Genetic Stock Identification Reveals That Angler Harvest Is Representative of Cryptic Stock Proportions in a High‐Profile Kokanee Fishery

Abstract

Estimating fishery harvest and spawning escapement (spawning stock size) are critical components of fisheries management; however, they can be particularly challenging to measure in systems where visually indistinguishable, but reproductively isolated populations mix within a single fishing area. Genetic stock identification is a common tool used in such mixed‐stock fisheries to improve estimates of spawning escapement and productivity; however, there are few references for management applications, particularly for inland recreational fisheries. The kokanee Oncorhynchus nerka population in Wood Lake, British Columbia, is a highly productive and valuable mixed‐stock fishery that includes two reproductively distinct ecotypes: shore‐ and stream‐spawning. Enumeration of shore‐spawning kokanee is logistically challenging, as the spawning population is not confined to a defined area or depth like stream‐spawners. Here, we combined in‐lake sampling (angler harvest and age‐0 trawl samples) over a 9‐year period (2008–2016) with genetic stock identification and Bayesian statistics to develop a new method for enumerating shore‐spawning kokanee. Our results suggest that angler‐harvested kokanee are representative of the spawner age structure and stock proportions. Therefore, we used the angler harvest sample combined with known stream‐spawner escapement to reconstruct the shore‐spawner escapement time series. Shore‐spawner abundance varied between 2,040 spawners and 13,460 spawners across years, which is over four times that previously predicted using the peak estimate of visual survey counts. Our results demonstrate the recovery of both the shore‐ and stream‐spawning kokanee in Wood Lake following a well‐documented crash in 2011 and suggest that a larger harvestable surplus is available for this high‐value kokanee fishery.

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

“…To compare assignment results across methods, we selected previously extracted DNA samples from [ 7 ] that were previously genotyped at 10 microsatellite loci (2012 trawl survey, n = 105) and at 24 SNP loci via TaqMan ® genotyping assays (2014 angler survey, n = 84). We genotyped these samples using the final optimized GT-seq panel and a Mid Output Reagent Kit (300 cycles) on an Illumina MiniSeq.…”

“…All individuals were genotyped by locus and individual, and filtered at a 50% missing data threshold in PLINK [ 49 ], as the identification of reproductive ecotypes within this system was sufficient at this threshold and allowed for the retention of samples that may have missing data due to lower quality DNA. In order to stay consistent with the stock assignment approaches used in the long-term time-series [ 7 ], we calculated the probability that an individual belongs to Wood Lake shore- or stream-spawning kokanee using the reference populations from the RADseq_kokanee baseline and the Rannala and Mountain (1997) method in ONCOR [ 46 , 47 ]. In addition, we used a Bayesian method to assign individuals to Wood Lake shore or stream-spawning kokanee as implemented in STRUCTURE 2.3.3 [ 42 , 43 ].…”

“…For mixed-stock fish populations, traditional survey methods can be inaccurate due to overlaps in morphology between closely-related life history forms [ 7 ]. In response, genetic stock identification (GSI) techniques have been developed to assess stock proportions by delineating individuals by genetic origin and considering barriers to gene flow [ 8 – 10 ].…”

Extirpation of a native population following a stocking program: genetic population structure and demographics of kokanee (Oncorhynchus nerka) in a large impounded watershed

“…Okanagan Lake and Wood Lake in the south-central region of B.C. have also experienced dramatic declines in Kokanee populations in recent years (Taylor et al 2000;Askey and Johnston 2013;Askey 2016;Ward et al 2019).…”

“…Both systems are composed of multiple reproductively-isolated Kokanee ecotypes, and current management protocols are compelled to recognize these ecotypes as discrete management units to ensure the recovery and persistence of Kokanee as a whole (Taylor et al 2000;Ward et al 2019). The preservation of spawning habitat specific to each ecotype in conjunction with the implementation of adaptive harvest regulations has been valuable in the recovery plans for these populations (Taylor et al 2000;Askey 2016;Ward et al 2019). if the latter still persist in the watershed.…”