메뉴 건너뛰기




Volumn 13, Issue 4, 2013, Pages 706-714

A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

Author keywords

Effective population size; Population genomics; RAD sequencing; SNP discovery

Indexed keywords

ANGUILLA (FISH); ANIMAL; ARTICLE; BIOLOGY; DNA SEQUENCE; GENETICS; GENOME; GENOMICS; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84879420457     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12117     Document Type: Article
Times cited : (67)

References (57)
  • 2
    • 79953059633 scopus 로고    scopus 로고
    • All roads lead to home: panmixia of European eel in the Sargasso Sea
    • Als TD, Hansen MM, Maes GE et al. (2011) All roads lead to home: panmixia of European eel in the Sargasso Sea. Molecular Ecology, 20, 1333-1346.
    • (2011) Molecular Ecology , vol.20 , pp. 1333-1346
    • Als, T.D.1    Hansen, M.M.2    Maes, G.E.3
  • 3
    • 54449098752 scopus 로고    scopus 로고
    • Rapid SNP discovery and genetic mapping using sequenced RAD markers
    • Baird NA, Etter PD, Atwood TS, et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 3, e3376.
    • (2008) PLoS ONE , vol.3
    • Baird, N.A.1    Etter, P.D.2    Atwood, T.S.3
  • 4
    • 77949787771 scopus 로고    scopus 로고
    • A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)
    • Ball AD, Stapley J, Dawson SA, Birkhead TR, Burke T, Slate J (2010) A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata). BMC Genomics, 11, 218.
    • (2010) BMC Genomics , vol.11 , pp. 218
    • Ball, A.D.1    Stapley, J.2    Dawson, S.A.3    Birkhead, T.R.4    Burke, T.5    Slate, J.6
  • 6
    • 37349046444 scopus 로고    scopus 로고
    • Fluctuations in European eel (Anguilla anguilla) recruitment resulting from environmental changes in the Sargasso Sea
    • Bonhommeau S, Chassot E, Rivot E (2008) Fluctuations in European eel (Anguilla anguilla) recruitment resulting from environmental changes in the Sargasso Sea. Fisheries Oceanography, 17, 32-44.
    • (2008) Fisheries Oceanography , vol.17 , pp. 32-44
    • Bonhommeau, S.1    Chassot, E.2    Rivot, E.3
  • 8
    • 84872452098 scopus 로고    scopus 로고
    • Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach
    • Bruneaux M, Johnston SE, Herczeg G et al. (2013) Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach. Molecular Ecology, 22, 565-582.
    • (2013) Molecular Ecology , vol.22 , pp. 565-582
    • Bruneaux, M.1    Johnston, S.E.2    Herczeg, G.3
  • 9
    • 71949101266 scopus 로고    scopus 로고
    • Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library
    • Castaño-Sanchez C, Smith TPL, Wiedmann RP et al. (2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics, 10, 559.
    • (2009) BMC Genomics , vol.10 , pp. 559
    • Castaño-Sanchez, C.1    Smith, T.P.L.2    Wiedmann, R.P.3
  • 11
    • 78149493335 scopus 로고    scopus 로고
    • Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel
    • Coppe A, Pujolar JM, Maes GE et al. (2010) Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel. BMC Genomics, 11, 635.
    • (2010) BMC Genomics , vol.11 , pp. 635
    • Coppe, A.1    Pujolar, J.M.2    Maes, G.E.3
  • 13
    • 79959435199 scopus 로고    scopus 로고
    • Genome-wide genetic marker discovery and genotyping using next-generation sequencing
    • Davey JW, Hohenlohe PA, Etter PD, et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499-510.
    • (2011) Nature Reviews Genetics , vol.12 , pp. 499-510
    • Davey, J.W.1    Hohenlohe, P.A.2    Etter, P.D.3
  • 16
    • 79955783956 scopus 로고    scopus 로고
    • A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    • Elshire RJ, Glaubitz JC, Sun Q et al. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6, e19379.
    • (2011) PLoS ONE , vol.6
    • Elshire, R.J.1    Glaubitz, J.C.2    Sun, Q.3
  • 18
  • 19
    • 34447531831 scopus 로고    scopus 로고
    • Oceanic changes in the Sargasso Sea and declines in recruitment of the European eel
    • Friedland KD, Miller MI, Knights B (2007) Oceanic changes in the Sargasso Sea and declines in recruitment of the European eel. ICES Journal of Marine Science, 64, 519-530.
    • (2007) ICES Journal of Marine Science , vol.64 , pp. 519-530
    • Friedland, K.D.1    Miller, M.I.2    Knights, B.3
  • 20
    • 84857419830 scopus 로고    scopus 로고
    • The genetic consequences of spatially varying selection in the panmictic American eel (Anguilla rostrata)
    • Gagnaire PA, Normandeau E, Côté C et al. (2012) The genetic consequences of spatially varying selection in the panmictic American eel (Anguilla rostrata). Genetics, 190, 725-736.
    • (2012) Genetics , vol.190 , pp. 725-736
    • Gagnaire, P.A.1    Normandeau, E.2    Côté, C.3
  • 21
    • 84858080216 scopus 로고    scopus 로고
    • Monitoring adaptive genetic responses to environmental change
    • Hansen MM, Olivieri I, Waller DM et al. (2012) Monitoring adaptive genetic responses to environmental change. Molecular Ecology, 21, 1311-1329.
    • (2012) Molecular Ecology , vol.21 , pp. 1311-1329
    • Hansen, M.M.1    Olivieri, I.2    Waller, D.M.3
  • 22
    • 79951736104 scopus 로고    scopus 로고
    • An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population
    • Hauser L, Baird M, Hilborn R, Seeb LW, Seeb JE (2011) An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Molecular Ecology Resources, 11, 150-161.
    • (2011) Molecular Ecology Resources , vol.11 , pp. 150-161
    • Hauser, L.1    Baird, M.2    Hilborn, R.3    Seeb, L.W.4    Seeb, J.E.5
  • 23
    • 79951759855 scopus 로고    scopus 로고
    • Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges
    • Helyar SJ, Hemmer-Jansen J, Bekkevold D et al. (2011) Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources, 11, 123-136.
    • (2011) Molecular Ecology Resources , vol.11 , pp. 123-136
    • Helyar, S.J.1    Hemmer-Jansen, J.2    Bekkevold, D.3
  • 24
    • 84857509392 scopus 로고    scopus 로고
    • Primitive duplicate hox clusters in the European eel's genome
    • Henkel CV, Burgerhout E, Danielle L et al. (2012) Primitive duplicate hox clusters in the European eel's genome. PLoS ONE, 7, e32231.
    • (2012) PLoS ONE , vol.7
    • Henkel, C.V.1    Burgerhout, E.2    Danielle, L.3
  • 25
    • 79951745279 scopus 로고    scopus 로고
    • Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of chinook salmon in the Columbia River Basin
    • Hess J, Matala AP, Narum SR (2011) Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of chinook salmon in the Columbia River Basin. Molecular Ecology Resources, 11, 137-149.
    • (2011) Molecular Ecology Resources , vol.11 , pp. 137-149
    • Hess, J.1    Matala, A.P.2    Narum, S.R.3
  • 28
    • 79951748696 scopus 로고    scopus 로고
    • Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westlope cutthroat trout
    • Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westlope cutthroat trout. Molecular Ecology Resources, 11, 117-122.
    • (2011) Molecular Ecology Resources , vol.11 , pp. 117-122
    • Hohenlohe, P.A.1    Amish, S.J.2    Catchen, J.M.3    Allendorf, F.W.4    Luikart, G.5
  • 29
    • 84879409519 scopus 로고    scopus 로고
    • ICES Report of the Joint EIFAAC/ICES Working Group on Eels (WGEEL), 5-9 September 2011, Lisbon, Portugal. ICES CM 2011/ACOM:18. International Council for the Exploration of the Seas, Copenhagen, Denmark.
    • ICES (2011) Report of the Joint EIFAAC/ICES Working Group on Eels (WGEEL), 5-9 September 2011, Lisbon, Portugal. ICES CM 2011/ACOM:18. International Council for the Exploration of the Seas, Copenhagen, Denmark.
    • (2011)
  • 30
    • 84859462157 scopus 로고    scopus 로고
    • The genomics basis of adaptive evolution in threespine sticklebacks
    • Jones FC, Grabherr MG, Chan YF et al. (2012a) The genomics basis of adaptive evolution in threespine sticklebacks. Nature, 484, 55-61.
    • (2012) Nature , vol.484 , pp. 55-61
    • Jones, F.C.1    Grabherr, M.G.2    Chan, Y.F.3
  • 31
    • 84855708550 scopus 로고    scopus 로고
    • A genome-wide SNP genotyping array reveals patterns of local and repeated species-pair divergence in sticklebacks
    • Jones FC, Chan YF, Schmutz M et al. (2012b) A genome-wide SNP genotyping array reveals patterns of local and repeated species-pair divergence in sticklebacks. Current Biology, 22, 83-90.
    • (2012) Current Biology , vol.22 , pp. 83-90
    • Jones, F.C.1    Chan, Y.F.2    Schmutz, M.3
  • 32
    • 0038615856 scopus 로고    scopus 로고
    • A review of the possible impacts of long-term oceanic and climatic changes and fishing mortality on recruitment of anguillid eels of the Northern hemisphere
    • Knights B (2003) A review of the possible impacts of long-term oceanic and climatic changes and fishing mortality on recruitment of anguillid eels of the Northern hemisphere. Science of the Total Environment, 310, 237-244.
    • (2003) Science of the Total Environment , vol.310 , pp. 237-244
    • Knights, B.1
  • 33
    • 33645108873 scopus 로고    scopus 로고
    • LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
    • Kuhner MK (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics, 22, 768-770.
    • (2006) Bioinformatics , vol.22 , pp. 768-770
    • Kuhner, M.K.1
  • 34
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25.
    • (2009) Genome Biology , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 35
    • 33846874137 scopus 로고    scopus 로고
    • Rapid and cost-effective polymorphism identification and genotyping using restriction-site associated DNA (RAD) markers
    • Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction-site associated DNA (RAD) markers. Genome Research, 17, 240-248.
    • (2007) Genome Research , vol.17 , pp. 240-248
    • Miller, M.R.1    Dunham, J.P.2    Amores, A.3    Cresko, W.A.4    Johnson, E.A.5
  • 37
    • 49249097861 scopus 로고    scopus 로고
    • Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce
    • Namroud MC, Beaulieu J, Juge N, Larouche J, Bousquet J (2008) Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Molecular Ecology, 17, 3599-3613.
    • (2008) Molecular Ecology , vol.17 , pp. 3599-3613
    • Namroud, M.C.1    Beaulieu, J.2    Juge, N.3    Larouche, J.4    Bousquet, J.5
  • 38
    • 56549112524 scopus 로고    scopus 로고
    • Waking the dead: the value of population genetic analyses of historical samples
    • Nielsen EE, Hansen MM (2008) Waking the dead: the value of population genetic analyses of historical samples. Fish and Fisheries, 9, 450-461.
    • (2008) Fish and Fisheries , vol.9 , pp. 450-461
    • Nielsen, E.E.1    Hansen, M.M.2
  • 39
    • 84861691274 scopus 로고    scopus 로고
    • Double Digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species
    • Peterson BK, Weber JN, Kay EH et al. (2012) Double Digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7, e37135.
    • (2012) PLoS ONE , vol.7
    • Peterson, B.K.1    Weber, J.N.2    Kay, E.H.3
  • 40
    • 58949095496 scopus 로고    scopus 로고
    • Isolation and characterization of expressed sequence tag-linked microsatellite loci for the European eel, Anguilla anguilla
    • Pujolar JM, Maes GE, Van Houdt JK, Zane L (2008) Isolation and characterization of expressed sequence tag-linked microsatellite loci for the European eel, Anguilla anguilla. Molecular Ecology Resources, 9, 233-235.
    • (2008) Molecular Ecology Resources , vol.9 , pp. 233-235
    • Pujolar, J.M.1    Maes, G.E.2    Van Houdt, J.K.3    Zane, L.4
  • 41
    • 79955855896 scopus 로고    scopus 로고
    • No apparent genetic bottleneck in the demographically declining European eel using molecular genetics and forward-time simulations
    • Pujolar JM, Bevacqua D, Cappocioni F, Ciccotti E, De Leo GA, Zane L (2011) No apparent genetic bottleneck in the demographically declining European eel using molecular genetics and forward-time simulations. Conservation Genetics, 12, 813-825.
    • (2011) Conservation Genetics , vol.12 , pp. 813-825
    • Pujolar, J.M.1    Bevacqua, D.2    Cappocioni, F.3    Ciccotti, E.4    De Leo, G.A.5    Zane, L.6
  • 42
    • 84866560252 scopus 로고    scopus 로고
    • Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel
    • Pujolar JM, Marino IAM, Milan M et al. (2012) Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel. BMC Genomics, 13, 507.
    • (2012) BMC Genomics , vol.13 , pp. 507
    • Pujolar, J.M.1    Marino, I.A.M.2    Milan, M.3
  • 45
    • 0036006020 scopus 로고    scopus 로고
    • Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model
    • Storz JF, Beaumont MA (2002) Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution, 56, 154-166.
    • (2002) Evolution , vol.56 , pp. 154-166
    • Storz, J.F.1    Beaumont, M.A.2
  • 46
    • 0021066244 scopus 로고
    • Evolutionary relationship of DNA sequences in finite populations
    • Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437-460.
    • (1983) Genetics , vol.105 , pp. 437-460
    • Tajima, F.1
  • 48
    • 84879410722 scopus 로고    scopus 로고
    • Reproduction of European eel in aquaculture (REEL): consolidation and new production methods. DTU Aqua Report No 249-2012. National Institute of Aquatic Resources, Technical University of Denmark
    • Tomkiewicz J (2012) Reproduction of European eel in aquaculture (REEL): consolidation and new production methods. DTU Aqua Report No 249-2012. National Institute of Aquatic Resources, Technical University of Denmark, 47 p.
    • (2012) , pp. 47
    • Tomkiewicz, J.1
  • 49
    • 24944471763 scopus 로고    scopus 로고
    • Genomic islands of speciation in Anopheles gambiae
    • Turner TL, Han MW, Nuzhdin SV (2005) Genomic islands of speciation in Anopheles gambiae. PLoS Biology, 3, e285.
    • (2005) PLoS Biology , vol.3
    • Turner, T.L.1    Han, M.W.2    Nuzhdin, S.V.3
  • 50
    • 52049084856 scopus 로고    scopus 로고
    • Genomic analysis of adaptive differentiation in Drosophila melanogaster
    • Turner TL, Levine MT, Eckert ML, Begun DJ (2008) Genomic analysis of adaptive differentiation in Drosophila melanogaster. Genetics, 179, 455-473.
    • (2008) Genetics , vol.179 , pp. 455-473
    • Turner, T.L.1    Levine, M.T.2    Eckert, M.L.3    Begun, D.J.4
  • 51
    • 77649191883 scopus 로고    scopus 로고
    • Population resequencing reveals local adaptation in Arabidopsis lyrata to serpentine soils
    • Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV (2010) Population resequencing reveals local adaptation in Arabidopsis lyrata to serpentine soils. Nature Genetics, 42, 260-263.
    • (2010) Nature Genetics , vol.42 , pp. 260-263
    • Turner, T.L.1    Bourne, E.C.2    Von Wettberg, E.J.3    Hu, T.T.4    Nuzhdin, S.V.5
  • 52
    • 77749324529 scopus 로고    scopus 로고
    • Genome-wide SNP detection in the great tit Parus major using high throughtput sequencing
    • Van Bers NEM, Van Oers K, Kerstens HHD (2010) Genome-wide SNP detection in the great tit Parus major using high throughtput sequencing. Molecular Ecology, 19, 89-99.
    • (2010) Molecular Ecology , vol.19 , pp. 89-99
    • Van Bers, N.E.M.1    Van Oers, K.2    Kerstens, H.H.D.3
  • 53
    • 84872480881 scopus 로고    scopus 로고
    • Genome-wide RAD sequence data provide unprecedented resolution in species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
    • Wagner CE, Keller I, Wittwer S et al. (2012) Genome-wide RAD sequence data provide unprecedented resolution in species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology, 22, 787-798.
    • (2012) Molecular Ecology , vol.22 , pp. 787-798
    • Wagner, C.E.1    Keller, I.2    Wittwer, S.3
  • 54
    • 33644878743 scopus 로고    scopus 로고
    • Genetic estimates of contemporary effective population size: to what time periods do the estimates apply?
    • Waples RS (2005) Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? Molecular Ecology, 14, 3335-3352.
    • (2005) Molecular Ecology , vol.14 , pp. 3335-3352
    • Waples, R.S.1
  • 55
    • 55149117555 scopus 로고    scopus 로고
    • Isolation and characterization of 12 dinocleotide microsatellites in the European eel, Anguilla anguilla, and tests for amplification in other species of eels
    • Wielgoss S, Wirth T, Meyer A (2008) Isolation and characterization of 12 dinocleotide microsatellites in the European eel, Anguilla anguilla, and tests for amplification in other species of eels. Molecular Ecology Resources, 8, 1382-1385.
    • (2008) Molecular Ecology Resources , vol.8 , pp. 1382-1385
    • Wielgoss, S.1    Wirth, T.2    Meyer, A.3
  • 56
    • 77953642090 scopus 로고    scopus 로고
    • Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies
    • Willing EM, Bentzen P, van Oosterhout C et al. (2010) Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies. Molecular Ecology, 19, 968-984.
    • (2010) Molecular Ecology , vol.19 , pp. 968-984
    • Willing, E.M.1    Bentzen, P.2    van Oosterhout, C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.