The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure

By Steven T. Kalinowski. Heredity, 2011

387 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/7b2f7728673c9189aa2a84d164c5248b372506f5

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In Genetics

Citations in the corpus

Assessing population structure in the face of isolation by distance: Are we neglecting the problem? (2018, background): “Results obtained indicate that sampling from pre- defined populations affects more the results of analyses than sampling individuals evenly distributed across the landscape (Aurelle & Ledoux, 2013; Kalinowski, 2011; Rosenberg et al., 2005; Schwartz & McKelvey, 2009).”
The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem (2016, methodology): “…other subpopulations, STRUCTURE tends to place individuals from this subpopulation into their own cluster while individuals belonging to the less sampled subpopulations (although not necessarily the most related in terms of evolutionary history) are merged into another cluster (Kalinowski 2011).”
An overview of STRUCTURE: applications, parameter settings, and supporting software (2013, background): “Kalinowski (2011) notes that better clusters are created applying the most realistic K values, so it is prudent to obtain the smallest value of K that maximizes the global likelihood of data— an approach capturing the major underlying population structure in the data without overestimating it.”
Widespread genetic introgression of escaped farmed Atlantic salmon in wild salmon populations (2016, methodology): “This method uses the STRUCTURE program (Pritchard et al., 2000) in a manner that avoids bias from the level of heterogeneity and different sample sizes as described by Kalinowski (2011) and standardizes the estimates of admixture when introgression occurs from several farmed populations.”
The computer program structure for assigning individuals to populations: easy to use but easier to misuse (2017, methodology): “A close inspection of the simulation studies (Kalinowski 2011; Neophytou 2014; Puechmaille 2016) described above shows that they invariably used the default ancestry prior in analysing the simulated data.”