Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecological questions, the scarcity of available DNA sequence data for most species has limited marker development. As the number and diversity of species being targeted for large-scale sequencing has increased, so has the potential for using sequence from sister taxa for marker development in species of interest. We evaluated the use of Oncorhynchus mykiss and Salmo salar sequence data to identify SNPs in three other species (Oncorhynchus tshawytscha, Oncorhynchus nerka and Oncorhynchus keta). Primers designed based on O. mykiss and S. salar alignments were more successful than primers designed based on Oncorhynchus-only alignments for sequencing target species, presumably due to the much larger number of potential targets available from the former alignments and possibly greater sequence conservation in those targets. In sequencing approximately 89 kb we observed a frequency of 4.30 x 10(-3) SNPs per base pair. Approximately half (53/101) of the subsequently designed validation assays resulted in high-throughput SNP genotyping markers. We speculate that this relatively low conversion rate may reflect the duplicated nature of the salmon genome. Our results suggest that a large number of SNPs could be developed for Pacific salmon using sequence data from other species. While the costs of DNA sequencing are still significant, these must be compared to the costs of using other marker classes for a given application.

Single-nucleotide polymorphisms (SNPs) exhibit several attributes that make them appealing as a class of genetic markers for applications in ecology and evolution. Two commonly cited limitations of SNPs in this capacity are that ascertainment bias and natural selection may shape allele frequencies of these markers, thus biasing estimates of population structure. The impacts of ascertainment bias and selection on estimates of population parameters have been demonstrated in a few model species, but their impacts relative to locusspecific variability and other potential complications on structure inferences in wild populations are unclear. We examined 22 allozymes, 9 short tandem repeats (STRs), and 41 SNPs in approximately 1,300 Chinook salmon Oncorhynchus tshawytscha representing 16 collections. We used plots of the genetic differentiation index F ST versus heterozygosity and sequence criteria to identify SNPs that might be under natural selection. We then calculated several measures of population structure based on the three marker sets and a subset of the SNPs from which loci identified as likely targets of natural selection had been removed. Correlation of genetic distances between collections was stronger between allozymes and SNPs than between either of these markers and STRs, suggesting that the influences of marker class bias (e.g., selection and ascertainment bias) were smaller than impacts of locus-specific effects. Divergence estimates between SNP ascertainment populations were not significantly higher when based on SNPs than when based on other markers. Overall divergence (F ST ) was higher for SNPs than for allozymes; however, the choice of F ST estimator influenced the relative values for STRs and SNPs. Estimates of within-population diversity based on allozymes and STRs correlated better with each other than with estimates based on SNPs; such estimates based on SNPs were relatively low for collections from populations outside the geographic coverage of the SNP ascertainment sample.

We report the characterization of 13 single nucleotide polymorphism (SNP) genotyping assays for chum salmon (Oncorhynchus keta). These assays are based on the 5′‐nuclease reaction and thus facilitate high‐throughput genotyping with minimal optimization time. Because data generated using these markers may be transported and combined across laboratories, SNPs offer the potential to reduce the amount of redundant work being done in mixture and migratory studies of chum salmon.

We characterize 38 single nucleotide polymorphism genotyping assays for chum salmon ( Oncorhynchus keta ), an important species for both commercial and subsistence fisheries in western Alaska. These assays are based on the 5′ ′ ′ ′ -nuclease reaction and thus facilitate high-throughput genotyping with minimal optimization time. Minor allele frequency differences (∆ ∆ ∆ ∆ q ) among collections were between 0.01 and 0.50 resulting in per locus F ST estimates of 0.00-0.08 with an average of 0.03.

We characterize 32 single nucleotide polymorphism genotyping assays for resolving genotypic variation in sockeye salmon Oncorhynchus nerka in the Pacific Rim. These assays are based on the 5′ ′ ′ ′ -nuclease reaction and thus facilitate high-throughput genotyping with minimal optimization time. Minor allele frequency differences (∆ ∆ ∆ ∆ q) among collections were between 4.7% and 97.9%, resulting in per locus F ST estimates of 0.02-0.71 with an average of 0.22.