DOI: 10.5061/dryad.2tm29
title: Data from: Landscape features along migratory routes influence adaptive genomic variation in anadromous steelhead (Oncorhynchus mykiss)

description: Organisms typically show evidence of adaptation to features within their
 local environment. However, many species undergo long-distance dispersal
 or migration across larger geographical regions that consist of highly
 heterogeneous habitats. Therefore, selection may influence adaptive
 genetic variation associated with landscape features at residing sites and
 along migration routes in migratory species. We tested for genomic
 adaptation to landscape features at natal spawning sites and along
 migration paths to the ocean of anadromous steelhead trout (Oncorhynchus
 mykiss) in the Columbia River Basin. Results from multivariate ordination,
 gene-environment association, and outlier analyses using 24,526
 single-nucleotide polymorphisms (SNPs) provided evidence that adaptive
 allele frequencies were more commonly associated with landscape features
 along migration paths than features at natal sites (91.2% versus 8.8% of
 adaptive loci, respectively). Among the 45 landscape variables tested,
 migration distance to the ocean and mean annual precipitation along
 migration paths were significantly associated with adaptive genetic
 variation in three distinct genetic clusters. Additionally, variables such
 as minimum migration water temperature and mean migration slope were
 significant only in inland stocks of steelhead that migrate up to 1200 km
 farther than those near the coast, indicating regional differences in
 migratory selective pressures. This study provides novel approaches for
 investigating migratory corridors and some of the first evidence that
 environment along migration paths can lead to substantial divergent
 selection. Consequently, our approach to understand genetic adaptation to
 migration conditions can be applied to other migratory species when
 migration or dispersal paths are generally known.
description: All landscape variable
 valuesMeasurements for all
 landscape variables both at natal site and along migration paths for every
 collection locality.all_env_Values.xlsxFull RAD Loci StatsLarge table including stats for each RAD locus globally and by population. The RAD sequence, mapping position to the O. mykiss assembly, and outlier classification are included for each locus. Additionally, the genotype success rate, observed heterozygosity, expected heterozygosity, minor allele frequency, and HWE corrected P.val (FDR) are included globally and for each population.full_loci_table.xlsxTop BLAST hitsTop BLAST hits for loci identified by the majority of outlier tests (3/4) and GEA analyses (2/3). For each SNP, the environmental association and category (if applicable) are included. Additionally, the top BLAST hit and nearest gene (within 10 kb) are included with their GO terms.Blast_table_V2.xlsxIndividual Read StatisticsRead statistics for each individual after process_radtags was performed.dry_ind_read_stats.xlsxPairwise FST TablePairwise population FST calculated by hierfstat. FST values are represented between each cluster (k=3), globally between populations, and between populations within each genetic cluster.FST_tables.xlsx