DOI: 10.5061/dryad.pd827
title: Data from: Genetic evidence for ecological divergence in kokanee salmon

description: The evolution of locally adapted phenotypes among populations that
 experience divergent selective pressures is a central mechanism for
 generating and maintaining biodiversity. Recently, the advent of
 high-throughput DNA sequencing technology has provided tools for
 investigating the genetic basis of this process in natural populations of
 non-model organisms. Kokanee, the freshwater form of sockeye salmon
 (Oncorhynchus nerka), occurs as two reproductive ecotypes, which differ in
 spawning habitat (tributaries vs. shorelines), however outside of the
 spawning season the two ecotypes co-occur in many lakes and lack
 diagnostic morphological characteristics. We used restriction site
 associated DNA (RAD) sequencing to identify 6,145 SNPs and genotype
 kokanee from multiple spawning sites in Okanagan Lake (British Columbia,
 Canada). Outlier tests revealed 18 loci putatively under divergent
 selection between ecotypes, all of which exhibited temporally stable
 allele frequencies within ecotypes. Six outliers were annotated to
 sequences in the NCBI database, two of which matched genes associated with
 early development. There was no evidence for neutral genetic
 differentiation, however, outlier loci demonstrated significant structure
 with respect to ecotype and had high assignment accuracy in mixed
 composition simulations. The absence of neutral structure combined with a
 small number of highly divergent outlier loci is consistent with
 theoretical predictions for the early stages of ecological divergence.
 These outlier loci were then applied to a realistic fisheries scenario in
 which additional RAD sequencing was used to genotype kokanee collected by
 trawl in Okanagan Lake, providing preliminary evidence that this approach
 may be an effective tool for conservation and management.
description: Data S1. All
 SNPsMulti-locus SNP data for
 all individuals of known ecotype (stream-spawning and shore-spawning) at
 6,145 SNP loci identified in this study. Data are presented in two-row
 Structure format; the first column contains sample names, the second
 column contains a number indicating the ecotype of origin (1=stream,
 2=shore), the remaining columns contain genotypes with “-9” used to
 indicate missing data. Sample names use the following convention: -The
 first two characters indicate either the Stream (St) or Shore (Sh)
 ecotype. -The second two characters indicate the sample location: Mission
 Creek (MK), Peachland Creek (PA), Powers Creek (PW), Penticton Creek (PN),
 Northeast shore (NE), Northwest shore (NW), Southeast shore (SE). -The
 four characters following the underscore indicate the year that samples
 were collected (either 2007 or 2010). -The final characters following the
 hyphen indicate the unique sample ID number for the ecotype, location, and
 year.Data S2. Oultier
 LociMulti-locus SNP data for
 all individuals of known ecotype and all trawl samples at the 18 outlier
 loci identified in this study. Data are presented in two-row Structure
 format; the first column contains sample names, the second column contains
 a number indicating the treatment (1=stream, 2=shore, 3=trawl), the
 remaining columns contain genotypes with “-9” used to indicate missing
 data. Sample names use the following convention: -The first two characters
 indicate either the Stream (St) or Shore (Sh) ecotype. -The second two
 characters indicate the sample location: Mission Creek (MK), Peachland
 Creek (PA), Powers Creek (PW), Penticton Creek (PN), Northeast shore (NE),
 Northwest shore (NW), Southeast shore (SE). -The four characters following
 the underscore indicate the year that samples were collected (either 2007
 or 2010). -The final characters following the hyphen indicate the unique
 sample ID number for the ecotype, location, and year. -'Tr' is
 used to indicate samples of unknown ecotype that were collected by
 trawl.