메뉴 건너뛰기




Volumn 9, Issue 1, 2018, Pages

A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; ALGORITHM; ANCESTRY; DATA; DEMOGRAPHIC HISTORY; GENETIC DRIFT; MODEL; RECONSTRUCTION;

EID: 85051476734     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-018-05257-7     Document Type: Article
Times cited : (316)

References (33)
  • 1
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • PID: 10835412
    • Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 2
    • 69749099417 scopus 로고    scopus 로고
    • Fast model-based estimation of ancestry in unrelated individuals
    • PID: 19648217
    • Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1655-1664
    • Alexander, D.H.1    Novembre, J.2    Lange, K.3
  • 3
    • 17644402806 scopus 로고    scopus 로고
    • Estimation of individual admixture: analytical and study design considerations
    • PID: 15712363
    • Tang, H. et al. Estimation of individual admixture: analytical and study design considerations. Genet. Epidemiol. 28, 289–301 (2005).
    • (2005) Genet. Epidemiol. , vol.28 , pp. 289-301
    • Tang, H.1
  • 4
    • 0037147189 scopus 로고    scopus 로고
    • Genetic structure of human populations
    • PID: 12493913
    • Rosenberg, N. et al. Genetic structure of human populations. Science 298, 2381–2385 (2002).
    • (2002) Science , vol.298 , pp. 2381-2385
    • Rosenberg, N.1
  • 5
    • 66249116333 scopus 로고    scopus 로고
    • The Genetic structure and history of Africans and African Americans
    • PID: 19407144
    • Tishkoff, S. et al. The Genetic structure and history of Africans and African Americans. Science 324, 1035–1044 (2009).
    • (2009) Science , vol.324 , pp. 1035-1044
    • Tishkoff, S.1
  • 6
    • 0034759330 scopus 로고    scopus 로고
    • Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds
    • PID: 11606545
    • Rosenberg, N. et al. Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159, 699–713 (2001).
    • (2001) Genetics , vol.159 , pp. 699-713
    • Rosenberg, N.1
  • 7
    • 84991434233 scopus 로고    scopus 로고
    • Pritchard, Stephens, and Donnelly on population structure
    • PID: 27729489
    • Novembre, J. Pritchard, Stephens, and Donnelly on population structure. Genetics 204, 391–393 (2016).
    • (2016) Genetics , vol.204 , pp. 391-393
    • Novembre, J.1
  • 8
    • 73349108482 scopus 로고    scopus 로고
    • A Genealogical interpretation of principal components analysis
    • PID: 19834557
    • McVean, G. A Genealogical interpretation of principal components analysis. PLoS Genet. 5, e1000686 (2009).
    • (2009) PLoS Genet. , vol.5
    • McVean, G.1
  • 9
    • 84869026948 scopus 로고    scopus 로고
    • Inference of population splits and mixtures from genome-wide allele frequency data
    • PID: 23166502
    • Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).
    • (2012) PLoS Genet. , vol.8
    • Pickrell, J.K.1    Pritchard, J.K.2
  • 10
    • 85021333511 scopus 로고    scopus 로고
    • admixture graph: an R package for admixture graph manipulation and fitting
    • PID: 28158333
    • Leppala, K., Nielsen, S. V. & Mailund, T. admixture graph: an R package for admixture graph manipulation and fitting. Bioinformatics 33, 1738–1740 (2017).
    • (2017) Bioinformatics , vol.33 , pp. 1738-1740
    • Leppala, K.1    Nielsen, S.V.2    Mailund, T.3
  • 11
    • 84857477622 scopus 로고    scopus 로고
    • Inference of population structure using dense haplotype data
    • PID: 22291602
    • Lawson, D. J. et al. Inference of population structure using dense haplotype data. PLoS Genet. 8, e1002453 (2012).
    • (2012) PLoS Genet. , vol.8
    • Lawson, D.J.1
  • 12
    • 84893945338 scopus 로고    scopus 로고
    • A genetic atlas of human admixture history
    • PID: 24531965
    • Hellenthal, G. et al. A genetic atlas of human admixture history. Science 343, 747–751 (2014).
    • (2014) Science , vol.343 , pp. 747-751
    • Hellenthal, G.1
  • 13
    • 84869057650 scopus 로고    scopus 로고
    • Ancient admixture in human history
    • PID: 22960212
    • Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
    • (2012) Genetics , vol.192 , pp. 1065-1093
    • Patterson, N.1
  • 14
    • 0041817568 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies
    • PID: 12930761
    • Falush, D., Stephens, M. & Pritchard, J. K. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164, 1567–1587 (2003).
    • (2003) Genetics , vol.164 , pp. 1567-1587
    • Falush, D.1    Stephens, M.2    Pritchard, J.K.3
  • 15
    • 84863986908 scopus 로고    scopus 로고
    • Ethiopian genetic diversity reveals linguistic stratification and complex influences on the ethiopian gene pool
    • PID: 22726845
    • Pagani, L. et al. Ethiopian genetic diversity reveals linguistic stratification and complex influences on the ethiopian gene pool. Am. J. Hum. Genet. 91, 83–96 (2012).
    • (2012) Am. J. Hum. Genet. , vol.91 , pp. 83-96
    • Pagani, L.1
  • 16
    • 84940785634 scopus 로고    scopus 로고
    • Evidence for a common origin of blacksmiths and cultivators in the ethiopian ari within the last 4500 years: lessons for clustering-based inference
    • PID: 26291793
    • van Dorp, L. et al. Evidence for a common origin of blacksmiths and cultivators in the ethiopian ari within the last 4500 years: lessons for clustering-based inference. PLoS Genet. 11, e1005397 (2015).
    • (2015) PLoS Genet. , vol.11
    • van Dorp, L.1
  • 17
    • 84903487421 scopus 로고    scopus 로고
    • Early back-to-Africa migration into the horn of Africa
    • PID: 24921250
    • Hodgson, J. A. et al. Early back-to-Africa migration into the horn of Africa. PLoS Genet. 10, e1004393 (2014).
    • (2014) PLoS Genet. , vol.10
    • Hodgson, J.A.1
  • 18
    • 38949170720 scopus 로고    scopus 로고
    • The genetic structure of Pacific islanders
    • PID: 18208337
    • Friedlaender, J. et al. The genetic structure of Pacific islanders. PLoS Genet. 4, e19 (2008).
    • (2008) PLoS Genet. , vol.4
    • Friedlaender, J.1
  • 19
    • 33750437374 scopus 로고    scopus 로고
    • Clines, clusters, and the effect of study design on the inference of human population structure
    • PID: 16355252
    • Rosenberg, N. et al. Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genet. 1, e70 (2005).
    • (2005) PLoS Genet. , vol.1
    • Rosenberg, N.1
  • 20
    • 33846006923 scopus 로고    scopus 로고
    • Population structure and eigenanalysis
    • PID: 17194218
    • Patterson, N., Price, A. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
    • (2006) PLoS Genet. , vol.2
    • Patterson, N.1    Price, A.2    Reich, D.3
  • 21
    • 84957837279 scopus 로고    scopus 로고
    • Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure
    • PID: 26811443
    • Basu, A., Sarkar-Roy, N. & Majumder, P. Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure. Proc. Natl Acad. Sci. USA 113, 1594–1599 (2016).
    • (2016) Proc. Natl Acad. Sci. USA , vol.113 , pp. 1594-1599
    • Basu, A.1    Sarkar-Roy, N.2    Majumder, P.3
  • 22
    • 21244479740 scopus 로고    scopus 로고
    • Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study
    • PID: 15969739
    • Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620 (2005).
    • (2005) Mol. Ecol. , vol.14 , pp. 2611-2620
    • Evanno, G.1    Regnaut, S.2    Goudet, J.3
  • 23
    • 55149118958 scopus 로고    scopus 로고
    • The influence of family groups on inferences made with the program Structure
    • PID: 21586009
    • Anderson, E. C. & Dunham, K. K. The influence of family groups on inferences made with the program Structure. Mol. Ecol. Resour. 8, 1219–1229 (2008).
    • (2008) Mol. Ecol. Resour. , vol.8 , pp. 1219-1229
    • Anderson, E.C.1    Dunham, K.K.2
  • 24
    • 61449263230 scopus 로고    scopus 로고
    • Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance?
    • Frantz, A. C. et al. Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance? J. Appl. Ecol. 46, 493–505 (2009).
    • (2009) J. Appl. Ecol. , vol.46 , pp. 493-505
    • Frantz, A.C.1
  • 25
    • 85020728652 scopus 로고    scopus 로고
    • The K=2 conundrum
    • PID: 28544181
    • Janes, J. K. et al. The K=2 conundrum. Mol. Ecol. 26, 3594–3602 (2017).
    • (2017) Mol. Ecol. , vol.26 , pp. 3594-3602
    • Janes, J.K.1
  • 26
    • 84959305535 scopus 로고    scopus 로고
    • The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem
    • PID: 26856252
    • Puechmaille, S. The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem. Mol. Ecol. Resour. 16, 608–627 (2016).
    • (2016) Mol. Ecol. Resour. , vol.16 , pp. 608-627
    • Puechmaille, S.1
  • 27
    • 78049415423 scopus 로고    scopus 로고
    • Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis
    • PID: 20862358
    • Engelhardt, B. E. & Stephens, M. Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet. 6, e1001117 (2010).
    • (2010) PLoS Genet. , vol.6
    • Engelhardt, B.E.1    Stephens, M.2
  • 28
    • 76749141381 scopus 로고    scopus 로고
    • Ancient human genome sequence of an extinct Palaeo-Eskimo
    • PID: 20148029
    • Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).
    • (2010) Nature , vol.463 , pp. 757-762
    • Rasmussen, M.1
  • 29
    • 84860132302 scopus 로고    scopus 로고
    • Origins and genetic legacy of neolithic farmers and hunter-gatherers in Europe
    • PID: 22539720
    • Skoglund, P. et al. Origins and genetic legacy of neolithic farmers and hunter-gatherers in Europe. Science 336, 466–469 (2012).
    • (2012) Science , vol.336 , pp. 466-469
    • Skoglund, P.1
  • 30
    • 61449135985 scopus 로고    scopus 로고
    • Fast and flexible simulation of DNA sequence data
    • PID: 19029539
    • Chen, G., Marjoram, P. & Wall, J. Fast and flexible simulation of DNA sequence data. Genome Res. 19, 136–142 (2009).
    • (2009) Genome Res. , vol.19 , pp. 136-142
    • Chen, G.1    Marjoram, P.2    Wall, J.3
  • 31
    • 84925238671 scopus 로고    scopus 로고
    • The fine-scale genetic structure of the British population
    • PID: 25788095
    • Leslie, S. et al. The fine-scale genetic structure of the British population. Nature 519, 309–314 (2015).
    • (2015) Nature , vol.519 , pp. 309-314
    • Leslie, S.1
  • 32
    • 67651225410 scopus 로고    scopus 로고
    • Sensitive detection of chromosomal segments of distinct ancestry in admixed populations
    • PID: 19543370
    • Price, A. L. et al. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 5, e1000519 (2009).
    • (2009) PLoS Genet. , vol.5
    • Price, A.L.1
  • 33
    • 34548292504 scopus 로고    scopus 로고
    • PLINK: A tool set for whole-genome association and population-based linkage analyses
    • PID: 17701901
    • Purcell, S. et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 559-575
    • Purcell, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.