Kootenay Lake kokanee (Oncorhynchus nerka) collapse into a predator pit

Kootenay Lake is a large, oligotrophic waterbody in southern British Columbia renowned for recreational fisheries for piscivorous rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus). Long-term datasets showed a build-up of large-bodied (>2 kg) piscivore abundance followed by a collapse of the kokanee (Oncorhynchus nerka) prey population in 2013 and subsequent decline of large-bodied piscivores. An unprecedented post-collapse state formed in 2015-2018, characterized by low kokanee spawner abundance and biomass and high catch rates for small-bodied (<2 kg), slow growing piscivores. Bioenergetics model estimates of average historic (1961-2008) piscivore consumption was 29.3% of the average historic (1993-2008) kokanee prey supply (biomass and production), but increased to 78.7% in 2011, immediately preceding kokanee collapse. From 2015-2018, kokanee did not recover due to persistently poor juvenile survival; estimated piscivore consumption relative to prey supply remained high (73.0%), suggesting that kokanee were trapped in a predator pit. Although the ultimate and interacting causes of the initial predator build-up remain uncertain, overcoming current depensatory dynamics may be aided by kokanee stocking or increasing harvest on still-abundant, unsatiated piscivores.

Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss)

Background Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhynchus mykiss)—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence. Results Genomic divergence was high between sympatric insectivores and piscivores ($$F_{\text{ST}}$$ F ST = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River ($$F_{\text{ST}}$$ F ST = 0.159) that are > 500 km apart. A window-based $$F_{\text{ST}}$$ F ST analysis did not reveal “islands” of genomic differentiation; however, the window with highest $$F_{\text{ST}}$$ F ST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs. Conclusion Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences.

Growth Genes Are Implicated in The Evolutionary Divergence of Sympatric Piscivorous and Insectivorous Rainbow Trout (Oncorhynchus Mykiss)

Background: Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding the traits associated with population divergence. We used genome-wide data to identify genomic regions associated with a key trait that distinguishes two ecotypes of rainbow trout (Oncorhynchus mykiss) – insectivores and piscivores – that coexist in Kootenay Lake, southeastern British Columbia, for the non-breeding portion of the year. “Gerrards” are large-bodied (breeding maturity at >60cm) piscivores that spawn ~50km north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data covering ~60% of the genome to assess the level of genomic divergence between ecotypes, test for genotype-phenotype associations, and identify loci that may play functional or selective roles in their divergence. Results: Analysis of nearly seven million SNPs provided a genome-wide mean FST estimate of 0.18, indicating a high level of reproductive isolation between populations. The window-based FST analysis did not reveal “islands” of genomic differentiation; however, the window with highest FST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~20%). Gene Ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~200 most divergent genomic windows, indicating the importance of genetically-based growth and growth-related metabolic functions in the divergence of these ecotypes. Conclusions: In spite of their sympatric coexistence, a high degree of genomic differentiation separates the populations of piscivores and insectivores, indicating little to no contemporary genetic exchange between ecotypes. Our results further indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect, rather it may be controlled by several loci of small effect, thus highlighting the power of whole-genome low-coverage sequencing in phenotypic association studies.

Dynamic analysis of the 2012 Johnsons Landing landslide at Kootenay Lake, British Columbia: the importance of undrained flow potential

The Johnsons Landing landslide occurred on 12 July 2012 on the shores of Kootenay Lake, British Columbia. The landslide consisted of poorly sorted, low-plasticity debris that initially descended a steep channel, before avulsing onto a glaciofluvial terrace. This event destroyed three homes and killed four people who lived on this terrace. This paper presents a back-analysis of this event using numerical runout modelling. It is shown that undrained flow can explain the observed channel avulsion with fewer model parameters than needed by previous analyses. This mechanism should be considered in similar settings, as ignoring it can lead to underestimation of runup and overtopping of natural and anthropogenic flow obstacles, such as landslide protection structures.

Characterizing the phytoplankton and zooplankton communities in Kootenay Lake: a time series analysis of 24 years of nutrient addition

Large-scale seasonal addition of limiting nutrients has been used for restoration in Kootenay Lake, British Columbia, since 1992 to mitigate cultural oligotrophication resulting from upstream hydropower development, river channelization, mysid shrimp introduction, and extensive tributary floodplain loss. Historical (1949) in-lake nutrient levels were targeted to stimulate bottom-up carbon transfer from native plankton communities to planktivorous and piscivorous fish populations that support popular fisheries. Analysis of 24 years of monitoring data assessed the effects of nutrient addition on the phytoplankton and zooplankton communities. Assessment involved comparisons of plankton community metric data from North Arm (1992–2003) and North + South arms (2004–2015) nutrient addition periods. A before–after, control–impact (BACI) analysis adjusted for these effects involved a series of phytoplankton and zooplankton metrics across the two lake arms. Time series analyses revealed significant serial correlation structure, significant increases in phytoplankton and zooplankton abundance and biomass, and increased stability within the phytoplankton and zooplankton communities. Results confirmed that adaptively managed nutrient restoration can effectively restore biological productivity and community structure in a large culturally oligotrophic lake.

The fishing and natural mortality of large, piscivorous Bull Trout and Rainbow Trout in Kootenay Lake, British Columbia (2008–2013)

BackgroundEstimates of fishing and natural mortality are important for understanding, and ultimately managing, commercial and recreational fisheries. High reward tags with fixed station acoustic telemetry provides a promising approach to monitoring mortality rates in large lake recreational fisheries. Kootenay Lake is a large lake which supports an important recreational fishery for large Bull Trout and Rainbow Trout.MethodsBetween 2008 and 2013, 88 large (≥500 mm) Bull Trout and 149 large (≥500 mm) Rainbow Trout were marked with an acoustic transmitter and/or high reward ($100) anchor tags in Kootenay Lake. The subsequent detections and angler recaptures were analysed using a Bayesian individual state-space Cormack–Jolly–Seber (CJS) survival model with indicator variable selection.ResultsThe final CJS survival model estimated that the annual interval probability of being recaptured by an angler was 0.17 (95% CRI [0.11–0.23]) for Bull Trout and 0.14 (95% CRI [0.09–0.19]) for Rainbow Trout. The annual interval survival probability for Bull Trout was estimated to have declined from 0.91 (95% CRI [0.76–0.97]) in 2009 to just 0.46 (95% CRI [0.24–0.76]) in 2013. Rainbow Trout survival was most strongly affected by spawning. The annual interval survival probability was 0.77 (95% CRI [0.68–0.85]) for a non-spawning Rainbow Trout compared to 0.41 (95% CRI [0.30–0.53]) for a spawner. The probability of spawning increased with the fork length for both species and decreased over the course of the study for Rainbow Trout.DiscussionFishing mortality was relatively low and constant while natural mortality was relatively high and variable. The results indicate that angler effort is not the primary driver of short-term population fluctations in the Rainbow Trout abundance. Variation in the probability of Rainbow Trout spawning suggests that the spring escapement at the outflow of Trout Lake may be a less reliable index of abundance than previously assumed. Multi-species stock assessment models need to account for the fact that large Bull Trout are more abundant than large Rainbow Trout in Kootenay Lake.

The fishing and natural mortality of large, piscivorous Bull Trout and Rainbow Trout in Kootenay Lake, British Columbia (2008-2013)

ABSTRACTBackgroundEstimates of fishing and natural mortality are important for understanding, and ultimately managing, commercial and recreational fisheries. High reward tags with fixed station acoustic telemetry provides a promising approach to monitoring mortality rates in large lake recreational fisheries. Kootenay Lake is a large lake which supports an important recreational fishery for large Bull Trout and Rainbow Trout.MethodsBetween 2008 and 2013, 88 large (≥ 500 mm) Bull Trout and 149 large (≥ 500 mm) Rainbow Trout were marked with an acoustic transmitter and/or high reward ($100) anchor tags in Kootenay Lake. The subsequent detections and angler recaptures were analysed using a Bayesian individual state-space Cormack-Jolly-Seber (CJS) survival model with indicator variable selection.ResultsThe final CJS survival model estimated that the annual interval probability of being recaptured by an angler was 0.17 (95% CRI 0.11 - 0.23) for Bull Trout and 0.14 (95% CRI 0.09 - 0.19) for Rainbow Trout. The annual interval survival probability for Bull Trout was estimated to have declined from 0.91 (95% CRI 0.77 - 0.97) in 2009 to just 0.45 (95% CRI 0.24 - 0.73) in 2013. Rainbow Trout survival was most strongly affected by spawning. The annual interval survival probability was 0.77 (95% CRI 0.68 - 0.85) for a non-spawning Rainbow Trout compared to 0.42 (95% CRI 0.31 - 0.54) for a spawner. The probability of spawning increased with the fork length for both species and decreased over the course of the study for Rainbow Trout.DiscussionFishing mortality was relatively low and constant while natural mortality was relatively high and variable. The results are consistent with Kokanee abundance as opposed to angler effort as the primary driver of short-term population fluctations in Rainbow Trout abundance. Multi-species stock assessment models need to account for the fact that large Bull Trout are more abundant than large Rainbow Trout in Kootenay Lake.