An international multi‐laboratory project was conducted to develop a standardized DNA database for Chinook salmon (Oncorhynchus tshawytscha). This project was in response to the needs of the Chinook Technical Committee of the Pacific Salmon Commission to identify stock composition of Chinook salmon caught in fisheries during their oceanic migrations. Nine genetics laboratories identified 13 microsatellite loci that could be reproducibly assayed in each of the laboratories. To test that the loci were reproducible among laboratories, blind tests were conducted to verify scoring consistency for the nearly 500 total alleles. Once standardized, a dataset of over 16,000 Chinook salmon representing 110 putative populations was constructed ranging throughout the area of interest of the Pacific Salmon Commission from Southeast Alaska to the Sacramento River in California. The dataset differentiates the major known genetic lineages of Chinook salmon and provides a tool for genetic stock identification of samples collected from mixed fisheries. A diverse group of scientists representing the disciplines of fishery management, genetics, fishery administration, population dynamics, and sampling theory are now developing recommendations for the integration of these genetic data into ocean salmon management.

Low genetic divergence at neutral loci among populations is often the result of high levels of contemporary gene flow. Western Alaskan summer-run chum salmon (Oncorhynchus keta) populations demonstrate weak genetic structure, but invoking contemporary gene flow as the basis for the low divergence is problematic because salmon home to their natal streams and some of the populations are thousands of kilometers apart. We used genotypes from microsatellite and single nucleotide polymorphism loci to investigate alternative explanations for the current genetic structure of chum salmon populations from western Alaska. We also estimated current levels of gene flow among Kuskokwim River populations. Our results suggest that weak genetic structure is best explained by physical connections that occurred after the Holocene Thermal Maximum among the Yukon, Kuskokwim, and Nushagak drainages that allowed gene flow to occur among now distant populations.

Summary Genetic tools are commonly used for conservation and management of at‐risk species. Individuals are often sampled from mixtures that are composed of many populations, which creates a need to assign individuals to their source. This can be problematic when the genetic divergence among source populations is weak but can be improved using adaptive genetic loci, which should show stronger levels of divergence. We previously reported a signature of positive selection in the mitochondrial‐encoded ND5 subunit of complex I in diverse taxa. The respiratory machinery of the mitochondria in salmonids is composed of more than 80 nuclear genes and there is substantial interaction between nuclear and mitochondrial expressed gene products. Recent studies report adaptive variation in mitochondrial function as well as co‐evolution between mitochondrial and nuclear genomes. We used potentially adaptive ND5‐based mitochondrial haplotypes to identify nuclear loci that would display increased levels of genetic divergence compared to neutral nuclear loci in chum salmon (Oncorhynchus keta). Populations in a geographic area the size of France have previously demonstrated weak genetic divergence even after substantial discovery efforts by multiple laboratories for allozymes, microsatellites and SNPs over the last two decades. We used RAD‐based next‐generation sequencing and identified a nuclear‐encoded subunit of mitochondrial complex I that was a significant FST outlier and 14 other divergent nuclear markers that improve genetic assignment of individuals to their population of origin relative to assignments based on neutral markers alone. This work demonstrates how a known adaptive marker can be leveraged to increase the probability of identifying divergent markers for applied genetics tools that may be biologically linked to it.

Chinook salmon Oncorhynchus tshawytscha support important subsistence and commercial fisheries throughout the Yukon River. Low returns and diverse user groups have made management of these fisheries contentious and have necessitated information on the origin of the spawning migration and harvest. Here we compare estimates of individual assignment and stock composition derived from genetic and radiotelemetry data collected from the same Chinook salmon. Radiotelemetry and genetic individual assignments were highly concordant. Agreement between methods for individual assignment was 79% to region and 93% to country when using the most probable genetic criterion, improving to 94% for region and 98% for country when using the ≥95% probability genetic criterion; however, under the more stringent criterion, fewer individuals could be assigned. Further analysis showed that estimates of stock composition based on radiotelemetry and genetic methods were within 6% of each other and were not significantly different. The concordance between estimates of individual assignment and stock composition from the radiotelemetry and genetic methods indicates that both methods are credible tools for fishery assessment of Yukon River Chinook salmon. Received October 14, 2011; accepted April 17, 2012

We present an application of the genetic mark–recapture technique to estimate salmon run size in a large river. Application of this technique requires modifications to estimation methodology. Under a typical Lincoln–Petersen mark–recapture estimation of salmon run size (N = M/p), individual fish are captured and marked (M) in the lower river and are recaptured (m) at escapement (E: the number of fish reached spawning ground) monitoring sites selected upriver where the proportion of marked individuals (p = m/E) is estimated. In this genetic mark–recapture technique, the marked individuals are not captured and recaptured, but rather the naturally distinctive genetic (marked) population is captured and recaptured. Genetically, the lower river population is a mixture of multiple genetic stocks, whereas the upriver escapement population consists of a single genetic stock. Hence, the mark–recapture experiment (N = M/pm) is reversed. The proportion of “marked” genetic stock (pm) is estimated in the lower river, and size of the “marked” stock in the lower river (M) is estimated by summing its upriver escapement (Em) and harvest (Cm) between the lower and upper portions of river (M = Em+Cm). The harvest is calculated as a product of total upriver harvest (C) and the proportion of the “marked” stock (pcm) in the harvest (Cm = C·pcm). Further, when the proportion of multiple genetic stocks (pk) is identified, stock‐specific run size (Nk = N·pk), escapement (Ek = Nk−Ck, where Ck = C ·pck), and exploitation rate (Exk = Ck /Nk) can also be estimated, which provides substantially more information than does the conventional approach. We illustrate an application of this technique for estimating run size of Chinook Salmon Oncorhynchus tshawytscha in the Yukon River, Alaska. Received June 6, 2013; accepted November 20, 2013