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Data and scripts from: Experimental evidence of size-selective harvest and environmental stochasticity effects on population demography, fluctuations, and nonlinearity
Rogers, Luke; Moore, Zack; Daigle, Abby; Luijckx, Pepijn; Krkosek, Martin — 2023-01-11 <p class="MsoNormal">Theory and analyses of fisheries datasets indicate that harvesting can alter population structure  and destabilize nonlinear processes, which increases population fluctuations. We conducted a factorial experiment on the population dynamics of <em>Daphnia magna</em> in relation to size-selective harvesting and stochasticity of food supply. Harvesting and stochasticity treatments both increased population fluctuations. Timeseries analysis indicated that fluctuations in control populations were nonlinear, and nonlinearity increased substantially in response to harvesting. Both harvesting and stochasticity induced population juvenescence, but harvesting did so via depletion of adults whereas stochasticity increased the abundance of juveniles. A fitted fisheries model indicated that harvesting shifted populations towards higher reproductive rates and larger-magnitude damped oscillations that amplify demographic noise. These findings provide experimental evidence that harvesting increases nonlinearity of population fluctuations and that both harvesting and stochasticity increase population variability and juvenescence.</p>
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Hakai Institute Juvenile Salmon Program Time Series
Hakai Institute / Hakai Institut
Johnson, Brett; Gan, Julian; Godwin, Sean; Bachen, Krystal; van der Stap, Tim; Krkosek, Martin; Rogers, Luke A.; Portner, Lauren; Janusson, Carly; Hunt, Brian P. V.; Hakai Institute — 2017-05-11 The Hakai Institute Juvenile Salmon program is an ongoing initiative that was established in 2015 in partnership with the University of British Columbia, University of Toronto, Simon Fraser University and Salmon Coast Field Station. This program researches the early life history of juvenile salmon in coastal British Columbia. Primary research objectives are determining: 1) Migration timing rates and routes; 2) Migration habitat, including physical and chemical oceanographic conditions, and availability of plankton prey; 3) The impacts of prey phenology, quantity and quality on juvenile salmon growth and condition; 4) Species and stock-specific feeding biology and competitive interactions; 5) Pathogen and parasite infection dynamics; and 6) Mortality estimates. The program targets Fraser River sockeye, and pink and chum salmon, but additionally provides information on coho, chinook, and herring through incidental capture. The field program operates between May and July during the peak of the juvenile sockeye outward migration. Purse seine and oceanographic sampling are conducted in the northern Strait of Georgia / Discovery Islands region (~ 220 km from the Fraser River mouth) and the Johnstone Strait / Queen Charlotte Strait region (~ 180 km from the northern Strait of Georgia. As such, this program informs early life history across two critical legs of the Fraser salmon northward migration. Data packages are updated annually. Versioned datasets are available through the links below. This data package is freely available to everyone, following the principles of equitable access and benefit sharing. However, we expect all data users to give attribution to the data providers (read our data license) and the use of these data should happen in the light of fair use, i.e.: 1) respect the data providers, and provide helpful feedback on data quality, and 2) communicate and/or collaborate with the providers if you are considering using this dataset for manuscripts or other forms of reporting. Le programme sur le saumon juvénile du Hakai Institute est une initiative permanente qui a été créée en 2015 en partenariat avec l'Université de la Colombie-Britannique, l'Université de Toronto, l'Université Simon Fraser et la station de terrain de Salmon Coast. Ce programme étudie le début du cycle biologique des saumons juvéniles sur la côte de la Colombie-Britannique. Les principaux objectifs de recherche sont de déterminer : 1) Délais et itinéraires de migration ; 2) L'habitat de migration, y compris les conditions océanographiques physiques et chimiques et la disponibilité de proies planctoniques ; 3) Les impacts de la phénologie, de la quantité et de la qualité des proies sur la croissance et la condition des saumons juvéniles ; 4) Biologie alimentaire et interactions compétitives spécifiques aux espèces et aux stocks ; 5) Dynamique des infections par les agents pathogènes et les parasites ; et 6) Estimations de la mortalité. Le programme cible le saumon rouge du fleuve Fraser, le saumon rose et le saumon kéta, mais fournit également des informations sur le coho, le quinnat et le hareng grâce à des captures fortuites. Le programme sur le terrain se déroule entre mai et juillet, au plus fort de la migration vers l'extérieur des saumons rouges juvéniles. Des échantillonnages océanographiques et à la senne coulissante sont effectués dans la région nord du détroit de Géorgie et des îles Discovery (à environ 220 km de l'embouchure du fleuve Fraser) et dans la région du détroit de Johnstone et du détroit de la Reine-Charlotte (à environ 180 km du nord du détroit de Géorgie). À ce titre, ce programme éclaire le début du cycle biologique de deux étapes critiques de la migration du saumon du Fraser vers le nord. Les packages de données sont mis à jour chaque année. Les ensembles de données versionnés sont disponibles via les liens ci-dessous. Cet ensemble de données est librement accessible à tous, conformément aux principes d'accès équitable et de partage des avantages. Cependant, nous attendons de tous les utilisateurs de données qu'ils attribuent leurs fournisseurs de données (lisez notre licence de données) et que l'utilisation de ces données doit se faire dans le cadre d'une utilisation équitable, c'est-à-dire : 1) respecter les fournisseurs de données et fournir des commentaires utiles sur la qualité des données, et 2) communiquer et/ou collaborer avec les fournisseurs si vous envisagez d'utiliser cet ensemble de données pour des manuscrits ou d'autres formes de rapports. https://creativecommons.org/licenses/by/4.0/
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Data for: Dynamic coastal pelagic habitat drives rapid changes in growth and condition of juvenile sockeye salmon (Oncorhynchus nerka) during early marine migration
Dryad
Garzke, Jessica; Forester, Ian; Godwin, Sean; Johnson, Brett; Krkosek, Martin; Mahara, Natalie; Pakhomov, Evgeny; Rogers, Luke — 2022-11-09 <p>Migrating marine taxa encounter diverse habitats that differ environmentally and in foraging conditions over a range of spatial scales. We examined body (RNA/DNA, length-weight residuals) and nutritional (fatty acid composition) condition of juvenile sockeye salmon (<em>Oncorhynchus</em> nerka) in British Columbia while migrating through oceanographically variable waters. Fish were sampled in the stratified northern Strait of Georgia (NSoG); the highly mixed Johnstone Strait (JS); and the transitional zone of Queen Charlotte Strait (QCS). In 2015, body and nutritional condition were high in the NSoG but rapidly declined to reach the lowest levels in JS where prey availability was low, before showing signs of compensatory growth in QCS. In 2016, juvenile salmon had a significantly lower condition in the NSoG than in 2015, although zooplankton biomass was similar, condition remained low in JS, and no compensatory growth was observed in QCS. We provide evidence that differences in juvenile salmon condition between the two years were due to changes in the food quality available to juvenile fish. We propose that existing hypotheses about fish survival need to be extended to incorporate food quality in addition to quantity to understand changes in fish condition and survival between years.</p>
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Juvenile salmon migration observations in the Discovery Islands and Johnstone Strait in British Columbia, Canada in 2018
Hakai Institute / Hakai Institut
Johnson, Brett; Gan, Julian; Godwin, Sean; Krkosek, Martin; Hunt, Brian — 2019-12-05 The Hakai Institute Juvenile Salmon Program has been monitoring juvenile salmon migrations in the Discovery Islands and Johnstone Strait since 2015 with the specific purpose to understand how ocean conditions experienced by juvenile salmon during their early marine migration impacts their growth, health and ultimately survival. We found that during the two of the warmest years of sea-surface temperature recorded in British Columbia waters, juvenile sockeye, pink, and chum left the Strait of Georgia one to two weeks earlier than previously. The temporal distribution of sockeye migration timing out of the Strait of Georgia north through the Discovery Islands was skewed right, indicating that many sockeye migrate together in late May and abundance tails off late into June and July. Pink and chum migrations are more protracted, lasting from early May to late July. Our results indicate that juvenile sockeye exit the Strait of Georgia en masse, likely in response to ocean temperature and foraging conditions. This report summarizes migration timing, fish length and weight, sea-louse loads, purse seine catch composition, and ocean temperatures observed from the first four years of this research and monitoring program. Combining key variables from this research program with observations from freshwater and high-seas sampling will provide, for some stocks, a complete account of the conditions salmon experience during their migration from their natal river to the high seas. These measures will further our knowledge of what drives early marine mortality, and better our understanding of how salmon are adapting to climate change. Le programme du saumon juvénile de l'Institut Hakai surveille les migrations de saumons juvéniles dans les îles Discovery et le détroit de Johnstone depuis 2015 dans le but spécifique de comprendre comment les conditions océaniques vécues par les saumons juvéniles au cours de leur migration marine précoce influent sur leur croissance, leur santé et leur santé. finalement, la survie. Nous avons constaté que pendant les deux années les plus chaudes de température à la surface de la mer enregistrées dans les eaux de la Colombie-Britannique, le saumon rouge juvénile, le rose et le kéta ont quitté le détroit de Georgia une à deux semaines plus tôt qu'auparavant. La répartition temporelle de la migration du saumon rouge à partir du détroit de Georgia au nord par les îles Discovery était asymétrique, ce qui indique que de nombreux saumons rouges migrent ensemble à la fin du mois de mai et que l'abondance s'est éloignée fin juin et juillet. Les migrations roses et kénues sont plus longues, allant du début mai à la fin juillet. Nos résultats indiquent que le saumon rouge juvénile quitte massivement le détroit de Georgia, probablement en réponse à la température de l'océan et aux conditions de nourriture. Ce rapport résume le moment de la migration, la longueur et le poids du poisson, les charges de pou de mer, la composition des prises de senne coulissante et les températures océaniques observées depuis les quatre premières années de ce programme de recherche et de surveillance. La combinaison des variables clés de ce programme de recherche avec des observations d'échantillonnage en eau douce et en haute mer fournira, pour certains stocks, un compte rendu complet des conditions que connaissent le saumon pendant leur migration de leur rivière natale vers la haute mer. Ces mesures permettront d'approfondir nos connaissances sur ce qui motive la mortalité marine précoce et de mieux comprendre comment le saumon s'adapte au changement climatique. https://creativecommons.org/licenses/by/4.0/
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Differential infestation of juvenile Pacific salmon by parasitic sea lice in British Columbia, Canada
Hakai Institute / Hakai Institut
Brookson, Cole; Krkosek, Martin; Hunt, Brian; Johnson, Brett; Rogers, Luke; Godwin, Sean; Hakai Institute — 2020-09-04 Fraser River Pacific salmon have declined in recent decades possibly from parasitism by sea lice (Caligus clemensi and Lepeophtheirus salmonis). We describe the abundance of both louse species infesting co-migrating juvenile pink (Oncorhynchus gorbuscha), chum (O. keta), and sockeye (O. nerka) salmon over five years in the Discovery Islands and Johnstone Strait, British Columbia. The generalist louse, C. clemensi, was 5-, 7-, and 39-times more abundant than the salmonid specialist, L. salmonis, on pink , chum, and sockeye salmon, respectively. Caligus clemensi abundance was higher on pinks (0.45, 95% CI: 0.38-0.55) and sockeye (0.39 95% CI 32 0.33-0.47) than chum. L. salmonis abundance was highest on pinks (0.09, 95% CI = 0.06-0.15). Caligus clemensi had higher abundances in Johnstone Strait than the Discovery Islands. These results suggest differences in host specialization and transmission dynamics between louse species. Because both lice infest farmed salmon, but only C. clemensi infests Pacific herring (Clupea pallasii), conservation science and management regarding lice and Fraser River salmon should further consider C. clemensi and transmission from farmed salmon and wild herring. Le saumon du Pacifique du fleuve Fraser a diminué ces dernières décennies, probablement en raison du parasitisme du pou du poisson (Caligus clemensi et Lepeophtheirus salmonis). Nous décrivons l'abondance des deux espèces de pou infestant le saumon rose juvénile co-migrant (Oncorhynchus gorbuscha), le saumon kéta (O. keta) et le saumon rouge (O. nerka) pendant cinq ans dans les îles Discovery et le détroit de Johnstone, en Colombie-Britannique. Le pou généraliste, C. clemensi, était 5, 7 et 39 fois plus abondant que le spécialiste des salmonidés, L. salmonis, sur le saumon rose, le saumon kéta et le saumon rouge, respectivement. L'abondance de Caligus clemensi était plus élevée chez les roses (0,45, IC à 95 % : 0,38-0,55) et le saumon rouge (0,39 IC à 95 % 32 0,33-0,47) que le kéna. L'abondance de L. salmonis était la plus élevée chez les roses (0,09, IC à 95 % = 0,06-0,15). Caligus clemensi avait une abondance plus élevée dans le détroit de Johnstone que dans les îles Discovery. Ces résultats suggèrent des différences dans la spécialisation des hôtes et la dynamique de transmission entre les espèces de pou. Étant donné que les deux poux infestent le saumon d'élevage, mais que seul C. clemensi infeste le hareng du Pacifique (Clupea pallasii), la science de la conservation et la gestion des poux et du saumon du fleuve Fraser devraient examiner davantage le C. clemensi et la transmission du saumon d'élevage et du hareng sauvage. https://creativecommons.org/licenses/by/4.0/
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Data to replicate: "Environmental variability can promote parasite diversity within hosts and transmission among hosts".
Federated Research Data Repository / dépôt fédéré de données de recherche
Jarvis-Cross, Madeline; Krkosek, Martin — 2023-07-06 Mathematical models and simulations are used to ask how environmental variability may affect the viability and longevity of within-host parasite diversity and among-host transmission. These data can be used to replicate the analyses in "Environmental variability can promote parasite diversity within hosts and transmission among hosts". The scripts to run such analyses can be found here: https://github.com/MadelineJC/EnvironmentalVariability_Repo.
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Data for: Temperature variation and life history drive nonlinear dynamics of marine fish populations
Zenodo
Hechler, Robert; Krkosek, Martin — 2025-01-16 Description: This repository contains the data needed to reproduce our analyses. All code has been made available to reviewers and will be publicly released upon manuscript acceptance. The raw data come from: Fish time series from the RAM Legacy Stock Assessment Data Base (Ricard et al. 2011; Fish and Fisheries) Fish species life history traits from FishLife (Thorson et al. 2023; Methods in Ecology Evolution) Sea surface temperature time series from NOAA OI SST V2 High Resolution Dataset (https://psl.noaa.gov/data/gridded/data.noaa.oisst.v2.highres.html) Sea surface temperature time series from COBE-SST 2 Dataset (https://psl.noaa.gov/data/gridded/data.cobe2.html) Data files: timeseries_ssb.csv - time series of spawner biomass timeseries_rec.csv - time series of recruitment  timeseries_tc.csv - time series of total catch  mean_annual_SST_noaa.oisst.v2.csv - time series of mean SST for each population from noaa.oisst.v2 variation_annual_SST_noaa.oisst.v2.csv - time series of within year SST variation for each population from noaa.oisst.v2 data_correlates_sst_traits_ssb_r_tc.csv - dataframe of the life history and temperature correlates for all populations  df_ccm_recruits.csv - time series of recruitment and matching SST for convergent cross mapping  df_ccm_spawners.csv - time series of spawner biomass and matching SST for convergent cross mapping  df_ccm_totalCatch.csv - time series of total catch and matching SST for convergent cross mapping  SST_annualMean_timeseries_donors_COBE_ForSensitivityAnalysis.csv - time series of mean SST from COBE  SST_annual_intraVariation_timeseries_donors_COBE_ForSensitivityAnalysis.csv - time series of within year SST variation from COBE datassb_forModels.csv - data for spawner mixed models  datarec_forModels.csv - data for recruit mixed models https://creativecommons.org/licenses/by/4.0/legalcode

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