Admixture in New Zealand isolates
In founder events involving a few initial founders, the small effective population size will result in strong effect of genetic drift and increased linkage disequilibrium, often resulting in large changes in allele and haplotype frequencies. Thus, founder events complicate estimates of the relationship between populations using allele frequency-based methods, such as Admixture. However, the haplotype structure contains information that may be used to identify the relationship between populations. To utilize the haplotype structure to infer the relationship between the New Zealand population and the European and Japanese populations we performed a local ancestry assignment using PCAdmix (Brisbin et al. 2012) with both Europe and Japan as ancestral groups and the New Zealand isolates as an admixed population. PCAdmix uses phased haplotypes derived from both reference panels and the admixed isolates to infer the ancestry of genomic windows. We used Beagle 4.0 (Browning & Browning 2007) to phase the data for each population, without imputation, using default settings. The local ancestry was inferred with PCAdmix, which uses principal components analysis in windows of 10 SNPs along the genome to identify ancestry from a set of predefined potential ancestral populations. Thus, in the case of the two individuals from New Zealand, the populations from Europe and Japan were defined as the ancestral populations.