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Introduction to the program structure About Structure Download Software: /structure.html Additional plotting software: distruct, CLUMPP: see Noah Rosenberg’s website. Contributors: Peter Donnelly, Daniel Falush, Jonathan Pritchard, Matthew Stephens, Xiaoquan “William” Wen. Descriptions of the Methods: Inference of population structure using multilocus genotype data. Pritchard, Stephens, Donnelly, 2000. Genetics 155: 945-959. [Basic models] Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies.? Falush, Stephens and Pritchard. 2003. Genetics, 164: 1567-1587. [F model, linkage model] Inference of population structure using multilocus genotype data: dominant markers and null alleles. Falush, Stephens and Pritchard. 2007 Molecular Ecology Notes. [models for AFLPs, etc] Documentation for structure software: Version 2.2. Pritchard, Wen, Falush. 2007. Structure website. [documentation and miscellaneous nuggets of wisdom] Background: defining populations In applications of population genetics it is often useful to classify individuals in a sample into subpopulations. Subjective approaches based on: geographic location linguistic, cultural or physical characters It is difficult to know whether such criteria give rise to a natural assignment in genetic terms. Structure uses multi-locus genotype data to infer population structure Identify subpopulations subsets of the sample with distinct allele frequencies Assign individuals probabilistically to subpopulations Typical data: Individual Locus 1 Locus 2 Locus 3 Locus 4 1 A,A A,A A,C A,A 2 A,B A,A A,B A,A 3 B,B A,B A,A A,A 4 C,C D,E D,E B,C 5 C,C C,D D,D B,D 6 B,C E,E A,E C,E 7 A,C D,D C,D A,D A,B,C,D,E are labels for the different alleles at each locus. A simple model of population structure Individuals in our sample represent a mixture of K unknown populations. Each population is characterized by unknown allele frequencies at each locu