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Volumn 11, Issue SUPPL. 1, 2011, Pages 218-225

Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod, Gadus morhua

Author keywords

Ascertainment bias; Assignment; Atlantic Ocean; Single nucleotide polymorphism

Indexed keywords

ANIMAL; ARTICLE; ATLANTIC COD; EXPRESSED SEQUENCE TAG; GENETICS; GENOTYPE; GEOGRAPHY; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 79951742194     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2010.02949.x     Document Type: Article
Times cited : (50)

References (56)
  • 1
    • 0038529784 scopus 로고    scopus 로고
    • Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis
    • Alland D, Whittam TS, Murray MB et al. (2003) Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. Journal of Bacteriology, 185, 3392-3399.
    • (2003) Journal of Bacteriology , vol.185 , pp. 3392-3399
    • Alland, D.1    Whittam, T.S.2    Murray, M.B.3
  • 2
    • 0034727107 scopus 로고    scopus 로고
    • An SNP map of the human genome generated by reduced representation shotgun sequencing
    • Altshuler D, Pollara VJ, Cowles CR et al. (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature, 407, 513-516.
    • (2000) Nature , vol.407 , pp. 513-516
    • Altshuler, D.1    Pollara, V.J.2    Cowles, C.R.3
  • 3
    • 0030404875 scopus 로고    scopus 로고
    • Microsatellite polymorphism and the population structure of Atlantic cod (Gadus morhua) in the northwest Atlantic
    • Bentzen P, Taggart CT, Ruzzante DE, Cook D (1996) Microsatellite polymorphism and the population structure of Atlantic cod (Gadus morhua) in the northwest Atlantic. Canadian Journal of Fisheries and Aquatic Sciences, 53, 2706-2721.
    • (1996) Canadian Journal of Fisheries and Aquatic Sciences , vol.53 , pp. 2706-2721
    • Bentzen, P.1    Taggart, C.T.2    Ruzzante, D.E.3    Cook, D.4
  • 6
    • 33749414405 scopus 로고    scopus 로고
    • Mouse SNPs for evolutionary biology: beware of ascertainment biases
    • Boursot P, Belkhir K (2006) Mouse SNPs for evolutionary biology: beware of ascertainment biases. Genome Research, 16, 1191-1192.
    • (2006) Genome Research , vol.16 , pp. 1191-1192
    • Boursot, P.1    Belkhir, K.2
  • 7
    • 79955527472 scopus 로고    scopus 로고
    • An integrated approach to gene discovery and marker development in Atlantic cod (Gadus morhua)
    • Bowman S, Hubert S, Higgins B et al. (2010) An integrated approach to gene discovery and marker development in Atlantic cod (Gadus morhua). Marine Biotechnology, 11 (191), 1-14.
    • (2010) Marine Biotechnology , vol.11 , Issue.191 , pp. 1-14
    • Bowman, S.1    Hubert, S.2    Higgins, B.3
  • 8
    • 0033728327 scopus 로고    scopus 로고
    • Transport and development of eggs and larvae of Atlantic cod, Gadus morhua, in relation to spawning time and location in coastal Newfoundland
    • Bradbury IR, Snelgrove PVR, Fraser S (2000) Transport and development of eggs and larvae of Atlantic cod, Gadus morhua, in relation to spawning time and location in coastal Newfoundland. Canadian Journal of Fisheries and Aquatic Sciences, 57, 1761-1772.
    • (2000) Canadian Journal of Fisheries and Aquatic Sciences , vol.57 , pp. 1761-1772
    • Bradbury, I.R.1    Snelgrove, P.V.R.2    Fraser, S.3
  • 9
    • 43049152791 scopus 로고    scopus 로고
    • Discrete spatial dynamics and essential habitat of coastal cod populations: conservation and management implications
    • Bradbury IR, Laurel B, Robichaud D et al. (2008) Discrete spatial dynamics and essential habitat of coastal cod populations: conservation and management implications. Fisheries Research, 9, 299-309.
    • (2008) Fisheries Research , vol.9 , pp. 299-309
    • Bradbury, I.R.1    Laurel, B.2    Robichaud, D.3
  • 10
    • 70449435667 scopus 로고    scopus 로고
    • Structural and functional connectivity of marine fishes within a semi-enclosed Newfoundland fjord
    • Bradbury IR, Snelgrove PVR, Bentzen P et al. (2009) Structural and functional connectivity of marine fishes within a semi-enclosed Newfoundland fjord. Journal of Fish Biology, 75, 1398-1409.
    • (2009) Journal of Fish Biology , vol.75 , pp. 1398-1409
    • Bradbury, I.R.1    Snelgrove, P.V.R.2    Bentzen, P.3
  • 11
    • 78650061856 scopus 로고    scopus 로고
    • Parallel adaptive evolution of Atlantic cod in the eastern and western Atlantic Ocean in response to ocean temperature
    • Bradbury IR, Hubert S, Higgins B et al. (2010) Parallel adaptive evolution of Atlantic cod in the eastern and western Atlantic Ocean in response to ocean temperature. Proceedings of the Royal Society of London Biological Sciences B, 277, 3725-3734.
    • (2010) Proceedings of the Royal Society of London Biological Sciences B , vol.277 , pp. 3725-3734
    • Bradbury, I.R.1    Hubert, S.2    Higgins, B.3
  • 12
    • 56049094112 scopus 로고    scopus 로고
    • Intraspecific phylogeographic genomics from multiple complete mtDNA genomes in Atlantic Cod (Gadus morhua): origins of the "Codmother," trans-Atlantic vicariance, and mid-glacial population expansion
    • Carr SM, Marshall HD (2008) Intraspecific phylogeographic genomics from multiple complete mtDNA genomes in Atlantic Cod (Gadus morhua): origins of the "Codmother, " trans-Atlantic vicariance, and mid-glacial population expansion. Genetics, 108, 381-389.
    • (2008) Genetics , vol.108 , pp. 381-389
    • Carr, S.M.1    Marshall, H.D.2
  • 14
    • 0032711229 scopus 로고    scopus 로고
    • New methods employing multilocus genotypes to select or exclude populations as origins of individuals
    • Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M (1999) New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics, 153, 1989-2000.
    • (1999) Genetics , vol.153 , pp. 1989-2000
    • Cornuet, J.M.1    Piry, S.2    Luikart, G.3    Estoup, A.4    Solignac, M.5
  • 15
    • 79951729279 scopus 로고    scopus 로고
    • COSEWIC Assessment and Status Report on the Atlantic cod Gadus morhua in Canada
    • COSEWIC (ed. Canada CotSoEWi), COSEWIC, Ottawa
    • COSEWIC (2010) COSEWIC Assessment and Status Report on the Atlantic cod Gadus morhua in Canada (ed. Canada CotSoEWi), COSEWIC, Ottawa, pp. 1-116.
    • (2010) , pp. 1-116
  • 16
    • 0037792156 scopus 로고    scopus 로고
    • An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies
    • Elphinstone MS, Hinten GN, Anderson MJ, Nock CJ (2003) An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies. Molecular Ecology, 3, 317-320.
    • (2003) Molecular Ecology , vol.3 , pp. 317-320
    • Elphinstone, M.S.1    Hinten, G.N.2    Anderson, M.J.3    Nock, C.J.4
  • 18
    • 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
  • 19
    • 43749104435 scopus 로고    scopus 로고
    • Mapping the spawning grounds of North Sea cod (Gadus morhua) by direct and indirect means
    • Fox CJ, Taylor M, Dickey-Collas M et al. (2009) Mapping the spawning grounds of North Sea cod (Gadus morhua) by direct and indirect means. Proceedings of the Royal Society of London B, 275, 1543-1548.
    • (2009) Proceedings of the Royal Society of London B , vol.275 , pp. 1543-1548
    • Fox, C.J.1    Taylor, M.2    Dickey-Collas, M.3
  • 20
    • 33749254083 scopus 로고    scopus 로고
    • The effects of isolation and colonization history on the genetic structure of Atlantic cod (Gadus morhua) in the Canadian Arctic
    • Hardie DC, Gillett RM, Hutchings JA (2006) The effects of isolation and colonization history on the genetic structure of Atlantic cod (Gadus morhua) in the Canadian Arctic. Canadian Journal of Fisheries and Aquatic Sciences, 63, 1830-1839.
    • (2006) Canadian Journal of Fisheries and Aquatic Sciences , vol.63 , pp. 1830-1839
    • Hardie, D.C.1    Gillett, R.M.2    Hutchings, J.A.3
  • 21
    • 33748603762 scopus 로고    scopus 로고
    • An empirical verification of population assignment methods by marking and parentage data: hatchery and wild steelhead (Oncorhynchus mykiss) in Forks Creek, Washington, USA
    • Hauser L, Seamons TR, Dauer M, Naish KA, Quinn TP (2006) An empirical verification of population assignment methods by marking and parentage data: hatchery and wild steelhead (Oncorhynchus mykiss) in Forks Creek, Washington, USA. Molecular Ecology, 15, 3157-3173.
    • (2006) Molecular Ecology , vol.15 , pp. 3157-3173
    • Hauser, L.1    Seamons, T.R.2    Dauer, M.3    Naish, K.A.4    Quinn, T.P.5
  • 22
    • 79951759855 scopus 로고    scopus 로고
    • Application of SNPs for population genetics of non-model organisms: new opportunities and challenges
    • Helyar SJ, Hemmer-Hansen J, Bekkevold D et al. (2011) Application of SNPs for population genetics of non-model organisms: new opportunities and challenges. Molecular Ecology Resources, 11 (Suppl. 1), 123-136.
    • (2011) Molecular Ecology Resources , vol.11 , Issue.SUPPL. 1 , pp. 123-136
    • Helyar, S.J.1    Hemmer-Hansen, J.2    Bekkevold, D.3
  • 24
    • 70249102114 scopus 로고    scopus 로고
    • Development of single nucleotide polymorphism markers for Atlantic cod (Gadus morhua) using expressed sequences
    • Hubert S, Tarrant Bussey J, Higgins B, Curtis BA, Bowman S (2009) Development of single nucleotide polymorphism markers for Atlantic cod (Gadus morhua) using expressed sequences. Aquaculture, 296, 7-14.
    • (2009) Aquaculture , vol.296 , pp. 7-14
    • Hubert, S.1    Tarrant Bussey, J.2    Higgins, B.3    Curtis, B.A.4    Bowman, S.5
  • 25
    • 77951241851 scopus 로고    scopus 로고
    • Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua)
    • Hubert S, Higgins B, Borza T, Bowman S (2010) Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua). BMC Genomics, 11, 191.
    • (2010) BMC Genomics , vol.11 , pp. 191
    • Hubert, S.1    Higgins, B.2    Borza, T.3    Bowman, S.4
  • 28
    • 0036268487 scopus 로고    scopus 로고
    • Detecting wildlife poaching: identifying the origin of individuals using Bayesian assignment tests and multi-locus genotypes
    • Manel S, Berthier P, Luikart G (2002) Detecting wildlife poaching: identifying the origin of individuals using Bayesian assignment tests and multi-locus genotypes. Conservation Biology, 16, 650-659.
    • (2002) Conservation Biology , vol.16 , pp. 650-659
    • Manel, S.1    Berthier, P.2    Luikart, G.3
  • 29
    • 13844320121 scopus 로고    scopus 로고
    • Assignment methods: matching biological questions with appropriate techniques
    • Manel S, Gaggiotti O, Waples RS (2005) Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology & Evolution, 20, 136-142.
    • (2005) Trends in Ecology & Evolution , vol.20 , pp. 136-142
    • Manel, S.1    Gaggiotti, O.2    Waples, R.S.3
  • 30
    • 0242684410 scopus 로고    scopus 로고
    • Balancing selection at the prion protein gene consistent with prehistoric kurulike epidemics
    • Mead S, Stumpf MPH, Whitfield J et al. (2003) Balancing selection at the prion protein gene consistent with prehistoric kurulike epidemics. Science, 300, 640-643.
    • (2003) Science , vol.300 , pp. 640-643
    • Mead, S.1    Stumpf, M.P.H.2    Whitfield, J.3
  • 32
    • 0033965571 scopus 로고    scopus 로고
    • Estimation of population parameters and recombination rates from single nucleotide polymorphisms
    • Nielsen R (2000) Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics, 154, 931-942.
    • (2000) Genetics , vol.154 , pp. 931-942
    • Nielsen, R.1
  • 33
    • 3442885665 scopus 로고    scopus 로고
    • Population genetic data of ascertained SNP data
    • Nielsen R (2004) Population genetic data of ascertained SNP data. Human Genomics, 1, 218-224.
    • (2004) Human Genomics , vol.1 , pp. 218-224
    • Nielsen, R.1
  • 35
    • 33748619762 scopus 로고    scopus 로고
    • Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms
    • Nielsen E, Hansen M, Meldrup D (2006) Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms. Molecular Ecology, 15, 3219-3229.
    • (2006) Molecular Ecology , vol.15 , pp. 3219-3229
    • Nielsen, E.1    Hansen, M.2    Meldrup, D.3
  • 36
    • 73149122326 scopus 로고    scopus 로고
    • Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)
    • Nielsen E, Hemmer-Hansen J, Poulsen N et al. (2009) Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua). BMC Evolutionary Biology, 9, 276.
    • (2009) BMC Evolutionary Biology , vol.9 , pp. 276
    • Nielsen, E.1    Hemmer-Hansen, J.2    Poulsen, N.3
  • 38
    • 33644871292 scopus 로고    scopus 로고
    • Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
    • Peakall R, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295.
    • (2006) Molecular Ecology Notes , vol.6 , pp. 288-295
    • Peakall, R.1    Smouse, P.E.2
  • 39
    • 6044264968 scopus 로고    scopus 로고
    • GeneClass2: a software for genetic assignment and first-generation migrant detection
    • Piry S, Alapetite A, Cornuet JM et al. (2004) GeneClass2: a software for genetic assignment and first-generation migrant detection. Journal of Heredity, 95, 536-539.
    • (2004) Journal of Heredity , vol.95 , pp. 536-539
    • Piry, S.1    Alapetite, A.2    Cornuet, J.M.3
  • 40
    • 0035148464 scopus 로고    scopus 로고
    • Nucleotide polymorphism and natural selection at the pantophysin (Pan I) locus in the Atlantic cod, Gadus morhua (L.)
    • Pogson GH (2001) Nucleotide polymorphism and natural selection at the pantophysin (Pan I) locus in the Atlantic cod, Gadus morhua (L.). Genetics, 157, 317-330.
    • (2001) Genetics , vol.157 , pp. 317-330
    • Pogson, G.H.1
  • 41
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945.
    • (2000) Genetics , vol.155 , pp. 945
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 42
    • 62449095842 scopus 로고    scopus 로고
    • Correcting estimators of {theta} and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process
    • Ramirez-Soriano A, Nielsen R (2009) Correcting estimators of {theta} and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process. Genetics, 181, 701-710.
    • (2009) Genetics , vol.181 , pp. 701-710
    • Ramirez-Soriano, A.1    Nielsen, R.2
  • 44
    • 4444286353 scopus 로고    scopus 로고
    • Migratory behaviour and range in the Atlantic cod: inference from a century of tagging
    • Robichaud D, Rose GA (2004) Migratory behaviour and range in the Atlantic cod: inference from a century of tagging. Fish and Fishery, 5, 185-214.
    • (2004) Fish and Fishery , vol.5 , pp. 185-214
    • Robichaud, D.1    Rose, G.A.2
  • 45
    • 58549093168 scopus 로고    scopus 로고
    • How accurate is the current picture of human genetic variation?
    • Romero G, Manica A, Goudet J, Handley LL, Balloux F (2009) How accurate is the current picture of human genetic variation? Heredity, 102, 120-126.
    • (2009) Heredity , vol.102 , pp. 120-126
    • Romero, G.1    Manica, A.2    Goudet, J.3    Handley, L.L.4    Balloux, F.5
  • 46
    • 0027788213 scopus 로고
    • Cod spawning on a migration highway in the North-west Atlantic
    • Rose GA (1993) Cod spawning on a migration highway in the North-west Atlantic. Nature, 366, 458-461.
    • (1993) Nature , vol.366 , pp. 458-461
    • Rose, G.A.1
  • 47
    • 0031742917 scopus 로고    scopus 로고
    • Nuclear DNA basis for shelf- and bank scale population structure in northwest Atlantic cod (Gadus morhua): Labrador to Georges bank
    • Ruzzante DE, Taggart CT, Cook DA (1998) Nuclear DNA basis for shelf- and bank scale population structure in northwest Atlantic cod (Gadus morhua): Labrador to Georges bank. Molecular Ecology, 7, 1663-1680.
    • (1998) Molecular Ecology , vol.7 , pp. 1663-1680
    • Ruzzante, D.E.1    Taggart, C.T.2    Cook, D.A.3
  • 49
    • 63849205170 scopus 로고    scopus 로고
    • Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios
    • Saenz-Agudelo P, Jones GP, Thorrold SR, Planes S (2009) Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios. Molecular Ecology, 18, 1765-1776.
    • (2009) Molecular Ecology , vol.18 , pp. 1765-1776
    • Saenz-Agudelo, P.1    Jones, G.P.2    Thorrold, S.R.3    Planes, S.4
  • 51
    • 79751491452 scopus 로고    scopus 로고
    • Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon
    • Seeb LW, Templin WD, Sato S et al. (2011) Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon. Molecular Ecology Resources, 11 (Suppl. 1), 184-206.
    • (2011) Molecular Ecology Resources , vol.11 , Issue.SUPPL. 1 , pp. 184-206
    • Seeb, L.W.1    Templin, W.D.2    Sato, S.3
  • 52
    • 45249120404 scopus 로고    scopus 로고
    • Number of alleles as a predictor of the relative assignment accuracy of short tandem repeat (STR) and single-nucleotide-polymorphism (SNP) baselines for chum salmon
    • Smith CT, Seeb LW (2008) Number of alleles as a predictor of the relative assignment accuracy of short tandem repeat (STR) and single-nucleotide-polymorphism (SNP) baselines for chum salmon. Transactions of the American Fisheries Society, 137(3), 751-762.
    • (2008) Transactions of the American Fisheries Society , vol.137 , Issue.3 , pp. 751-762
    • Smith, C.T.1    Seeb, L.W.2
  • 53
    • 56249125642 scopus 로고    scopus 로고
    • Predicted extirpation of the dominant demersal fish in a large marine ecosystem: Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence
    • Swain DP, Chouinard GA (2008) Predicted extirpation of the dominant demersal fish in a large marine ecosystem: Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence. Canadian Journal of Fisheries and Aquatic Sciences, 65, 2315-2319.
    • (2008) Canadian Journal of Fisheries and Aquatic Sciences , vol.65 , pp. 2315-2319
    • Swain, D.P.1    Chouinard, G.A.2
  • 54
    • 33645859299 scopus 로고    scopus 로고
    • What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity
    • Waples RS, Gaggiotti O (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology, 15, 1419-1439.
    • (2006) Molecular Ecology , vol.15 , pp. 1419-1439
    • Waples, R.S.1    Gaggiotti, O.2
  • 55
    • 34347336584 scopus 로고    scopus 로고
    • Localizing recent adaptive evolution in the human genome
    • Williamson SH, Hubisz MJ, Clark AG et al. (2007) Localizing recent adaptive evolution in the human genome. PLoS Genetics, 3, e90.
    • (2007) PLoS Genetics , vol.3
    • Williamson, S.H.1    Hubisz, M.J.2    Clark, A.G.3
  • 56
    • 18444376793 scopus 로고    scopus 로고
    • Genomics: anthrax and the art of war (against ascertainment bias)
    • Worobey M (2005) Genomics: anthrax and the art of war (against ascertainment bias). Heredity, 94, 459-460.
    • (2005) Heredity , vol.94 , pp. 459-460
    • Worobey, M.1


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