2020

Permanent URI for this collectionhttps://hdl.handle.net/1807/98912

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Modeling Habitat Suitability and Management Options for Maintaining Round Whitefish (Prosopium cylindraceum) in Adirondack Ponds
(Canadian Science Publishing, 2020-12-24) Conley, Amy Kathleen; Schlesinger, Matthew D.; Daley, James G.; Holst, Lisa K.; Howard, Timothy G.
Habitat loss, acid precipitation, and nonnative species have drastically reduced the number of Adirondack waterbodies occupied by round whitefish (Prosopium cylindraceum). The goal of this study was to 1) increase the probability of reintroduction success by modeling the suitability of ponds for reintroduction and 2) better understand the effects of different rates of pond reclamation. We created a species distribution model that identified 70 waterbodies that were physically similar to occupied ponds. The most influential variables for describing round whitefish habitat included trophic, temperature, and alkalinity classes; waterbody maximum depth; maximum air temperature; and surrounding soil texture and impervious surface. Next, we simulated population dynamics under a variety of treatment scenarios and compared the probability of complete extirpation using a modified Markov model. Under almost all management strategies, and under pressure from nonnative competitors like that observed in the past 30 years, the number of occupied ponds will decline over the next 100 years. However, restoring one pond every 3 years would result in a 99% chance of round whitefish persistence after 100 years.
The translocation trade-off for eastern sand darter (Ammocrypta pellucida): balancing harm to source populations with the goal of re-establishment
(Canadian Science Publishing, 2020-12-21) Lamothe, Karl A; van der Lee, Adam S.; Drake, D. Andrew R.; Koops, Marten A
Using translocations to recover populations requires a sufficiently large number of individuals from source populations, but removing too many individuals could lead to source population collapse. To understand the trade-off between the probabilities of source population extirpation and translocation success, matrix population models that incorporate Allee effects, density-dependence, and demographic and environmental stochasticity were combined with a model that simulates removals from source populations. We apply these models to eastern sand darter (Ammocrypta pellucida; Threatened) translocation scenarios in Canada. Results suggest that translocations most often require source populations >20,000 individuals, as source population extirpation probability increased with the number and frequency of removals. Transport mortality or losses immediately following introduction further affected translocation success. Uncertainty around life-history parameters and the strength of Allee effects led to additional uncertainty about the required source population size. Although stochastic processes affected the probability of translocation success, factors such as stocking density and frequency can be controlled, and therefore, translocation may be a viable strategy for eastern sand darter recovery, even when applying cautious thresholds to guard against uncertainty.
It’s elemental, my dear Watson: validating seasonal patterns in otolith chemical chronologies
(Canadian Science Publishing, 2020-12-12) Hssy, Karin; Krger-Johnsen, Maria; Thomsen, Tonny Bernt; Heredia, Benjamin Dominguez; Naeraa, Tomas; Limburg, Karin E.; Heimbrand, Yvette; McQueen, Kate; Haase, Stefanie; Krumme, Uwe; Casini, Michele; Mion, Monica; Radtke, Krzysztof
Accurate age data is essential for reliable fish stock assessment. Yet many stocks suffer from inconsistencies in age interpretation. A new approach to obtain age makes use of the chemical composition of otoliths. This study validates the periodicity of recurrent patterns in 25Mg, 31P, 34K, 55Mn, 63Cu, 64Zn, 66Zn, 85Rb, 88Sr, 138Ba, and 208Pb in Baltic cod (Gadus morhua) otoliths from tag-recapture and known-age samples. Otolith P concentrations showed the highest consistency in seasonality over the years, with minima co-occurring with otolith winter zones in the known-age otoliths and in late winter/early spring when water temperatures are coldest in tagged cod . The timing of minima differs between stocks, occurring around February in western Baltic cod and one month later in eastern Baltic cod; seasonal maxima are also stock-specific, occurring in August and October, respectively. The amplitude in P is larger in faster-growing western compared to eastern Baltic cod. Seasonal patterns with minima in winter/late spring were also evident in Mg and Mn, but less consistent over time and fish size than P. Chronological patterns in P, and to a lesser extent Mg and Mn, may have the potential to supplement traditional age estimation or to guide the visual identification of translucent and opaque otolith patterns used in traditional age estimation
Environmental and genetic influences on fitness-related traits in a hatchery coho salmon population.
(Canadian Science Publishing, 2020-12-26) Devlin, Robert H.; Supernault, K. Janine; Gezan, Salvador A.; Chan, Michelle T.T.; Wetklo, Mike; Biagi, Carlo A.; Sakhrani, Dionne; Barnetson, Stu; Dixon, Glen; Tattersall, Evelyn; Davidson, William S; Koop, Ben F; Willis, David M.; Withler, Ruth E.
Many natural and managed organisms will require substantial functional genetic variation to respond to selection in the face of rapid environmental change. Pacific salmon have experienced strong fluctuations in critical fitness traits over the past five decades. We examined genetic and phenotypic variability over three generations in a pedigreed hatchery population of coho salmon (Oncorhynchus kisutch) by monitoring seven fitness-related traits. Three-year-old adult return numbers varied more than five-fold, and jack (2-year old males) numbers varied 13-fold. Body sizes of Inch Creek coho salmon decreased consistently such that fish were only 40.7% as heavy in 2015 as in 2006 and female reproductive traits also decreased. During the study period, the majority of families produced returning adult progeny and effective population size was relatively constant. Heritability estimates for phenotypic traits were significantly greater than zero except for condition factor, and the estimated heritability for jacking was 0.42. The Inch Creek coho salmon population harbours substantial heritability for fitness and reproductive traits and thus likely retains significant capacity for adaptation despite many years of hatchery propagation.
Reduced recruitment of Chinook salmon in a leveed bar-built estuary
(Canadian Science Publishing, 2020-11-08) Chen, Emily K; Henderson, Mark J.
Estuaries are commonly touted as nurseries for salmonids, providing numerous advantages for smolts prior to ocean entry. In bar-built estuaries, sandbars form at the mouth of rivers during periods of low stream flow, closing access to the ocean and preventing outmigration. We evaluated how summer residency in a leveed bar-built estuary affects the growth, survival, and recruitment of a Chinook salmon (Oncorhynchus tshawytscha) population. We performed a mark-recapture study on outmigrants to determine juvenile estuary abundance, growth, and survival. We used returning adult scales and otoliths to determine the relative proportion of summer estuary residents in spawning adults. Juveniles in the estuary grew less after mouth closure, and ultimately summer estuary residents had lower smolt-to-adult survival and contributed disproportionately less to the spawning population than juveniles that reared in the ocean their first summer. Mouth closure may lower food availability and deteriorate estuary conditions by reducing marine prey influx and estuary circulation. This research demonstrates the complexity of estuary dynamics and function as salmonid nurseries, particularly when considering the extensive modification of estuaries.
Tide gates form physical and ecological obstacles to river herring (Alosa spp.) spawning migrations
(Canadian Science Publishing, 2020-12-26) Alcott, Derrick James; Goerig, Elsa; Rillahan, Christopher; He, Pingguo; Castro-Santos, Theodore
River herring (Alosa spp.) are anadromous fish that enter North American Atlantic coastal rivers and lakes each spring to spawn. Anthropogenic structures such as dams and tide gates serve as physical obstacles that limit river herring access to spawning habitat. This study examined the physical and ecological components affecting herring passage through a tide gate by applying a time-to-event analysis framework to multiple movement behaviors derived from telemetry data. Herring had higher passage success early in the season (78%) than later on (16%). Key behaviors that govern passage varied with diel period, tide, and flow direction through the gates. Furthermore, these behaviors shifted as the season progressed, consistent with the hypothesis that predator avoidance may be driving passage failure late in the spawning season.
Linking Demographic Transitions to Population Dynamics in a Fluctuating Environment
(Canadian Science Publishing, 2020-12-22) Gatto, John V.; Kline, Jeffrey L.; Loftus, William F.; Trexler, Joel C
Recruitment has been linked to decreases in the ratio of age-specific mortality (M’) to mass-specific growth (G’), and year-class strength may be predicted by the age when M’/G’=1. Hydrological stress adversely affects these parameters for species inhabiting floodplains; however, the relationship between M’ and G’ in hydrologically variable environments is poorly understood. We evaluated age-specific mortality for six species from a 20-year time series, and growth curves from otolith length-at-age data. We assessed the effect of hydrology on the transitional age (age M’/G’=1) at 21 sites representing a hydrological gradient. Disturbance intensity influenced age-specific mortality but had no effect on mass-specific growth. The transitional age was inversely correlated with annual density, but weakly associated with population biomass. Hydrological disturbance shifted the transition age to older ages, reducing recruitment overall. We demonstrated that the M’/G’ transition was affected adversely by hydrological stress and can be applied to a diverse group of taxa. Growth, survivorship, and the transitional age should be evaluated to improve population modelling efforts used to predict the influence of future restoration actions.
Comparison of Larval Fish Detections Using Morphology-Based Taxonomy versus High-Throughput Sequencing for Invasive Species Early Detection
(Canadian Science Publishing, 2020-12-21) Hoffman, Joel; Meredith, Christy; Pilgrim, Erik; Trebitz, Anett S; Hatzenbuhler, Chelsea; Kelly, John Russell; Peterson, Greg S; Lietz, Julie; Okum, Sara; Martinson, John
When first introduced, invasive species typically evade detection; DNA barcoding coupled with high-throughput sequencing (HTS) may be more sensitive and accurate than morphology-based taxonomy, and thereby improve invasive (or rare) species detection. We quantified the relative error of species detection between morphology-based and HTS-based taxonomic identification of ichthyoplankton collections from the Port of Duluth, Minnesota, an aquatic non-native species introduction ‘hot-spot’ in the Laurentian Great Lakes. We found HTS-based taxonomy identified 28 species and morphology-based taxonomy 30 species, of which 27 were common to both. Among samples, 76% of family-level taxonomic assignments agreed; however, only 42% of species assignments agreed. Most errors were attributed to morphology-based taxonomy, whereas HTS-based taxonomy error was low. For this study system, for most non-native fishes, the detection probability by randomized survey for larvae was similar to that by a survey that is optimized for non-native species early detection of juveniles and adults. We conclude that classifying taxonomic errors by comparing HTS results against morphology-based taxonomy is an important step toward incorporating HTS-based taxonomy into biodiversity surveys.
Comparison of staircase and asymmetrical before-after control impact (aBACI) experimental designs to test the effectiveness of stream restoration at increasing juvenile steelhead density
(Canadian Science Publishing, 2020-12-07) Loughin, Thomas M.; Bennett, Stephen N.; Bouwes, Nicolaas
Before-after-control-impact (BACI) experimental designs are commonly used in large-scale environmental experiments but these designs can be confounded by location and time interactions. Staircase designs, where replicate treatments are staggered temporally, have been suggested as an alternative to BACI designs. We performed a simulation study based on data from an ongoing watershed-scale restoration experiment within three streams to test the effectiveness of adding large wood to increase habitat complexity and abundance and productivity of juvenile steelhead (Oncorhynchus mykiss). We compared the power of two asymmetric BACI (aBACI) designs to two staircase designs for detecting changes in the density of steelhead (fish/m2). A staircase design where treatments were temporally staggered in one treatment section in each stream had the highest power and best precision, especially when the innate spatial and temporal variances of steelhead density were large. A traditional BACI performed the worst, and a variation on another BACI and staircase design had intermediate performance. Multi-stream staircase designs are also more logistically and economically feasible and can maximize learning by replicating experiments across different stream types.
Paradox of otolith shape indices: routine but overestimated use
(Canadian Science Publishing, 2020-12-10) Tuset, Vctor M.; Otero-Ferrer, Jos Luis; Siliprandi, Carolina; Manjabacas, Amalia; Mart-Puig, Pere; Lombarte, Antoni
The identification of fish species using otolith shape has been common in many fields of the marine science. Different analytical processes can be applied for the morphological discrimination, but reviewing the literature we have found conceptual and statistical limitations in the use of shape indices and wavelets (contour analysis), being specially worrying in the first case due to their widespread routine use. In the present study, 42 species were classified using otolith shape indices and wavelets and applying traditional and machine learning classifiers and performance measures (accuracy, Cohen’s kappa statistic, sensitivity and precision). Our results were conclusive, wavelets were a more adequate option for the classification of species than shape indices, independently of classifiers and performance measures considered. The artificial neural network and support vector machine provided the highest values for all performance measures using wavelets. In all cases, the measures of sensitivity and precision pointed out a higher confusion between some otolith patterns using shape indices. Therefore, we strongly discourage the routine use of shape indices for the identification of species.
Synchronous changes in length at maturity across four species of Lake Erie fish with different harvest histories
(Canadian Science Publishing, 2020-12-30) Gslason, Dav; McLaughlin, Robert L.; Robinson, Beren W
Decreases in size at maturation in harvested fish populations can reduce productivity and resilience. Delineating the causes for these changes in maturation is challenging. We assessed harvest and large-scale ecosystem variability as causes for changes in maturation in four Lake Erie fishes. Regulated harvests of Yellow Perch (Perca flavescens) and Walleye (Sander vitreus) are greater than unregulated harvests of White Perch (Morone americana) and White Bass (Morone chrysops). Our assessment considered cohort data from 1991-2012 for each species. We used a conceptual model of harvest-induced plasticity to show that changes in female length at 50% maturity (L50) were unrelated to harvest intensity in all species. We then demonstrated that changes in female L50 among cohorts were synchronous across species. Post-hoc analysis of variables capturing year-to-year variation in climatic and lake conditions suggested L50 was larger when water levels were near the norm for the study period and smaller at low and high levels. We conclude that changes in L50 were most strongly related to ecosystem changes unrelated to harvest intensity.
Mapping American lobster (Homarus americanus) habitat for use in marine spatial planning
(Canadian Science Publishing, 2020-12-01) McKee, Anne; Grant, Jon; Barrell, Jeffrey
Marine spatial planning (MSP) is a management tool which could help mitigate the conflict that exists between the American lobster (Homarus americanus) fishery and the net-pen salmon aquaculture industry in the Canadian Maritime provinces. We developed adult American lobster species distribution models (SDMs) for use in MSP in Liverpool, Nova Scotia, through remote sensing data collection methods. A single-beam echosounder was used to collect bathymetry and seafloor substrate data, and an aerial drone collected lobster presence data through the georeferenced photography of lobster trap buoys. The SDMs display trends in lobster presence likelihood that correspond with established patterns of habitat selection in adult lobsters. The areas where lobsters are predicted to have the highest likelihood of presence are sections of hard and rocky substrate, though that association is confounded by depth. The uncertainty of the SDMs was quantitatively assessed and the importance of explicitly analysing the effects of scale and resolution of spatial data is highlighted.
Landlocked Atlantic salmon in a large river-lake ecosystem: managing an endemic, large-bodied population of high conservation value
(Canadian Science Publishing, 2020-11-13) Greenberg, Larry A.; Norrgrd, Johnny R.; Gustafsson, Pr; Bergman, Eva
Managing and conserving threatened migratory salmonid populations in large river-lake ecosystems is challenging not only because of the ecosystems’ large size, but also because there is often more than one anthropomorphic stressor. The River Klarlven-Lake Vnern ecosystem, situated in Norway and Sweden, is a large highly modified ecosystem, home to a threatened, endemic, large-bodied population of landlocked salmon. With 11 dams, the salmon population has been maintained through extensive stocking and a truck and transport system for spawners. Here we review what we have learned about the salmon after 15 years of research, highlighting the major findings for each life stage. Our studies indicate that the salmon population is below carrying capacity, and we suggest measures to increase the number of spawners and downstream passage success. Habitat restoration to compensate for losses from former log driving activities is expected to further increase carrying capacity. Re-establishing salmon in Klarlven’s upper reaches in Norway, while possible, is fraught with both ecological and legislative hurdles. Substantial long-term funding is needed to foster co-management and ensure a sustainable fishery.
Growth during the first summer at sea modulates sex-specific maturation schedule in Atlantic salmon
(Canadian Science Publishing, 2020-12-12) Trehin, Cecile; Rivot, Etienne; Lamireau, Ludivine; Meslier, Lisa; Besnard, Anne-Laure; Gregory, Stephen D; Nevoux, Marie
Recent decline in abundance of Atlantic salmon and concomitant changes in life history may result from a decline in the growth conditions during marine migration. Available literature suggests the existence of a sex-specific reaction norm linking maturation with environmental growth conditions at sea. However the extent to which this mechanism explains variations in age at maturity remains unclear. Using a historical collection of scales (1987-2017) from the Slune River, France, we showed that marine growth declined over the first summer, and remained stable during the subsequent periods at sea among returning salmon. Results support the hypothesis of a sex-specific probabilistic reaction norm, with individual probability to return after one year at sea increasing when growth increases. Females may require higher growth than males to attain their maturation threshold. This mechanism is a good candidate to explain temporal variability in sea-age at return at both the individual and population level in the Slune population and in many other southern European populations.
Evaluating benthic impact of the Gulf of Maine lobster fishery using the swept area seabed impact (SASI) model
(Canadian Science Publishing, 2020-12-19) Goode, Andrew G; Grabowski, Jonathan H; Brady, Damian C.
The Magnuson-Stevens Fishery Conservation and Management Act mandates U.S. fisheries minimize adverse effects of fishing on essential fish habitat (EFH). The Gulf of Maine (GoM) American lobster fishery is the most valuable U.S. fishery, and can deploy more than three million traps annually. To date, the impact of this fishery on benthic EFH has not been addressed quantitatively. To evaluate the impact of the GoM lobster fishery on EFH, lobster fishing effort was incorporated into a model linking habitat susceptibility and recovery to area impacted by fishing gear; the Swept Area Seabed Impact model. Impact to EFH was localized along the coast and highest along mid-coast Maine. Upwards of 13% of the benthos is in the process of recovery, but between 99.92 – 99.96% of initially affected habitat fully recovers. These estimates suggest that lobster fishing negligibly contributes to accumulation of EFH damage in the GoM due to the expansive area fished and the small footprint of each trap. Identifying areas of persistent impact is crucial in developing effective fisheries management for critical marine habitats.
Trophic niche overlap and abundance reveal potential impact of interspecific interactions on a reintroduced fish
(Canadian Science Publishing, 2020-12-07) Larocque, Sarah M.; Johnson, Timothy B.; Fisk, Aaron T
Conceptually trophic niche overlap and species abundance can describe the strength and number of interspecific trophic interactions to determine the competitive impact on reintroduced species or other ecosystem changes. We use an example with young-of-year (YOY) Atlantic salmon (Salmo salar) reintroductions to determine if trophic niche overlaps and abundances limit restoration success. Using seasonal stable isotopes and abundance estimates for invertivorous fishes in three Lake Ontario tributaries, we assessed community isotopic structure, trophic niche overlap, and the impact of the niche overlap by incorporating relative abundance. Brown trout (Salmo trutta) YOY could be a strong competitor with a high trophic niche overlap with Atlantic salmon YOY but at lower abundances relative to Atlantic salmon minimizes impact. Stream resident fish communities appeared to partition resources across seasons such that abundant species had low trophic niche overlap to minimize overall competition with Atlantic salmon YOY given available resources, indicating niche complementarity. Through joint consideration of trophic overlap and abundance using our conceptual model, the competitive impact of community composition on a reintroduced species could be assessed.
Small biased body size of salmon fry preyed upon by piscivorous fish in riverine and marine habitats
(Canadian Science Publishing, 2020-12-26) Hasegawa, Koh; Honda, Kentaro; Yoshiyama, Taku; Suzuki, Kengo; Fukui, Sho
Predator-prey interactions must be considered when aiming to enhance populations by releasing artificially reared individuals into natural environments. Released individuals create an abundance of prey for predators, and a basic hypothesis of predator-prey interactions suggests that predators select large prey due to the high caloric content. An alternative hypothesis is that small individuals are vulnerable to predation due to their poor predator avoidance. This study tested these hypotheses using stocked chum (Oncorhynchus keta) and masu (O. masou) salmon fry and piscivorous salmonids in marine and riverine habitats in Hokkaido, Japan. Stomach contents were sampled from predators, and fork length of prey fry was measured. Then, their fork length was compared with whole stocked fry (range of mean fork length (SD): 45.82.55-49.22.76 mm) for each habitat. As a result, prey fry were ca. 3-6% smaller than whole stocked fry, even under a prey abundant condition (i.e. just after hatchery reared salmon fry were stocked). Piscivorous salmonids pursue schooling fry, and small fry may be easily caught due to their slow speed in avoiding predators.
Comparing a suite of surplus-production-based stock status identification approaches and management procedures
(Canadian Science Publishing, 2020-12-04) Xu, Luoliang; Hodgdon, Cameron Tyler; Sun, Ming; Mazur, Mackenzie Dale; Chen, Xinjun; Chen, Yong
Different approaches have been used to identify fishery stock status when only biomass and catch data are available. However, the performance of the approaches may be affected by the uncertainties derived from different sources (e.g., model misspecification, stock productivity changing, observation error). Here, we propose that the observed biomass associated with the highest calculated surplus production can be used as an indicator (Bhighest_S) to identify stock status. We develop a management procedure (MP) atop a widely used method (i.e., Gcontrol) by incorporating Bhighest_S in the harvest control rule. Two simulations are conducted to compare the stock status identification approaches and corresponding MPs. Using Bhighest_S to identify stock status performs better than surplus production modeling approaches in simulated regime shift scenarios. Compared with the old version of Gcontrol, incorporating Bhighest_S or estimated BMSY in the harvest control rule provides more stable and higher yields. This study contributes to the development and evaluation of indicator-based stock status identification approaches and MPs that only require biomass and catch data.
Importance of sample size for estimating prevalence: A case example of infectious hematopoietic necrosis viral RNA detection in mixed-stock Fraser River Sockeye salmon (Oncorhynchus nerka), British Columbia, Canada.
(Canadian Science Publishing, 2020-10-20) Laurin, Emilie; Bradshaw, Julia; Hawley, Laura; Gardner, Ian A.; Garver, Kyle A; Johnson, Stewart C; Thakur, Krishna K
Proper sample size must be considered when designing infectious-agent prevalence studies for mixed-stock fisheries, because bias and uncertainty complicate interpretation of apparent (test)-prevalence estimates. Sample size varies between stocks, often smaller than expected during wild-salmonid surveys. Our case example of 2010-2016 survey data of Sockeye salmon (Oncorhynchus nerka) from different stocks of origin in British Columbia, Canada, illustrated the effect of sample size on apparent-prevalence interpretation. Molecular testing (viral RNA RT-qPCR) for infectious hematopoietic necrosis virus (IHNv) revealed large differences in apparent-prevalence across wild salmon stocks (much higher from Chilko Lake) and sampling location (freshwater or marine), indicating differences in both stock and host life-stage effects. Ten of the 13 marine non-Chilko stock-years with IHNv-positive results had small sample sizes (
Chinook salmon exhibit long-term rearing and early marine growth in the Fraser River, B.C., a large urban estuary
(Canadian Science Publishing, 2020-12-09) Chalifour, Lia; Scott, David C; MacDuffee, Misty; Stark, Steven; Dower, John F; Beacham, Terry D.; Martin, Tara G; Baum, Julia K.
Estuaries represent a transition zone for salmon migrating from freshwater to marine waters, yet their contribution to juvenile growth is poorly quantified. Here, we use genetic stock identification and otolith analyses to quantify estuarine habitat use by Chinook salmon (Oncorhynchus tshawytscha) – the Pacific salmon species considered most reliant on this habitat – in Canada’s most productive salmon river, the Fraser. Two years of sampling revealed subyearling migrant (“ocean-type”) Chinook from the Harrison River to be the estuary’s dominant salmon population throughout the emigration period. These Chinook salmon were caught predominantly in the estuary’s brackish marshes but shifted to more saline habitats as they grew. Otolith analyses indicated that these Chinook salmon have wide-ranging entry timing (from February to May), and longer estuarine residency (weeks to months, mean 41.8 days) than estimated by prior studies, but similar daily growth rates (mean 0.57 mm +/- 0.13 SD) across entry dates and residency periods, implying sufficient foraging opportunities throughout the emigration period and habitats. Together, these results suggest that estuarine habitat is more important for early marine growth of subyearling migrant Chinook salmon than previously recognized.

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