Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.

By Daniel Falush, Matthew Stephens, J. K. Pritchard. Genetics, 2003

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View Paper: https://www.semanticscholar.org/paper/66ce7e4c2d44343513aac4088571e12337dadc0c

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Citations in the corpus

The estimation of population differentiation with microsatellite markers (2002, methodology): “Despite the development of alternative approaches such as methods assigning individuals to populations (Paetkau et al. 1995; Pritchard et al. 2000), differentiation estimators remain the most commonly used tools to describe population structuring.”
Inferring weak population structure with the assistance of sample group information (2009, methodology): “Although a model of linked loci has been developed (Falush et al. 2003), the methods in this paper are most useful when there is a scarcity of data.”
Association Mapping for Enhancing Maize (Zea mays L.) Genetic Improvement (2011, methodology): “…association analyses including genomic control (Devlin and Roeder, 1999; Mackay, and Powell, 2007), structured association (Pritchard et al., 2000; Falush et al., 2003), principal components analysis (PCA) (Patterson et al., 2006; Price et al., 2006), nonmetric multidimensional scaling (nMDS)…”
Association mapping of yield and its components in rice cultivars (2007, background): “When alpha is close to zero, most individuals are essentially from one population or another whereas alpha >1 means that most individuals are admixed (Falush et al. 2003).”
Estimation of individual admixture: Analytical and study design considerations (2005, methodology): “While the simulation parameters were chosen to approximate the population history of African-Americans [Falush et al., 2003], Simulation 4 is potentially unrepresentative in two important aspects.”
Genotype and environment effects on rice (Oryza sativa L.) grain arsenic concentration in Bangladesh (2010, unknown): “…sub-population identity was known (10 each of the temperate japonica, tropical japonica, indica, aus and basmati/aromatic (Garris et al. 2005)) using a model based Bayesian approach (Falush et al. 2003; Pritchard et al. 2000) and the C.S. Chord distance method (Cavalli-Sforza and Edwards 1967).”
Noninvasive sampling and genetic variability, pack structure, and dynamics in an expanding wolf population (2014, unknown): “3 (Falush et al. 2003).”
Population structure and long-range linkage disequilibrium in a durum wheat elite collection (2005, unknown): “Co-ancestry and population structure analyses, conducted on a genome-wide level using highly informative, well-distributed markers provide valuable information for association studies (Pritchard and Rosenberg 1999; Falush et al. 2003; Flint-Garcia et al. 2003).”
Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe (2010, unknown): “All simulations were independently replicated four times for each K, using the ‘‘admixture’’ and the ‘‘independent’’ allele frequency models (Falush et al. 2003).”
Reconstructing routes of invasion using genetic data: why, how and so what? (2010, methodology): “Standard methods of population structure analysis, such as Fst-based analysis and ⁄ or STRUCTURE (Pritchard et al. 2000), BAPS (Corander et al. 2003) or GENELAND (Guillot et al. 2005) analyses, may be used for this purpose.”
Efficiency of model‐based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci (2005, background): “In organisms where linkage maps are available and thus recombination rates between physically linked loci are known, increased efficiency and detection of older admixture events may be feasible by employing sets of linked markers (Falush et al. 2003).”
Streaming dynamic and distributed inference of latent geometric structures (2018, background): “, 2014) is a fundamental geometric object that underlies the presence of latent topic variables in topic and admixture models (Blei et al., 2003; Pritchard et al., 2000).”
A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective (2008, methodology): “Strictly speaking, the approach applies to an island model (Wright 1931) but it has also been used to describe a fission model (Falush et al. 2003).”
The computer program structure for assigning individuals to populations: easy to use but easier to misuse (2017, methodology): “Pritchard and coworkers (Pritchard et al. 2000; Falush et al. 2003, 2007; Hubisz et al. 2009) developed a Bayesian method to assign individuals with multilocus genotypes into discrete clusters, each corresponding to a Mendelian population characterized by a set of allele frequencies at each locus.”