Inferring weak population structure with the assistance of sample group information

By Melissa J. Hubisz, Daniel Falush, Matthew Stephens, J. K. Pritchard. Molecular Ecology Resources, 2009

3,465 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/92c15c860c4fd1248d720d676cbb04e6fb3fc718

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In Genetics

Citations in the corpus

Acute survivorship of the deep-sea coral Lophelia pertusa from the Gulf of Mexico under acidification, warming, and deoxygenation (2014, methodology): “We are also very grateful for the technical skills of the ROV Jason group and the captain and crew of the Ronald H. Brown.”
Association Mapping in Plant Genomes (2012, methodology): “Commonly used algorithms are those of Pritchard & Rosenberg (1999) implemented in the software STRUCTURE (Hubisz et al., 2009; Pritchard et al., 2000).”
Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo‐Pacific cauliflower corals (Pocillopora, Scleractinia) (2013, methodology): “3 (Pritchard et al., 2000; Falush et al., 2003; Hubisz et al., 2009) using 806 complete multilocus genotypes (MLGs).”
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.”
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets (2014, methodology): “STRUCTURE (Pritchard et al. 2000; Falush et al. 2003; Hubisz et al. 2009) takes a Bayesian approach to estimate global ancestry by sampling from the posterior distribution over global ancestry parameters using a Gibbs sampler that appropriately accounts for the conditional independence…”
Remarkably low genetic diversity and strong population structure in common bottlenose dolphins (Tursiops truncatus) from coastal waters of the Southwestern Atlantic Ocean (2014, methodology): “We assumed correlated allele frequencies and an admixture model using sampling location as prior information (LOCPRIOR function) (Hubisz et al. 2009).”
Sphagnum divinum (sp. nov.) and S. medium Limpr. and their relationship to S. magellanicum Brid. (2018, neutral): “3.4 (Pritchard et al., 2000; Falush et al., 2003, 2007; Hubisz et al., 2009).”
Clumpak: a program for identifying clustering modes and packaging population structure inferences across K (2015, methodology): “…Pella & Masuda 2006; Chen et al. 2007; Gao et al. 2007; Huelsen-beck & Andolfatto 2007; Guillot 2008; Alexander et al. 2009; Durand et al. 2009; Hubisz et al. 2009; Shringarpure used of which is S TRUCTURE (Pritchard et al. 2000; Falush et al. 2003, 2007; Hubisz et al. 2009), classify…”
The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem (2016, background): “…population structure in cases of low levels of divergence between subpopulations or when the data set Correspondence: Sebastien J. Puechmaille, Fax +49 3834 86 4252, E-mail: s.puechmaille@gmail.com © 2016 John Wiley & Sons Ltd is small, either in terms of individuals or loci (Hubisz et al. 2009).”
An overview of STRUCTURE: applications, parameter settings, and supporting software (2013, methodology): “Both models can be used with consideration for sampling location information by applying the prior model parameter: LOCPRIOR to the population model (Hubisz et al., 2009).”
Multi-population GWA mapping via multi-task regularized regression (2010, methodology): “We perform an extensive simulation study under various scenarios, using datasets simulated from HapMap genotypes, and demonstrate our method on a real dataset, the lactase-persistence phenotype with the WTCCC genotypes.”
Host population genetic structure and zooxanthellae diversity of two reef-building coral species along the Florida Reef Tract and wider Caribbean (2010, methodology): “The program performed 100,000 calculations (after discarding 10,000 as burn-in) for K = 1 to K = 5 with three repetitions each assuming correlated allele frequencies with a location prior (Hubisz et al. 2009).”
Genetic discontinuity among regional populations of Lophelia pertusa in the North Atlantic Ocean (2011, positive): “First, a Bayesian model-based clustering approach without a priori knowledge of populations (Pritchard et al. 2000) was implemented in STRUCTURE v. 2.3.2 (Hubisz et al. 2009).”
Phylogeography and genetic differentiation along the distributional range of the orchid Epidendrum fulgens: a Neotropical coastal species not restricted to glacial refugia (2011, methodology): “Bayesian assignment analysis (in structure 2.3.3; Hubisz et al., 2009) was used to assign individuals to genetic clusters (K) and estimate admixture proportions (Q) for each individual.”