Inference of population structure using multilocus genotype data: dominant markers and null alleles

TLDR

Dominant markers such as AFLPs are economical for surveying many loci, yet genotype uncertainty, null alleles, and polyploid calling issues limit conventional population‑structure analyses. The authors propose a simple method to account for genotypic ambiguity in population‑structure studies. They apply this method to AFLP data from whitefish and implement it in the structure software (v2.2). The method is available in structure v2.2 at http://pritch.bsd.uchicago.edu/structure.html.

Abstract

Abstract Dominant markers such as amplified fragment length polymorphisms (AFLPs) provide an economical way of surveying variation at many loci. However, the uncertainty about the underlying genotypes presents a problem for statistical analysis. Similarly, the presence of null alleles and the limitations of genotype calling in polyploids mean that many conventional analysis methods are invalid for many organisms. Here we present a simple approach for accounting for genotypic ambiguity in studies of population structure and apply it to AFLP data from whitefish. The approach is implemented in the program structure version 2.2, which is available from http://pritch.bsd.uchicago.edu/structure.html .