Contents

Introduction

The program structure implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers. The methods used are introduced in a paper by Pritchard, Stephens and Donnelly (2000), which is the appropriate citation for this program⁴. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, and identifying migrants and admixed individuals. Briefly, we assume 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. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers including microsatellites, SNPs and RFLPs, provided that they are unlinked (or at least, not so tightly linked that they are in linkage-disequilibrium; see section 1.2). While the computational approaches implemented here 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 on the part of the user. The user should consult the accompanying paper (Pritchard et al., 2000a) for a description of the uses and limitations of this method. This document describes the use of this software, and supplements the (Pritchard et al., 2000a) paper.