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.

Analysis of Sr and Ba profiles measured by ultra-high-resolution mass spectrometry LA-ICP-MS in otoliths of juvenile anadromous sockeye salmon Oncorhynchus nerka in the early marine life-history stage as a proxy for fresh to marine water transition

The strontium (Sr) and barium (Ba) profiles in otoliths of juvenile sockeye salmon Oncorhynchus nerka from British Columbia are measured using a Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) system and analyzed. The highest possible measurement resolution (near-daily) was used to assess variability and repeatability of the breakpoint (marine entry) estimates inferred from Sr:Ca and Ba:Ca ratios. Such resolution for the otolith chemical composition (to an accuracy of 2 μm) was reached using the rotating slit, which width was close to the daily circulus width of the otoliths. So, daily or 2-day changes in the elemental composition were recorded during the period of transition to the marine environment. Sr profiles were generally similar among the fish, starting with low values of Sr:Ca in the fresh water and increasing sharply after the marine entry. The Ba:Ca signal was more complex, showing in most cases a dramatic increase immediately before the breakpoint. Besides, multiple peaks in the Ba profiles were recorded prior to the marine transition with a significant difference of their number between fish from different populations. A breakpoint was detectable in the Ba profiles 3–11 µm prior to its appearance in the Sr profiles. The complexity of Ba profiles may cause erroneous estimates of the marine entry date; thus, the Sr signal is a more reliable marker of marine transition for juvenile sockeye.

Migration and survival of Okanagan River Sockeye Salmon Oncorhynchus nerka, 2012–2019

Background Okanagan River Sockeye Salmon Oncorhynchus nerka (Okanagan Sockeye) are one of two remaining self-sustaining Sockeye Salmon populations in the Columbia River Basin. We used detection histories of smolts implanted with passive integrated transponder (PIT) tags between 2012 and 2019 to estimate survival and behavioral metrics during reintroduction efforts and changing environmental conditions over the monitoring period. Results Smolts migrating to McNary Dam, whose route includes 130 km of the Okanagan River and 388 km of the Columbia River, generally had high survival (mean of 87.0% per 100 km) and fast migration speeds (up to 50 km/day) relative to other salmonids in the region. Smolt-to-adult returns (SARs) ranged from 0.4 to 6.1% and were greater for fish originating from Skaha Lake compared to cohorts tagged in Osoyoos Lake. Most adults returned after 2 years in the ocean (69%), followed by jacks (27%), and adults that spent 3 years at sea (4%), though Skaha Lake adults had a significantly younger age structure than cohorts from Osoyoos Lake. Survival of adults from Bonneville Dam (rkm 235) upstream to Wells Dam (rkm 830) was generally high (80–92%), and migration speed decreased in upstream reaches. Survival from Wells Dam to the Okanagan River was only estimable in 2018, where 64% of adults survived to the spawning grounds. The upstream migration of adult Okanagan Sockeye was significantly compromised during the drought of 2015 when less than 5% of Okanagan Sockeye that returned to the Columbia River reached spawning grounds. Conclusions Our results indicate that Okanagan Sockeye have exceptional survival and migratory ability relative to other salmonids, though poor ocean conditions combined with warming water temperatures in freshwater habitats in recent years have the potential to devastate the population. The success of reintroduction efforts to increase spatial structure and diversity of Okanagan Sockeye is, therefore, critical to maintaining the population in years to come.

The effect of total dissolved gas supersaturation on gas bubble trauma in juvenile rainbow trout (Oncorhynchus mykiss), juvenile kokanee (Oncorhynchus nerka) and two age classes of white sturgeon (Acipenser transmontanus).

Hydroelectric dams are an important source of electricity globally, but they can also cause total dissolved gas (TDG) supersaturation in rivers. Total dissolved gas supersaturation can harm fish through a condition called gas bubble trauma (GBT). Gas bubble trauma has been studied primarily in salmonids, such as rainbow trout and steelhead salmon (Oncorhynchus mykiss), but seldomly in non-salmonids like white sturgeon (Acipenser transmontanus). We assessed the vulnerability of juvenile rainbow trout (<1 year old), juvenile kokanee (Oncorhynchus nerka) (<1 year old), and two ages of white sturgeon (<1 year old and 3+ year old) to GBT. Bubble formation and the time to 50% loss of equilibrium (LOE) was quantified during exposure to nominal levels of 100, 115, 120 and 130% TDG. We predicted that all three species would show similar times to 50% LOE at a given TDG level. However, time to LOE was longer, the proportion of fish with external symptoms of GBT was lower and the proportion of fish with bubbles in the gills was higher or lower (dependant on age) in white sturgeon relative to rainbow trout and kokanee at a given TDG. The physiological basis for the difference is not known. However, it is important to consider species specific differences in TDG sensitivity in the conservation of vulnerable species