Structure
From Vd
Contents |
Structure
General information
The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including microsatellites, RFLPs, SNPs and AFLPs. This method was described in an article by Pritchard, Stephens & Donnelly (2000). Extensions to the method were published by Falush, Stephens and Pritchard (2003). Structure has been widely used for interpreting population structure of humans and other organisms. A selection of interesting references (mainly applications) is shown below.
Structure implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers. Briefly, it assumes a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. It is assumed that within populations, the loci are at Hardy-Weinberg equilibrium, and linkage equilibrium. Loosely speaking, individuals are assigned to populations in such a way as to achieve this. The model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers. The model assumes that markers are not in linkage disequilibrium (LD) within subpopulations, so it can not handle markers that are extremely close together. Starting with version 2.0, weakly linked markers can be used. While the computational approaches implemented are fairly powerful, some care is needed in running the program in order to ensure sensible answers. For example, it is not possible to determine suitable run-lengths theoretically, and this requires some experimentation. The user should consult the Structure manual and the accompanying papers for a description of the uses and limitations of this method.
Home page
http://pritch.bsd.uchicago.edu/structure.html
Manual and references about the method
- http://pritch.bsd.uchicago.edu/software/readme_structure2_1.pdf
- Inference of population structure using multilocus genotype data. J.K. Pritchard, M. Stephens and P. J. Donnelly, 2000. Genetics 155: 945-959.
- Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. D. Falush, M. Stephens and J.K. Pritchard. 2003. Genetics, 164: 1567-1587.
Visualization
Distruct is a program for visualizing Structure output.
Structure-sum is a collection of R scripts for visualizing results of Structure runs without predefined populations.
Examples of applications
- Traces of human migrations in Helicobacter pylori populations. D. Falush, T. Wirth, B. Linz, J.K. Pritchard, M. Stephens and 13 others, 2003. Science, 299: 1582-1585.
- The genetic structure of human populations. N.A. Rosenberg, J.K. Pritchard, J.L. Weber, H.M. Cann, K.K. Kidd, L.A. Zhivotovsky and M.W. Feldman, 2002. Science, 298: 2381-2385. (and technical comment, 2003).
- Dwarf8 polymorphisms associate with variation in flowering time. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES. Nat Genet. 2001 28:286-9.
- Origin of extant domesticated sunflowers in eastern North America. Harter AV, Gardner KA, Falush D, Lentz DL, Bye RA, Rieseberg LH. Nature. 2004 430:201-5.
- Emerging vectors in the Culex pipiens complex. Fonseca DM, Keyghobadi N, Malcolm CA, Mehmet C, Schaffner F, Mogi M, Fleischer RC, Wilkerson RC. Science. 2004 303:1535-8.
- Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Rosenberg NA et al. Genetics. 2001 159:699-713.