Low-coverage Whole Genome Sequencing (LCWGS) of DNA Sequences from White-Crowned Sparrows (Zonotrichia leucophrys) in Alberta and British Columbia (Canada) and Colorado and Oregon (U.S.)

This dataset contains low-coverage whole genome sequencing (lcWGS) data from multiple subspecies of white-crowned sparrows (Zonotrichia leucophrys) sampled across Alberta and British Columbia (Canada), and Colorado and Oregon (USA), between 2017 and 2021. The samples represent three focal subspecies (Z. l. gambelii, Z. l. oriantha, and Z. l. pugetensis) collected during the breeding season from riparian deciduous habitats to minimize environmental effects on genetic variation. Genomic DNA was extracted from blood or feather samples using a modified salt extraction method, and shotgun sequencing libraries were prepared without PCR amplification, incorporating 8 bp unique barcodes per sample. Sequencing was performed at Genome Quebec using Illumina NovaSeq 6000 S4 PE 150 chemistry. Each sample was sequenced at a depth of ~6.2x to 8.9x coverage. The data processing pipeline includes read alignment to the zebra finch (Taeniopygia guttata) reference genome using BWA, duplicate removal with Picard, indel realignment and overlap clipping, genotype likelihood estimation with SAMtools and BCFtools, and SNP calling with quality and frequency filters. ANGSD was used to infer major/minor alleles, allele frequencies, and to generate population-level variant data for downstream analysis of genetic structure and divergence. This dataset supports investigations into mitonuclear coevolution, population structure, and recent divergence patterns in white-crowned sparrows.