plant DNA analysis of white spruce, Alaska and adjacent Canada

The motivation of the study: We conducted a population genomics analysis of white spruce (Picea glauca) in Eastern Beringia (Alaska and adjacent Canada) in order to infer the location of putative glacial refugia during the last glacial maximum and assess postglacial spread of genetic lineages. Sampling was conducted in Alaska and adjacent Canada in the growing seasons of 2015 and 2016. We have completed DNA extraction using Nucleospin 96 Plant II (Macherey-Nagel Inc.) and use an Illumina custom Spruce SNP BeadChip Array with 6,000 beads to obtain genome-wide SNP (Single nucleotide polymorphism) data. We successfully genotyped samples from 79 locations at 4,205 SNP loci. The genetic ancestry of each individual was assessed with sparse Non-Negative Matrix Factorization (SNMF) algorithms and Discriminant Analysis of Principal Components (DAPC).