Data from: Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon

The genes of the major histocompatibility complex (MHC) are an important component of the vertebrate immune system and can provide insights into the role of pathogen-mediated selection in wild populations. Here we examined variation at the MHC class II peptide binding region in 27 populations of sockeye salmon (Oncorhynchus nerka), distributed among three distinct spawning ecotypes, from a complex of interconnected rivers and lakes in southwestern Alaska. We also obtained genotypes from 90 putatively neutral SNPs for each population to compare the relative roles of demography and selection in shaping the observed MHC variation. We found that MHC divergence was generally partitioned by spawning ecotype (lake beaches, rivers, and streams) and was 30 times greater than variation at neutral markers. Additionally, we observed substantial differences in modes of selection and diversity among ecotypes, with beach populations displaying higher levels of directional selection and lower MHC diversity than the other two ecotypes. Finally, the level of MHC differentiation in our study system was comparable to that observed over much larger geographic ranges, suggesting that MHC variation does not necessarily increase with increasing spatial scale and may instead be driven by fine-scale differences in pathogen communities or pathogen virulence. The low levels of neutral structure and spatial proximity of populations in our study system indicates that MHC differentiation can be maintained through strong selective pressure even when ample opportunities for gene flow exist.genotypes for 90 neutral SNPs for 27 populationsA genepop file containing the genotypes for 88 neutral SNPs from 27 populations. Three mitochondrial SNPs (One_CO1, One_Cytb_17, and One_Cytb_26) were phenotyped according to the methods of Habicht et al. (2010). SNP names correspond to those found in Dann et al. (2012, http://www.adfg.alaska.gov/FedAidpdfs/sp12-12.pdf). Population codes are found in the readme file.wr_88_snps_27_pops_genepop.txtMHC genotypes for 27 populationsGenepop file of MHC genotypes for 27 populations. Genotypes are coded as haplotypes 1-27 based on the order they were discovered. For example haplotype L1-16 in the manuscript would be coded with a 16 in this file. A description of the haplotypes including their sequence can be found in Table S1 of the manuscript. The readme file for this data file includes information on population abbreviations.MHC_genotypes_WR_27_pops_genepop.tx