Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon

Complex traits often exhibit complex underlying architectures by evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during adaptation is not understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American populations remains unclear, as does potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large SNP array and whole genome re-sequencing to explore the genomic basis of sea age in North American Atlantic Salmon. We found significant associations at the gene and SNP level with a known large-effect locus (vgll3), indicating genetic parallelism, ..., Atlantic Salmon Axiom SNP array data in plink format (.bed, .bim, .fam), and individually matched collected sea age phenotypes for population level and individual level trait association analyses., , # Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon

[https://doi.org/10.5061/dryad.g1jwstqz3](https://doi.org/10.5061/dryad.g1jwstqz3)

This repo contains metadata used in a genomic study of Atlantic Salmon at-sea maturation strategies across North America. The metadata here is as follows:

Salmon_Metadata_Bam_Unique_HD.txt - Individual sex, sea age, and river of origin information for 582 individuals sequenced with whole genome resequencing. Paired reads are available at NCBI with accession PRJNA1083490. Variables are:

* **BAM** - A BAM (Binary Alignment Map) file containing sequenced genomic data, typically used for storing aligned sequence reads from high-throughput sequencing.
* **FGL_ID** - Fisheries Genetics Lab identifier, a unique code assigned by the fisheries genetics laboratory for specimen tracking and database management.
* **RiverCode** - A standardized code representing the river or waterway where the salmon sample was...,