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G. Guillot (2008)
Inference of structure in subdivided populations at low levels of genetic differentiation - the correlated allele frequencies model revisitedBioinformatics, 24 19
D. Falush, M. Stephens, J. Pritchard (2007)
Inference of population structure using multilocus genotype data: dominant markers and null allelesMolecular Ecology Notes, 7
David Alexander, K. Lange (2011)
Enhancements to the ADMIXTURE algorithm for individual ancestry estimationBMC Bioinformatics, 12
C. Whitfield, S. Behura, S. Berlocher, A. Clark, J. Johnston, W. Sheppard, D. Smith, A. Suarez, Daniel Weaver, N. Tsutsui (2006)
Thrice Out of Africa: Ancient and Recent Expansions of the Honey Bee, Apis melliferaScience, 314
G. Evanno, S. Regnaut, J. Goudet (2005)
Detecting the number of clusters of individuals using the software structure: a simulation studyMolecular Ecology, 14
D. Falush, M. Stephens, J. Pritchard (2003)
Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.Genetics, 164 4
J. Corander, P. Waldmann, M. Sillanpää (2003)
Bayesian analysis of genetic differentiation between populations.Genetics, 163 1
S Ratnasingham, PD Hebert (2013)
A DNA‐based registry for all animal species: the Barcode index number (BIN) systemProceedings of the National Academy of Sciences of the United States of America, 8
Sijia Wang, Cecil Lewis, M. Jakobsson, Sohini Ramachandran, N. Ray, G. Bedoya, W. Rojas, M. Parra, J. Molina, C. Gallo, G. Mazzotti, G. Poletti, K. Hill, A. Hurtado, D. Labuda, W. Klitz, R. Barrantes, M. Bortolini, F. Salzano, M. Petzl-Erler, L. Tsuneto, E. Llop, F. Rothhammer, L. Excoffier, M. Feldman, N. Rosenberg, A. Ruiz-Linares (2007)
Genetic Variation and Population Structure in Native AmericansPLoS Genetics, 3
Hong Gao, S. Williamson, C. Bustamante (2007)
A Markov Chain Monte Carlo Approach for Joint Inference of Population Structure and Inbreeding Rates From Multilocus Genotype DataGenetics, 176
N. Rosenberg, T. Burke, K. Elo, M. Feldman, P. Freidlin, M. Groenen, J. Hillel, A. Mäki-Tanila, Michèle Tixier-Boichard, A. Vignal, K. Wimmers, S. Weigend (2001)
Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds.Genetics, 159 2
NA Rosenberg, E Woolf, JK Pritchard (2001b)
Distinctive genetic signatures in the Libyan JewsGenetic Epidemiology, 98
C. Driscoll, M. Menotti-Raymond, A. Roca, K. Hupe, W. Johnson, E. Geffen, E. Harley, M. Delibes, D. Pontier, A. Kitchener, N. Yamaguchi, S. O'Brien, D. Macdonald (2007)
The Near Eastern Origin of Cat DomesticationScience, 317
T. Pemberton, Chaolong Wang, Jun Li, N. Rosenberg (2010)
Inference of unexpected genetic relatedness among individuals in HapMap Phase III.American journal of human genetics, 87 4
Corander (2008a)
Enhanced Bayesian modelling in BAPS software for learning genetic structures of populationsBMC Bioinformatics, 9
Anton Enright, S. Dongen, C. Ouzounis (2002)
An efficient algorithm for large-scale detection of protein families.Nucleic acids research, 30 7
J. Pritchard, Matthew Stephens, P. Donnelly (2000)
Inference of population structure using multilocus genotype data.Genetics, 155 2
D. Shen, Alberto, Bardelli, J. Sager, Steve Szabo, J. Ptak, Natalie, Silliman, B. Peters, M. Heijden, G. Riggins, M. Steven, Powell, S. Markowitz, W. Kenneth, Kinzler (2004)
Genetic Structure of the Purebred Domestic Dog
Gilles Guillot, A. Estoup, F. Mortier, J. Cosson (2005)
A Spatial Statistical Model for Landscape GeneticsGenetics, 170
L. Kaufman, P. Rousseeuw (1991)
Finding Groups in Data: An Introduction to Cluster Analysis
N. Rosenberg (2003)
distruct: a program for the graphical display of population structureMolecular Ecology Notes, 4
Hua Tang, Jie Peng, Pei Wang, N. Risch (2005)
Estimation of individual admixture: Analytical and study design considerationsGenetic Epidemiology, 28
J. Huelsenbeck, P. Andolfatto, Edna Huelsenbeck (2011)
Structurama: Bayesian Inference of Population StructureEvolutionary Bioinformatics Online, 7
Karoline Faust, J. Sathirapongsasuti, J. Izard, N. Segata, D. Gevers, J. Raes, C. Huttenhower (2012)
Microbial Co-occurrence Relationships in the Human MicrobiomePLoS Computational Biology, 8
J. Pritchard, P. Donnelly (2001)
Case-control studies of association in structured or admixed populations.Theoretical population biology, 60 3
Y. Verkuil, T. Piersma, J. Jukema, L. Zwarts, A. Baker, J. Hooijmeijer (2012)
The interplay between habitat availability and population differentiationBiological Journal of The Linnean Society, 106
J. Corander, J. Siren, E. Arjas (2008)
Bayesian spatial modeling of genetic population structureComputational Statistics, 23
S. Ratnasingham, P. Hebert (2013)
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) SystemPLoS ONE, 8
O. François, S. Ancelet, G. Guillot (2006)
Bayesian Clustering Using Hidden Markov Random Fields in Spatial Population GeneticsGenetics, 174
E. Durand, F. Jay, O. Gaggiotti, O. François (2009)
Spatial inference of admixture proportions and secondary contact zones.Molecular biology and evolution, 26 9
K. Weiss, J. Long (2009)
Non-Darwinian estimation: my ancestors, my genes' ancestors.Genome research, 19 5
D. Altshuler, R. Gibbs, L. Peltonen, E. Dermitzakis, S. Schaffner, F. Yu, P. Bonnen, P. Bakker, P. Deloukas, S. Gabriel, R. Gwilliam, S. Hunt, M. Inouye, Xiaoming Jia, A. Palotie, Melissa Parkin, P. Whittaker, K. Chang, A. Hawes, L. Lewis, Yanru Ren, D. Wheeler, D. Muzny, Chris Barnes, K. Darvishi, M. Hurles, Joshua Korn, K. Kristiansson, Charles Lee, Steven McCarrol, J. Nemesh, A. Keinan, S. Montgomery, Samuela Pollack, A. Price, N. Soranzo, C. Gonzaga‐Jauregui, V. Anttila, W. Brodeur, M. Daly, S. Leslie, G. McVean, L. Moutsianas, Huy Nguyen, Qingrun Zhang, Mohammed Ghori, R. McGinnis, W. McLaren, F. Takeuchi, S. Grossman, I. Shlyakhter, E. Hostetter, Pardis Sabeti, C. Adebamowo, M. Foster, D. Gordon, J. Licinio, M. Manca, P. Marshall, I. Matsuda, D. Ngare, V. Wang, Deepa Reddy, C. Rotimi, C. Royal, R. Sharp, Changqing Zeng, L. Brooks, J. Mcewen (2010)
Integrating common and rare genetic variation in diverse human populationsNature, 467
J. Corander, P. Waldmann, P. Marttinen, M. Sillanpää (2004)
BAPS 2: enhanced possibilities for the analysis of genetic population structureBioinformatics, 20 15
Jeffry Thornsberry, M. Goodman, J. Doebley, S. Kresovich, D. Nielsen, E. Buckler (2001)
Dwarf8 polymorphisms associate with variation in flowering timeNature Genetics, 28
(2014)
The complex genealogy of jewish populations, pp. 148. The Department of Zoology
M. Jakobsson, Sonja Scholz, P. Scheet, J. Gibbs, Jenna Vanliere, H. Fung, Zachary Szpiech, J. Degnan, Kai Wang, R. Guerreiro, J. Bras, Jennifer Schymick, D. Hernandez, B. Traynor, J. Simón-Sánchez, M. Matarin, A. Britton, J. Leemput, Ian Rafferty, M. Bucan, H. Cann, J. Hardy, N. Rosenberg, A. Singleton (2008)
Genotype, haplotype and copy-number variation in worldwide human populationsNature, 451
Éric Frichot, François Mathieu, Théo Trouillon, Guillaume Bouchard, O. François (2014)
Fast and Efficient Estimation of Individual Ancestry CoefficientsGenetics, 196
(2009)
wrote the manuscript. Data Accessibility CLUMPAK is freely available for online use and for download at http
Kimberly Gilbert, R. Andrew, Dan Bock, Michelle Franklin, N. Kane, Jean-Sébastien Moore, Brook Moyers, S. Renaut, Diana Rennison, Thor Veen, T. Vines (2012)
Recommendations for utilizing and reporting population genetic analyses: the reproducibility of genetic clustering using the program structureMolecular Ecology, 21
J. Huelsenbeck, P. Andolfatto (2007)
Inference of Population Structure Under a Dirichlet Process ModelGenetics, 175
F. Breseghello, M. Sorrells (2006)
Association Mapping of Kernel Size and Milling Quality in Wheat (Triticum aestivum L.) CultivarsGenetics, 172
S. Manel, O. Gaggiotti, R. Waples (2005)
Assignment methods: matching biological questions with appropriate techniques.Trends in ecology & evolution, 20 3
C. Hoggart, E. Parra, M. Shriver, C. Bonilla, R. Kittles, D. Clayton, P. McKeigue (2003)
Control of confounding of genetic associations in stratified populations.American journal of human genetics, 72 6
S Manel, OE Gaggiotti, RS Waples (2005)
Assignment methods: matching biological questions with appropriate techniquesTheoretical Population Biology, 20
(2008)
BMC Bioinformatics BioMed Central Methodology article Enhanced Bayesian modelling in BAPS software for learning genetic
S. Dongen (2008)
Graph Clustering Via a Discrete Uncoupling ProcessSIAM J. Matrix Anal. Appl., 30
S. Dongen (2000)
Graph clustering by flow simulation
Dent Earl, B. Vonholdt (2012)
STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno methodConservation Genetics Resources, 4
Noah Rosenberg, Eilon Woolf, J. Pritchard, Tamar Schaap, D. Gefel, Isaac Shpirer, U. Lavi, Batsheva Bonne-Tamir, J. Hillel, Marcus Feldman (2001)
Distinctive genetic signatures in the Libyan Jews.Proceedings of the National Academy of Sciences of the United States of America, 98 3
JM Thornsberry, MM Goodman, J Doebley (2001)
Dwarf8 polymorphisms associate with variation in flowering timeGenome Research, 28
M. Jakobsson, N. Rosenberg (2007)
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structureBioinformatics, 23 14
JK Pritchard, P Donnelly (2001)
Case‐control studies of association in structured or admixed populationsMolecular Ecology Notes, 60
David Alexander, J. Novembre, K. Lange (2009)
Fast model-based estimation of ancestry in unrelated individuals.Genome research, 19 9
Anil Jain, R. Dubes (1988)
Algorithms for Clustering Data
Jun Li, D. Absher, Hua Tang, Audrey Southwick, A. Casto, Sohini Ramachandran, H. Cann, G. Barsh, M. Feldman, L. Cavalli-Sforza, R. Myers
Supporting Online Material Materials and Methods Figs. S1 to S3 Tables S1 to S5 References Worldwide Human Relationships Inferred from Genome-wide Patterns of Variation
J Pella, M Masuda (2006)
The Gibbs and split‐merge sampler for population mixture analysis from genetic data with incomplete baselinesPLoS ONE, 63
Z. Gompert, C. Buerkle (2013)
Analyses of genetic ancestry enable key insights for molecular ecologyMolecular Ecology, 22
Chibiao Chen, E. Durand, F. Forbes, O. François (2007)
Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison studyMolecular Ecology Notes, 7
J. Pella, M. Masuda (2006)
The Gibbs and splitmerge sampler for population mixture analysis from genetic data with incomplete baselinesCanadian Journal of Fisheries and Aquatic Sciences, 63
N. Kopelman, L. Stone, Chaolong Wang, D. Gefel, M. Feldman, J. Hillel, N. Rosenberg (2009)
Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populationsBMC Genetics, 10
Shancen Zhao, Pingping Zheng, S. Dong, Xiangjiang Zhan, Qi Wu, Xiaosen Guo, Yibo Hu, Weiming He, Shanning Zhang, Wei Fan, Lifeng Zhu, Dong Li, Xuemei Zhang, Quan Chen, He-min Zhang, Zhihe Zhang, Xue-lin Jin, Jinguo Zhang, Huanming Yang, J. Wang, Jun Wang, F. Wei (2012)
Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptationNature Genetics, 45
H Tang, J Peng, P Wang, NJ Risch (2005)
Estimation of individual admixture: analytical and study design considerationsPLoS Genetics, 28
NM Kopelman, L Stone, C Wang (2009)
Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populationsCanadian Journal of Fisheries and Aquatic Sciences, 10
N. Rosenberg, J. Pritchard, J. Weber, H. Cann, K. Kidd, L. Zhivotovsky, M. Feldman (2002)
Genetic Structure of Human PopulationsScience, 298
M. Hubisz, D. Falush, M. Stephens, J. Pritchard (2009)
Inferring weak population structure with the assistance of sample group informationMolecular Ecology Resources, 9
Noah Rosenberg (2006)
Standardized Subsets of the HGDP‐CEPH Human Genome Diversity Cell Line Panel, Accounting for Atypical and Duplicated Samples and Pairs of Close RelativesAnnals of Human Genetics, 70
S. Shringarpure, E. Xing (2009)
mStruct: Inference of Population Structure in Light of Both Genetic Admixing and Allele MutationsGenetics, 182
R. Horn, Charles Johnson (1991)
Topics in Matrix Analysis
Kevin Dawson, Khalid Belkhir (2001)
A Bayesian approach to the identification of panmictic populations and the assignment of individuals.Genetical research, 78 1
The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population‐genetic data analysis. Application of model‐based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model‐based population structure analyses. For analysing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp. Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak, available at http://clumpak.tau.ac.il, simplifies the use of model‐based analyses of population structure in population genetics and molecular ecology.
Molecular Ecology Resources – Wiley
Published: Jan 1, 2015
Keywords: ; ; ;
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