: Totowa, New Jersey, pp 365-386.
    • (2000) Bioinformatics Methods and Protocols: Methods in Molecular Biology , pp. 365-386
    • Rozen, S.1    Skaletsky, H.J.2
  • 36
    • 13844270527 scopus 로고    scopus 로고
    • Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation
    • DOI 10.1086/428594
    • Stephens M, Scheet P (2005). Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet 76:449-462. (Pubitemid 40250525)
    • (2005) American Journal of Human Genetics , vol.76 , Issue.3 , pp. 449-462
    • Stephens, M.1    Scheet, P.2
  • 37
    • 0035071957 scopus 로고    scopus 로고
    • A new statistical method for haplotype reconstruction from population data
    • DOI 10.1086/319501
    • Stephens M, Smith NJ, Donnelly P (2001). A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989. (Pubitemid 32289743)
    • (2001) American Journal of Human Genetics , vol.68 , Issue.4 , pp. 978-989
    • Stephens, M.1    Smith, N.J.2    Donnelly, P.3
  • 38
    • 38549103015 scopus 로고    scopus 로고
    • Combining population genomics and quantitative genetics: Finding the genes underlying ecologically important traits
    • DOI 10.1038/sj.hdy.6800937, PII 6800937
    • Stinchcombe JR, Hoekstra HE (2008). Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100:158-170. (Pubitemid 351156869)
    • (2008) Heredity , vol.100 , Issue.2 , pp. 158-170
    • Stinchcombe, J.R.1    Hoekstra, H.E.2
  • 39
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
    • Tajima F (1989). Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595. (Pubitemid 19274682)
    • (1989) Genetics , vol.123 , Issue.3 , pp. 585-595
    • Tajima, F.1
  • 40
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680. (Pubitemid 24354800)
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 41
    • 0036007449 scopus 로고    scopus 로고
    • Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size
    • DOI 10.1046/j.0962-1083.2001.01415.x
    • Vekemans X, Beauwens T, Lemaire M, Roldán-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. Mol Ecol 11:139-151. (Pubitemid 34108478)
    • (2002) Molecular Ecology , vol.11 , Issue.1 , pp. 139-151
    • Vekemans, X.1    Beauwens, T.2    Lemaire, M.3    Roldan-Ruiz, I.4
  • 43
    • 45549108208 scopus 로고    scopus 로고
    • Sequence differentiation in regions identified by a genome scan for local adaptation
    • DOI 10.1111/j.1365-294X.2008.03755.x
    • Wood HM, Grahame JW, Humphray S, Rogers J, Butlin RK (2008). Sequence differentiation in regions identified by a genome scan for local adaptation. Mol Ecol 17:3123-3135. (Pubitemid 351861453)
    • (2008) Molecular Ecology , vol.17 , Issue.13 , pp. 3123-3135
    • Wood, H.M.1    Grahame, J.W.2    Humphray, S.3    Rogers, J.4    Butlin, R.K.5
  • 44
    • 0034881797 scopus 로고    scopus 로고
    • Characterization of AFLP markers in damselflies: Prevalence of codominant markers and implications for population genetic applications
    • DOI 10.1139/gen-44-4-677
    • Wong A, Forbes MR, Smith ML (2001). Characterization of AFLP markers in damselflies: prevalence of codominant markers and implications for population genetic applications. Genome 44:677-684. (Pubitemid 32773644)
    • (2001) Genome , vol.44 , Issue.4 , pp. 677-684
    • Wong, A.1    Forbes, M.R.2    Smith, M.L.3


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