An overview of STRUCTURE: applications, parameter settings, and supporting software

Abstract

Objectives: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE.Methods: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS.Conclusion: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data.

Hybridization in Plants: Old Ideas, New Techniques

“…Model-based methods are widely used to infer global (genomeaverage) and local (locus-specific) ancestry from population variation data (Gompert and Buerkle, 2013;Liu et al, 2013). For example, the program STRUCTURE uses a hierarchical Bayesian model to identify subpopulations and estimate global ancestry for each sampled individual based on allele frequency data (Pritchard et al, 2000;Porras-Hurtado et al, 2013) and has been extended to estimate locus-specific ancestry (Falush et al, 2003). Maximum likelihood-based programs, like ADMIXTURE (Alexander et al, 2009), allow for less computationally intensive estimates of genetic ancestry.…”

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

“…For example, a homozygote call with 15x coverage comprising 3x forward strand coverage and 12x reverse strand coverage was manually corrected to a no-call, whereas a homozygote call with 15x coverage split into 7x forward coverage and 8x reverse coverage was maintained. Population analyses with STRUCTURE v. 2.3.4 [37] were performed following previous guidelines [38]. One to nine populations (K=1 to K=9) were assumed and five replicate analyses were executed for each K value.…”

Variability and genetic structure of yellow passion fruit (Passiflora edulis f. flavicarpa Degener) in Colombia using microsatellite DNA markers

“…The used program Structure was v.2.3.4 (Pritchard et al, 2000). The number of subpopulations (K-value) was set from 2 to 10, using 20 independent runs with a burn-in period of 100,000 steps, and afterwards 200,000 Monte Carlo Markov Chain (MCMC) interactions after burn-ins, following the admixture ancestry model and correlated allele frequencies, which is appropriate for self-incompatible allogamous species (Porras-Hurtado et al, 2013). Results of runs with the highest ln Pr (G|K) value of the 20 runs were chosen and presented as bar plots according to the Evanno et al (2005) method.…”