Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales

The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the freshwater resident form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan® SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.

Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon

Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population history and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism genotypic data from archival scale samples, and applied this approach to a study of kokanee salmon (Oncorhynchus nerka) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (> 90% average genotyping across all individuals) and low genotyping error (< 0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrated GT-seq as a valuable tool for collecting genome-wide data from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.

Partitioning maternal and exogenous diet contributions to otolith 87Sr/86Sr in Kokanee Salmon (Oncorhynchus nerka)

Strontium isotopes (87Sr/86Sr) recorded in the otoliths of Pacific Salmon (Oncorhynchus spp.) are commonly used to identify natal origin. For species that migrate at or soon after emergence, the embryonic region of the otolith provides the only record of provenance. However, maternal contribution of Sr from the yolk can confound the isotopic signature of the natal site. We experimentally quantified maternal and exogenous diet contributions to otolith 87Sr/86Sr over embryonic development in Kokanee salmon (O. nerka). Eggs from two populations in isotopically distinct lakes were incubated and reared in a common water source. Timing of developmental events and proportional contribution from yolk to otolith 87Sr/86Sr differed significantly between the two populations. We suggest that the magnitude of difference in 87Sr/86Sr between yolk and water, the relative concentrations of Sr and Ca in these isotopic sources, and population-specific effects on otolith growth and composition contribute to this variation. Understanding how these factors affect otolith 87Sr/86Sr could extend the use of otolith geochemistry for determining provenance to species and populations in which natal site rearing is limited.

Age composition of Chukchi sockeye salmon Oncorhynchus nerka

Long-term data on age composition for Chukchi populations of sockeye salmon are presented. Spawners of 23 ages are recognized in the period 1970-2013 for 10 populations: 2+, 3+, 0.1+, 0.2+, 0.3+, 0.4+, 0.5+, 1.1+, 1.2+, 1.3+, 1.4+, 1.5+, 2.1+, 2.2+, 2.3+, 2.4+, 2.5+, 3.1+, 3.2+, 3.3+, 3.4+, 4.2+, and 4.3+. The brood stock basis is formed by five- and six-year fish of 1-2-year freshwater feeding and 3-year marine feeding. The greatest diversity in the age composition is observed at the northern limit of the Asian sockeye salmon natural habitat - i.e. in the Seutakan and Achchen lake-river systems. The spawners dropped into the sea at the age of 0+ and 1+ years are more common in the populations with prevailing limnophilous forms of sockeye (rivers Khatyrka, Tumanskaya and Anadyr, Seutakan lake-river system), and the spawners dropped at the age 2+ and 3+ years - in the populations with domination of its rheophilous form (Meinypilgyn lake-river system, Orianda and Amaam lagoons). As compared with the sockeye salmon from central spawning areas of the habitat, the Chukchi sockeye has more complicated age composition of reproductive part of stocks, greater duration of marine feeding, females predominance among fast-maturing fish returning after 2 years of marine life, higher portion of males in senior age groups, and minor level of kokanee salmon and jacks. Brief description of spawning and/or feeding ponds for Chukchi sockeye salmon is presented.