Christian T. Smith

Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon

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 ∼89 kb we observed a frequency of 4.30 × 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 Provide Rapid and Accurate Estimates of the Proportions of U.S. and Canadian Chinook Salmon Caught in Yukon River Fisheries

Abstract As anadromous Chinook salmon Oncorhynchus tshawytscha bound for U.S. and Canadian spawning grounds migrate through the U.S. portion of the Yukon River, they are targeted by several fisheries. To fulfill treaty obligations between the two countries, fishery managers need to know what portion of fish caught in the United States are of Canadian origin. Allozyme markers have been used to assign individuals in mixed fishery samples to U.S. and Canadian portions of the Yukon River; however, these markers are limited by sampling difficulties and by the number of available loci. Microsatellite DNA markers have been considered as an alternative; however, microsatellite data are not readily transportable among laboratories or countries. Here we present the use of single nucleotide polymorphism (SNP) markers that combine the ease of sampling and large potential number of loci of other DNA markers with universally transportable data. Simulations and analyses of known fish suggest that the SNP baseline can be...

Number of Alleles as a Predictor of the Relative Assignment Accuracy of Short Tandem Repeat (STR) and Single-Nucleotide-Polymorphism (SNP) Baselines for Chum Salmon

Abstract Short tandem repeat (STR) markers, which exhibit many alleles per locus, are commonly used to assign fish to their populations of origin. Single-nucleotide polymorphisms (SNPs), which have many technical advantages over STRs, typically exhibit only two alleles per locus. Simulation studies have indicated that the number of independent alleles is a good predictor of the accuracy of genetic markers for fishery applications. Extant STR baselines for salmon Oncorhynchus spp. contain hundreds of alleles, and it has been estimated that hundreds of SNP markers will need to be developed before the SNP baselines will be comparable to the STR baselines. We compared 15 STRs exhibiting 349 independent alleles with 61 SNPs exhibiting 66 independent alleles for accuracy in assigning individuals to closely related populations of chum salmon O. keta. The SNP baseline yielded slightly higher mean accuracies for proportional assignment and comparable accuracies for individual assignment. Based on the number of ind...

Impacts of Marker Class Bias Relative to Locus-Specific Variability on Population Inferences in Chinook Salmon: A Comparison of Single-Nucleotide Polymorphisms with Short Tandem Repeats and Allozymes

Abstract 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 locus-specific 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 populatio...

Use of the 5′-Nuclease Reaction for Single Nucleotide Polymorphism Genotyping in Chinook Salmon

Abstract Migratory and stock composition studies of Chinook salmon Oncorhynchus tshawytscha require genetic markers by which a large number of individuals can be processed in a relatively short time. Given the multijurisdictional geographic range of this species, it is further desirable that genetic markers and the corresponding data be transportable across laboratories. We developed 10 single nucleotide polymorphism (SNP) genotyping assays in Chinook salmon based on the 5′-nuclease reaction. Using these assays, a single technician with two thermal cyclers can generate thousands of genotypes per day. The genotyping assays described here are easy to standardize across laboratories, and the resulting genotype data are readily combined with those collected by means of any other sequence detection platform. The rapid rate at which genotyping may be done using these markers and the fact that SNP data are standardized across laboratories and platforms much more readily than are data from other genetic marker cl...

The genetic variability of the red king crab, Paralithodes camtschatica (Tilesius, 1815) (Anomura, Lithodidae) introduced into the Barents Sea compared with samples from the Bering Sea and Kamchatka region using eleven microsatellite loci

The intentional introduction of red king crab, Paralithodes camtschatica (Tilesius, 1815) in the Barents Sea represent one of a few successful cases and one that now supports a commercial fishery. Introductions of alien species into new environments are often associated with genetic bottlenecks, which cause a reduction in the genetic variation, and this could be important for the spreading potential of the species in the Atlantic Ocean. Red king crab samples collected in the Varangerfjord located on the Barents Sea (northern Norway) were compared with reference crab samples collected from the Bering Sea and Kamchatka regions in the Pacific Ocean. All samples were screened for eleven microsatellite loci, based on the development of species-specific primers. The observed number of alleles per locus was similar, and no reduction in genetic variation, including gene diversity and allelic richness, was detected between the Varangerfjord sample and the reference sample from Okhotsk Sea near Kamchatka, indicating no genetic bottlenecking at least for the microsatellite loci investigated. The same results were found in comparison with the sample from Bering Sea. The level of genetic differentiation among the samples, measured as overall FST across all loci, was relatively low (0.0238) with a range of 0.0035–0.1000 for the various loci investigated. The largest pairwise FST values were found between the Bering Sea and Varangerfjord/Barents Sea samples, with a value of 0.0194 across all loci tested. The lowest value (0.0101) was found between the Varangerfjord and Kamchatka samples. Genetic differentiation based on exact tests on allele frequencies revealed highly significant differences between all pairwise comparisons. The high level of genetic variation found in the Varangerfjord/Barents Sea sample could be of significance with respect to further spreading of the species to other regions in the North Atlantic Ocean.

A Rapid, High-Throughput Technique for Detecting Tanner Crabs Chionoecetes bairdi Illegally Taken in Alaska's Snow Crab Fishery

Abstract Tanner crabs Chionoecetes bairdi and snow crabs C. opilio are both important commercial species for Alaskan fisheries. The geographical ranges of Tanner and snow crabs overlap in the southeastern Bering Sea where a commercial fishery targets the more abundant snow crabs. Morphological identification of these species and of hybrids has proven difficult and impedes monitoring of the harvests. Techniques for the genetic identification of these species have been developed, but it may not be possible to process the desired number of samples because of throughput limitations and sample requirement constraints. Here we present a rapid, high-throughput assay for identifying these species based on single nucleotide polymorphisms (SNPs) in the nuclear rRNA internal transcribed spacer 1 region and the mitochondrial DNA 16S rRNA gene. These SNPs can also be used to infer the direction of hybridization (i.e., the species of each gender).