Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration

When populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift and accumulation of deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) is necessary to restore levels of genetic diversity and counteract inbreeding depression. Recent work in conservation genomics have studied these processes focusing on genetic diversity of single nucleotide polymorphisms. In contrast, our knowledge about structural genomic variation (insertions, deletions, duplications and inversions) in endangered species is limited. We analysed whole-genome, short-read sequences from 212 wolves from the inbred Scandinavian population, and from neighbouring populations in Finland and Russia, and detected >35,000 structural variants (SVs) after stringent quality and genotype frequency filtering; >26,000 high-confidence variants remained after manual curation. The majority of variants were shorter than 1 kb, with a..., , , # Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration

**Link to paper:**

**Citation:** Smeds, L., Huson, L.S.A. & Ellegren, H. (2024). *Evolutionary Applications*, **17**:e13652.

This datasets contain genotypes for structural variants for Scandinavian, Finnish and Russian wolves, both raw variants from the Smoove pipeline, and the final set of variants after quality filtering, genotype frequency filtering and manual curation.

## Description of the data and file structure

The genotypes are saved in vcf format, and the file structure and names are identical to what's described in the GitHub code.

Genotypes for 212 wolves generated by the Smoove pipeline: *data/smove/annotated/cohort.smoove.square.anno.vcf.gz*

Final variants divided into types (DEL=deletions, DUP=duplications, INV=inversions), quality filtered and manually inspected by 1 curator: *data/curated/1cur.strict.**.*...