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

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.

[1]  J. Brookfield.  A simple new method for estimating null allele frequency from heterozygote deficiency. , 1996 .

[2]  K. Roeder,et al.  Genomic Control for Association Studies , 1999, Biometrics.

[3]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[4]  M. Feldman,et al.  Genetic Structure of Human Populations , 2002, Science.

[5]  Dipak K Dey,et al.  A Bayesian approach to inferring population structure from dominant markers , 2002, Molecular ecology.

[6]  M. Stephens,et al.  Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. , 2003, Genetics.

[7]  M. Stephens,et al.  Traces of Human Migrations in Helicobacter pylori Populations , 2003, Science.

[8]  P. Taberlet,et al.  The power and promise of population genomics: from genotyping to genome typing , 2003, Nature Reviews Genetics.

[9]  Pierre Duchesne,et al.  AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites , 2003, Molecular ecology.

[10]  O. Hardy,et al.  Estimation of pairwise relatedness between individuals and characterization of isolation‐by‐distance processes using dominant genetic markers , 2003, Molecular ecology.

[11]  P. Hollingsworth,et al.  Neighbour joining trees, dominant markers and population genetic structure , 2004, Heredity.

[12]  B. Weir,et al.  Moment estimation of population diversity and genetic distance from data on recessive markers * , 2004, Molecular ecology.

[13]  L. Bernatchez,et al.  Generic scan using AFLP markers as a means to assess the role of directional selection in the divergence of sympatric whitefish ecotypes. , 2004, Molecular biology and evolution.

[14]  K. Leonard,et al.  Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species , 2005, Molecular ecology.

[15]  C. Camilleri,et al.  Evidence for a large‐scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium , 2006, Molecular ecology.

[16]  L. Bernatchez,et al.  Natural hybrids in Atlantic eels (Anguilla anguilla, A. rostrata): evidence for successful reproduction and fluctuating abundance in space and time , 2006, Molecular ecology.

[17]  E. Randi,et al.  Bayesian analyses of admixture in wild and domestic cats (Felis silvestris) using linked microsatellite loci , 2005, Molecular ecology.