메뉴 건너뛰기




Volumn 11, Issue 6, 2011, Pages 1068-1075

Genotyping HapSTR loci: Phase determination from direct sequencing of PCR products

Author keywords

Gametic phase; Haplotype reconstruction; Microsatellite; Nuclear loci; Vidua

Indexed keywords

MICROSATELLITE DNA; PRIMER DNA;

EID: 80054073812     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2011.03036.x     Document Type: Article
Times cited : (7)

References (49)
  • 1
    • 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
  • 2
    • 1642285792 scopus 로고    scopus 로고
    • The incomplete natural history of mitochondria
    • Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Molecular Ecology, 13, 729-744.
    • (2004) Molecular Ecology , vol.13 , pp. 729-744
    • Ballard, J.W.O.1    Whitlock, M.C.2
  • 3
    • 0036007847 scopus 로고    scopus 로고
    • The estimation of population differentiation with microsatellite markers
    • Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Molecular Ecology, 11, 155-165.
    • (2002) Molecular Ecology , vol.11 , pp. 155-165
    • Balloux, F.1    Lugon-Moulin, N.2
  • 4
    • 0033831392 scopus 로고    scopus 로고
    • Microsatellites can be misleading: an empirical and simulation study
    • Balloux F, Brunner H, Lugon-Moulin N, Hausser J, Goudet J (2000) Microsatellites can be misleading: an empirical and simulation study. Evolution, 54, 1414-1422.
    • (2000) Evolution , vol.54 , pp. 1414-1422
    • Balloux, F.1    Brunner, H.2    Lugon-Moulin, N.3    Hausser, J.4    Goudet, J.5
  • 5
    • 1842842603 scopus 로고    scopus 로고
    • Evolution of a perfect simple sequence repeat locus in the context of its flanking sequence
    • Blankenship SM, May B, Hedgecock D (2002) Evolution of a perfect simple sequence repeat locus in the context of its flanking sequence. Molecular Biology and Evolution, 19, 1943-1951.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 1943-1951
    • Blankenship, S.M.1    May, B.2    Hedgecock, D.3
  • 6
    • 65449133181 scopus 로고    scopus 로고
    • Multilocus phylogeography and phylogenetics using sequence-based markers
    • Brito P, Edwards SV (2009) Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica, 135, 439-455.
    • (2009) Genetica , vol.135 , pp. 439-455
    • Brito, P.1    Edwards, S.V.2
  • 7
    • 35948952881 scopus 로고    scopus 로고
    • Gene sampling strategies for multi-locus population estimates of genetic diversity (theta)
    • Carling MD, Brumfield RT (2007) Gene sampling strategies for multi-locus population estimates of genetic diversity (theta). PLoS ONE, 2, e160.
    • (2007) PLoS ONE , vol.2
    • Carling, M.D.1    Brumfield, R.T.2
  • 8
    • 48249149566 scopus 로고    scopus 로고
    • Decoding of superimposed traces produced by direct sequencing of heterozygous indels
    • Dmitriev DA, Rakitov RA (2008) Decoding of superimposed traces produced by direct sequencing of heterozygous indels. PLoS Computational Biology, 4, e1000113.
    • (2008) PLoS Computational Biology , vol.4
    • Dmitriev, D.A.1    Rakitov, R.A.2
  • 9
    • 0034496840 scopus 로고    scopus 로고
    • Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies
    • Edwards SV, Beerli P (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution, 54, 1839-1854.
    • (2000) Evolution , vol.54 , pp. 1839-1854
    • Edwards, S.V.1    Beerli, P.2
  • 10
    • 0036718239 scopus 로고    scopus 로고
    • Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis
    • Estoup A, Jarne P, Cornuet JM (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Molecular Ecology, 11, 1591-1604.
    • (2002) Molecular Ecology , vol.11 , pp. 1591-1604
    • Estoup, A.1    Jarne, P.2    Cornuet, J.M.3
  • 11
    • 33244495782 scopus 로고    scopus 로고
    • Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?
    • Felsenstein J (2006) Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? Molecular Biology and Evolution, 23, 691-700.
    • (2006) Molecular Biology and Evolution , vol.23 , pp. 691-700
    • Felsenstein, J.1
  • 12
    • 35848964045 scopus 로고    scopus 로고
    • CHAMPURU 1.0: a computer software for unraveling mixtures of two DNA sequences of unequal lengths
    • Flot JF (2007) CHAMPURU 1.0: a computer software for unraveling mixtures of two DNA sequences of unequal lengths. Molecular Ecology Notes, 7, 974-977.
    • (2007) Molecular Ecology Notes , vol.7 , pp. 974-977
    • Flot, J.F.1
  • 13
    • 33747401249 scopus 로고    scopus 로고
    • Phase determination from direct sequencing of length-variable DNA regions
    • Flot JF, Tillier A, Samadi S, Tillier S (2006) Phase determination from direct sequencing of length-variable DNA regions. Molecular Ecology Notes, 6, 627-630.
    • (2006) Molecular Ecology Notes , vol.6 , pp. 627-630
    • Flot, J.F.1    Tillier, A.2    Samadi, S.3    Tillier, S.4
  • 14
    • 77951536651 scopus 로고    scopus 로고
    • Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation
    • Garrick RC, Sunnucks P, Dyer RJ (2010) Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation. BMC Evolutionary Biology, 10, 118.
    • (2010) BMC Evolutionary Biology , vol.10 , pp. 118
    • Garrick, R.C.1    Sunnucks, P.2    Dyer, R.J.3
  • 15
    • 78650304994 scopus 로고    scopus 로고
    • Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites
    • Haasl RJ, Payseur BA (2011) Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites. Heredity, 106, 158-171.
    • (2011) Heredity , vol.106 , pp. 158-171
    • Haasl, R.J.1    Payseur, B.A.2
  • 16
    • 27244436959 scopus 로고    scopus 로고
    • A simple method to score single nucleotide polymorphisms based on allele-specific PCR and primer-induced fragment-length variation
    • Hansson B, Kawabe A (2005) A simple method to score single nucleotide polymorphisms based on allele-specific PCR and primer-induced fragment-length variation. Molecular Ecology Notes, 5, 692-696.
    • (2005) Molecular Ecology Notes , vol.5 , pp. 692-696
    • Hansson, B.1    Kawabe, A.2
  • 17
    • 55149104619 scopus 로고    scopus 로고
    • Computation vs. cloning: evaluation of two methods for haplotype determination
    • Harrigan RJ, Mazza ME, Sorenson MD (2008) Computation vs. cloning: evaluation of two methods for haplotype determination. Molecular Ecology Resources, 8, 1239-1248.
    • (2008) Molecular Ecology Resources , vol.8 , pp. 1239-1248
    • Harrigan, R.J.1    Mazza, M.E.2    Sorenson, M.D.3
  • 18
    • 77952297997 scopus 로고    scopus 로고
    • The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses
    • Hey J (2010a) The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. Molecular Biology and Evolution, 27, 921-933.
    • (2010) Molecular Biology and Evolution , vol.27 , pp. 921-933
    • Hey, J.1
  • 19
    • 77952294620 scopus 로고    scopus 로고
    • Isolation with migration models for more than two populations
    • Hey J (2010b) Isolation with migration models for more than two populations. Molecular Biology and Evolution, 27, 905-920.
    • (2010) Molecular Biology and Evolution , vol.27 , pp. 905-920
    • Hey, J.1
  • 20
    • 3142714474 scopus 로고    scopus 로고
    • Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis
    • Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics, 167, 747-760.
    • (2004) Genetics , vol.167 , pp. 747-760
    • Hey, J.1    Nielsen, R.2
  • 21
    • 33847253975 scopus 로고    scopus 로고
    • Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
    • Hey J, Nielsen R (2007) Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences of the United States of America, 104, 2785-2790.
    • (2007) Proceedings of the National Academy of Sciences of the United States of America , vol.104 , pp. 2785-2790
    • Hey, J.1    Nielsen, R.2
  • 22
    • 1642326524 scopus 로고    scopus 로고
    • Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species
    • Hey J, Won YJ, Sivasundar A, Nielsen R, Markert JA (2004) Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species. Molecular Ecology, 13, 909-919.
    • (2004) Molecular Ecology , vol.13 , pp. 909-919
    • Hey, J.1    Won, Y.J.2    Sivasundar, A.3    Nielsen, R.4    Markert, J.A.5
  • 24
    • 0022211482 scopus 로고
    • Statistical properties of the number of recombination events in the history of a sample of DNA sequences
    • Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics, 111, 147-164.
    • (1985) Genetics , vol.111 , pp. 147-164
    • Hudson, R.R.1    Kaplan, N.L.2
  • 25
    • 70349210121 scopus 로고    scopus 로고
    • Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes)
    • Irwin DE, Rubtsov AS, Panov EN (2009) Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes). Biological Journal of the Linnean Society, 98, 422-438.
    • (2009) Biological Journal of the Linnean Society , vol.98 , pp. 422-438
    • Irwin, D.E.1    Rubtsov, A.S.2    Panov, E.N.3
  • 26
    • 25644452054 scopus 로고    scopus 로고
    • Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees
    • Jennings WB, Edwards SV (2005) Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution, 59, 2033-2047.
    • (2005) Evolution , vol.59 , pp. 2033-2047
    • Jennings, W.B.1    Edwards, S.V.2
  • 27
    • 0032052803 scopus 로고    scopus 로고
    • Stimulation and suppression of PCR-mediated recombination
    • Judo MSB, Wedel AB, Wilson C (1998) Stimulation and suppression of PCR-mediated recombination. Nucleic Acids Research, 26, 1819-1825.
    • (1998) Nucleic Acids Research , vol.26 , pp. 1819-1825
    • Judo, M.S.B.1    Wedel, A.B.2    Wilson, C.3
  • 28
    • 0014494672 scopus 로고
    • The number of heterozygous nucleotide sites maintained in a finite population due to steady influx of mutations
    • Kimura M (1969) The number of heterozygous nucleotide sites maintained in a finite population due to steady influx of mutations. Genetics, 61, 893-903.
    • (1969) Genetics , vol.61 , pp. 893-903
    • Kimura, M.1
  • 30
    • 0025305576 scopus 로고
    • Effects of primer template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies
    • Kwok S, Kellogg DE, Mckinney N et al. (1990) Effects of primer template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Research, 18, 999-1005.
    • (1990) Nucleic Acids Research , vol.18 , pp. 999-1005
    • Kwok, S.1    Kellogg, D.E.2    Mckinney, N.3
  • 32
    • 0036852236 scopus 로고    scopus 로고
    • SNPSTRs: empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes
    • Mountain JL, Knight A, Jobin M et al. (2002) SNPSTRs: empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes. Genome Research, 12, 1766-1772.
    • (2002) Genome Research , vol.12 , pp. 1766-1772
    • Mountain, J.L.1    Knight, A.2    Jobin, M.3
  • 33
    • 0034967295 scopus 로고    scopus 로고
    • Distinguishing migration from isolation: a Markov chain Monte Carlo approach
    • Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158, 885-896.
    • (2001) Genetics , vol.158 , pp. 885-896
    • Nielsen, R.1    Wakeley, J.2
  • 34
    • 33746361176 scopus 로고    scopus 로고
    • Integrating patterns of polymorphism at SNPs and STRs
    • Payseur BA, Cutter AD (2006) Integrating patterns of polymorphism at SNPs and STRs. Trends in Genetics, 22, 424-429.
    • (2006) Trends in Genetics , vol.22 , pp. 424-429
    • Payseur, B.A.1    Cutter, A.D.2
  • 35
    • 66249125357 scopus 로고    scopus 로고
    • A genomewide comparison of population structure at STRPs and nearby SNPs in humans
    • Payseur BA, Jing PC (2009) A genomewide comparison of population structure at STRPs and nearby SNPs in humans. Molecular Biology and Evolution, 26, 1369-1377.
    • (2009) Molecular Biology and Evolution , vol.26 , pp. 1369-1377
    • Payseur, B.A.1    Jing, P.C.2
  • 36
    • 44449119051 scopus 로고    scopus 로고
    • Multilocus phylogeography of a Holarctic duck: colonization of North America from Eurasia by gadwall (Anas strepera)
    • Peters JL, Zhuravlev YN, Fefelov I, Humphries EM, Omland KE (2008) Multilocus phylogeography of a Holarctic duck: colonization of North America from Eurasia by gadwall (Anas strepera). Evolution, 62, 1469-1483.
    • (2008) Evolution , vol.62 , pp. 1469-1483
    • Peters, J.L.1    Zhuravlev, Y.N.2    Fefelov, I.3    Humphries, E.M.4    Omland, K.E.5
  • 37
    • 4944227513 scopus 로고    scopus 로고
    • Precision and accuracy of divergence time estimates from STR and SNPSTR variation
    • Ramakrishnan U, Mountain JL (2004) Precision and accuracy of divergence time estimates from STR and SNPSTR variation. Molecular Biology and Evolution, 21, 1960-1971.
    • (2004) Molecular Biology and Evolution , vol.21 , pp. 1960-1971
    • Ramakrishnan, U.1    Mountain, J.L.2
  • 38
    • 0036245438 scopus 로고    scopus 로고
    • Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
    • Rosenberg NA, Nordborg M (2002) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics, 3, 380-390.
    • (2002) Nature Reviews Genetics , vol.3 , pp. 380-390
    • Rosenberg, N.A.1    Nordborg, M.2
  • 39
    • 25444438753 scopus 로고    scopus 로고
    • Inferring haplotypes at the NAT2 locus: the computational approach
    • Sabbagh A, Darlu P (2005) Inferring haplotypes at the NAT2 locus: the computational approach. BMC Genetics, 6, 30.
    • (2005) BMC Genetics , vol.6 , pp. 30
    • Sabbagh, A.1    Darlu, P.2
  • 40
    • 0000373654 scopus 로고    scopus 로고
    • Characterization of microsatellite loci in village indigobirds Vidua chalybeata and cross-species amplification in estrildid and ploceid finches
    • Sefc KM, Payne RB, Sorenson MD (2001) Characterization of microsatellite loci in village indigobirds Vidua chalybeata and cross-species amplification in estrildid and ploceid finches. Molecular Ecology Notes, 1, 252-254.
    • (2001) Molecular Ecology Notes , vol.1 , pp. 252-254
    • Sefc, K.M.1    Payne, R.B.2    Sorenson, M.D.3
  • 41
    • 17644416109 scopus 로고    scopus 로고
    • Genetic continuity of brood-parasitic indigobird species
    • Sefc KM, Payne RB, Sorenson MD (2005) Genetic continuity of brood-parasitic indigobird species. Molecular Ecology, 14, 1407-1419.
    • (2005) Molecular Ecology , vol.14 , pp. 1407-1419
    • Sefc, K.M.1    Payne, R.B.2    Sorenson, M.D.3
  • 42
    • 35649007346 scopus 로고    scopus 로고
    • TraceHaplotyper: using direct sequencing to determine the phase of an indel followed by biallelic SNPs
    • Seroussi Y, Seroussi E (2007) TraceHaplotyper: using direct sequencing to determine the phase of an indel followed by biallelic SNPs. BioTechniques, 43, 452-456.
    • (2007) BioTechniques , vol.43 , pp. 452-456
    • Seroussi, Y.1    Seroussi, E.2
  • 43
    • 0036053432 scopus 로고    scopus 로고
    • Factors affecting PCR-mediated recombination
    • Shafikhani S (2002) Factors affecting PCR-mediated recombination. Environmental Microbiology, 4, 482-486.
    • (2002) Environmental Microbiology , vol.4 , pp. 482-486
    • Shafikhani, S.1
  • 44
    • 0242691208 scopus 로고    scopus 로고
    • A comparison of Bayesian methods for haplotype reconstruction from population genotype data
    • Stephens M, Donnelly P (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics, 73, 1162-1169.
    • (2003) American Journal of Human Genetics , vol.73 , pp. 1162-1169
    • Stephens, M.1    Donnelly, P.2
  • 45
    • 0035071957 scopus 로고    scopus 로고
    • A new statistical method for haplotype reconstruction from population data
    • Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978-989.
    • (2001) American Journal of Human Genetics , vol.68 , pp. 978-989
    • Stephens, M.1    Smith, N.J.2    Donnelly, P.3
  • 47
    • 78651328464 scopus 로고    scopus 로고
    • A tale of two genomes: contrasting patterns of phylogeographic structure in a widely distributed bat
    • Turmelle AS, Kunz TH, Sorenson MD (2011) A tale of two genomes: contrasting patterns of phylogeographic structure in a widely distributed bat. Molecular Ecology, 20, 357-375.
    • (2011) Molecular Ecology , vol.20 , pp. 357-375
    • Turmelle, A.S.1    Kunz, T.H.2    Sorenson, M.D.3
  • 48
    • 0037350984 scopus 로고    scopus 로고
    • Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects
    • Zhang DX, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12, 563-584.
    • (2003) Molecular Ecology , vol.12 , pp. 563-584
    • Zhang, D.X.1    Hewitt, G.M.2
  • 49
    • 42449136665 scopus 로고    scopus 로고
    • Mitochondrial DNA under siege in avian phylogeography
    • Zink RM, Barrowclough GF (2008) Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology, 17, 2107-2121.
    • (2008) Molecular Ecology , vol.17 , pp. 2107-2121
    • Zink, R.M.1    Barrowclough, G.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.