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Data from: The genomic architecture of local adaptation in two connected populations of three-spined stickleback

Delaive, Sann1

Published Apr 06, 2026 on Dryad. https://doi.org/10.5061/dryad.cc2fqz6md

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Abstract

Populations often harbor extensive genetic variation shaped by both selection and connectivity, yet the genomic basis of this variation remains incompletely understood. We generated two complementary datasets in three-spined sticklebacks (Gasterosteus aculeatus) to characterize single-nucleotide polymorphisms (SNPs) and structural variants (SVs) across the genome. For SNP discovery, we used Illumina whole-genome sequencing data aligned to the most recent reference genome, including the Y chromosome for males, while excluding the pseudo-autosomal region to minimize alignment errors. Reads were processed to remove duplicates, clipped for overlaps, and locally realigned around indels, achieving an average coverage of 11.2×. After standardizing coverage and removing related individuals, we called SNPs chromosome by chromosome and filtered for biallelic sites with a minor allele frequency > 0.05, coverage between 4× and 35×, and a genotyping success rate exceeding 50%.

To complement this, we generated a structural variant dataset by combining long-read (Nanopore) and short-read (Illumina) sequencing. Nanopore reads >1 kb were mapped and filtered, and SVs were called independently with multiple algorithms for each dataset to maximize confidence. Only SVs detected by at least two callers per dataset were retained, and long- and short-read datasets were then merged. Structural variants were genotyped across all samples using a genome graph approach, with insertions primarily resolved from long-read data and inversions largely from short-read data.

Together, these datasets provide a high-resolution view of genomic variation, capturing both fine-scale SNPs and larger structural variants. They enable the study of recombination landscapes, patterns of differentiation, and the potential role of structural variation in local adaptation across connected populations of three-spined sticklebacks.