Geology topics

Thomas P. Quinn

Publications and source records attributed to Thomas P. Quinn.

15 recordsLinked to original sources

USGS2024

Differences in life history patterns of American shad, Alosa sapidissima, populations between ancestral, Atlantic coast, and non-native, Pacific coast rivers of North America

Organisms naturalized outside their native range can reveal new life history patterns in new environments. Here, we compare life history patterns of American shad, Alosa sapidissima, from five rivers along the U.S. Pacific coast (introduced range) with contemporary data from the Atlantic coast source populations. The Pacific coast fish grew slower, matured at a younger age, and were less often iteroparous than conspecifics from the Hudson River and Susquehanna River sources. Differences among the Pacific coast populations indicated that some combination of phenotypic plasticity and genetic adaptation has occurred since the transplants in the 1870s. Microchemical analysis of otoliths from returning adults demonstrated an immature, extended freshwater life history form, locally known as “mini-shad”. These fish remain in the river for at least 1 year or enter salt water briefly and then return to fresh water for several months prior to subsequent seaward migration and return as adults. This and other forms of variation (extent of estuary use and size at sea water entry) expand the understanding of Alosine migration and life history diversity.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2023

Seasonal shifts in diel vertical migrations by lake-dwelling coastal cutthroat trout, Oncorhynchus clarkii clarkii, reflect thermal regimes and prey distributions

Lakes provide important habitat for salmonids that may use them as a primary feeding area between periods of reproduction. The seasonal changes in vertical thermal structure in lakes can affect the distribution of salmonids on seasonal and diel time scales as they search for, consume, and digest prey that also exploits the water column's distribution of food, temperature and light. Our goal was to analyse the vertical distribution of wild, native coastal cutthroat trout ( Oncorhynchus clarkii clarkii ) in Lake Washington on daily and seasonal time scales. This lake is stratified in the summer and isothermal in winter, allowing us to compare vertical movements between periods with and without thermal structure in water 50 m deep. We predicted that trout would be deeper in the water column during stratified months and shallower during isothermal months, and shallower at night than in the day. Overall, the trout showed these patterns in the depths and temperatures they occupied, tending to be within or below the thermocline in the summer but not in the coolest water available, and closer to the surface when the lake was isothermal. The trout were also closer to the surface at night and deeper during the day. The vertical range of these diel movements shifted with the seasons–deepest in October, as the thermocline deepened and weakened, and shallowest in January when the lake was isothermal. These seasonal and diel vertical distribution patterns by the trout optimise metabolism for growth, and facilitate feeding on planktivorous fishes that also show seasonal and diel vertical distribution changes.

Washington↗

USGS2023

Who spawns where? Temperature, elevation, and discharge differentially affect the distribution of breeding by six Pacific salmonids within a large river basin

Within the geographic range of salmonid fishes, many apparently suitable rivers and streams are used for reproduction by some species but not others. This is widely known but seldom addressed, as studies often examine factors determining the distribution of one or only a few species. We examined physical factors associated with the spawning distribution of six native Pacific salmonids (pink, chum, coho, and Chinook salmon, bull trout, and steelhead) in the Skagit River basin, Washington. Annual mean temperature and catchment elevation had the strongest association with spawning assemblage distribution, but stream length, annual discharge, seasonal hydrology, and land use were also influential. Some species (e.g., pink and Chinook salmon) were more closely associated with each other and with common variables than others, and bull trout were the most distinctive. For interpretation, we investigated the roles of adult body size, timing of spawning, and duration of juvenile rearing, but none of these factors explained groupings in the data. Interspecific differences in habitat association remained, suggesting fundamental constraints on species distributions with implications for conservation and restoration.

Washington↗

USGS2022

Life-cycle model reveals sensitive life stages and evaluates recovery options for a dwindling Pacific salmon population

Population models, using empirical survival rates estimates for different life stages, can help managers explore whether various management options could stabilize a declining population or restore it to former levels of abundance. Here we used two decades of data on five life stages of the Cedar River, USA Sockeye Salmon, Oncorhynchus nerka , population to create and parameterize a life-cycle model. This formerly large but unproductive population is now in steep decline, despite hatchery enhancement. We gathered population-specific data on survival during five stages: 1) egg-to-fry, 2) fry-to-presmolt, 3) presmolt-to-adult return from the ocean, 4) adult en route from the ocean to the spawning grounds, and 5) reproduction. We ground-truthed the model to ensure its fit to the data, and then we modified survival and other parameters during various stages to examine future scenarios. Our analyses revealed that low survival of juveniles in Lake Washington (stage 2: averaging only 3% over the last 20 years), survival of adults returning to fresh water to spawn (stage 4), and survival of adults on spawning grounds to reproduce (stage 5) are likely limiting factors. Combined increases in these stages and others (specifically, the proportion of fish taken into the hatchery to be spawned) might also recover the population. As in other integrated hatchery populations, managers must weigh options relating to balancing the fraction of natural- and hatchery-origin fish, and our results showed that increasing the fraction of fish taken into the hatchery alone will not recover the population. Our model brings together population-specific data to help managers weigh conservation strategies and understand which stages and habitats are most limiting and how much survival must increase to achieve recovery targets. By extension, our analyses also reveal the utility of such models in other cases where stage-specific data are available.

North American Journal of Fisheries Management↗

USGS2022

Multidecadal trends in body size of Puget Sound Chinook Salmon: Analysis of data from the Tengu Derby, a culturally unique fishery

In Pacific salmon Oncorhynchus spp., downward trends in size and abundance have been reported for species and stocks for over 40 years, but the patterns are inconsistent among regions and species. Interpretation of these trends is complicated by many possible contributing factors, including short time series, data comprising a mix of stocks, and varying gear types. Here, we present data on the mass of individual Chinook Salmon Oncorhynchus tshawytscha caught in the winter from 1946 to 2019 in central Puget Sound, Washington, by participants in what may be the longest running Pacific salmon derby in North America, the Tengu Derby. In this annual recreational fishing competition, established by Japanese Americans immediately after release from internment camps at the end of World War II, participants follow strict gear, area, and methods regulations and catch almost exclusively salmonids originating from and remaining in Puget Sound. Records revealed an overall decline in fish mass over the decades, with a high degree of variability throughout the time series. Specifically, resident Chinook Salmon exhibited several shifts, including a decrease in size from a high in the 1950s to a low around 1980, followed by an increase to another high around 1990 and then a decline over the most recent 30 years. These size trends of residents differed from those of Puget Sound Chinook Salmon as a whole. We infer that the resident fish experienced ecological conditions affecting their growth that were distinct from those of fish feeding along the Pacific Ocean in the same periods. These distinct trends in size of Chinook Salmon from common origins indicate that the different migration patterns of fish within stocks must be considered in the analysis and interpretation of body size trends and also in patterns of survival.

Washington↗

USGS2020

Increased prespawning mortality threatens an integrated natural- and hatchery-origin sockeye salmon population in the Lake Washington Basin

The life cycle of diadromous fishes such as salmonids involves natural mortality in a series of distinct life history stages, occurring sequentially in different habitats. Decades of research have emphasized mortality at the embryo, juvenile, and sub-adult stages but it is increasingly clear that some adults that survive and return to freshwater habitats die during the final homeward migration or after they reach the spawning grounds, prior to breeding. These are termed “en route” and “prespawning” mortality, respectively, and can threaten populations depleted by mortality at previous stages. In this study, we present evidence that the sockeye salmon, Oncorhynchus nerka, population that returns to the Lake Washington Basin, in Washington State, USA, is experiencing both forms of adult mortality. Counts of the salmon entering the basin on their return migration in June and July were compared to counts in the major spawning grounds in September through November for 1995–2018. The disparity has increased markedly in recent years. The counts on the spawning grounds have decreased as a proportion of the number entering the system with an average 49 % of sockeye unaccounted for, consistent with increased en route mortality. In addition, prespawning mortality rates have increased in salmon that reach the Cedar River, the main spawning tributary, both at a hatchery holding adult fish in 1995–2018, and in the naturally spawning populations when monitored in the last five years. Hatchery records indicated <10 % prespawning mortality for 1995–2010, increasing to an average 43 % for 2014 – 2018. Recent carcass surveys in the Cedar River documented that 33.6% (2014), 22.3% (2015), 30.3% (2016) and 50.0% (2018) of female sockeye died before completing spawning. These recent increases in prespawning mortality have been associated with warm water during entry to freshwater, but comparably warm water in past decades had no such effect. Steady warming of river temperatures around the median run completion date from < 8.0 °C to > 13.0 °C was correlated with increased prespawning mortality rates at the hatchery from 1995–2018. We conclude that warming conditions during migration and spawning, in concert with other factors such as infections with pathogens, are responsible for the increased prespawning mortality of adult sockeye salmon that are high enough to threaten the population’s viability.

Washington↗

USGS2019

Trophic plasticity and the invasion of a renowned piscivore: A diet synthesis of northern pike (Esox lucius) from the native and introduced ranges in Alaska, U.S.A.

The invasion of non-native fishes is a leading cause of extinction and imperilment of native freshwater fishes. Evidence suggests that introduced species with generalist diets have the potential for greatest impacts through competition and predation even though populations are often comprised of specialist individuals. The northern pike (Esox lucius), a predatory fish, has been widely introduced outside its native range for recreational fishing purposes, especially in western North America, and it has been implicated in declines and extirpations of native fishes. We synthesized over 2,900 individual northern pike diet records across 31 waterbodies from the native and introduced ranges in Alaska to quantify the extent of diet specialization and generalization relative to freshwater prey communities. To control for effects of ontogenetic diet shifts, we separately analyzed major size classes of northern pike and inferred and visualized trophic plasticity from Prey-Specific Abundance indices and ordination. Diet generalization was common in northern pike among waterbodies and usually consisted of individuals consuming macroinvertebrates. However, when available, individual northern pike diets showed specialization on fishes, amphibians, small mammals, and dragonflies. The reliance on macroinvertebrate prey by northern pike from small, isolated lakes in the native and invasive ranges suggests that dietary plasticity facilitates persistence of these predators in the absence of preferred fish prey. Broadly, this synthesis supports the hypothesis that trophic plasticity and diet generalization widely occur among invasive and native populations of northern pike which is likely to enhance the probability of introduction success, exacerbate their environmental impacts, and complicate management of this potentially invasive freshwater predator.

Alaska↗

USGS2019

A Bayesian life-cycle model to estimate escapement at maximum sustained yield in salmon based on limited information

Life-cycle models combine several strengths for estimating population parameters and biological reference points of harvested species and are particularly useful for those exhibiting distinct habitat shifts and experiencing contrasting environments. Unfortunately, time series data are often limited to counts of adult abundance and harvest. By incorporating data from other populations and by dynamically linking the life-history stages, Bayesian life-cycle models can be used to estimate stage-specific productivities and capacities as well as abundance of breeders that produce maximum sustained yield (MSY). Using coho salmon ( Oncorhynchus kisutch ) as our case study, we show that incorporating information on marine survival variability from nearby populations can improve model estimates and affect management parameters such as escapement at MSY. We further show that the expected long-term average yield of a fishery managed for a spawner escapement target that produces MSY strongly depends on the average marine survival. Our results illustrate the usefulness of incorporating information from other sources and highlight the importance of accounting for variation in marine survival when making inferences about the management of Pacific salmon.

Washington↗

USGS2019

Influences of spawning timing, water temperature, and climatic warming on early life history phenology in western Alaska sockeye salmon

We applied an empirical model to predict hatching and emergence timing for 25 western Alaska sockeye salmon (Oncorhynchus nerka) populations in four lake-nursery systems to explore current patterns and potential responses of early life history phenology to warming water temperatures. Given experienced temperature regimes during development, we predicted hatching to occur in as few as 58 d to as many as 260 d depending on spawning timing and temperature. For a focal lake spawning population, our climate-lake temperature model predicted a water temperature increase of 0.7 to 1.4 °C from 2015 to 2099 during the incubation period, which translated to a 16 d to 30 d earlier hatching timing. The most extreme scenarios of warming advanced development by approximately a week earlier than historical minima and thus climatic warming may lead to only modest shifts in phenology during the early life history stage of this population. The marked variation in the predicted timing of hatching and emergence among populations in close proximity on the landscape may serve to buffer this metapopulation from climate change.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2018

Concentrations of environmental DNA (eDNA) reflect spawning salmon abundance at fine spatial and temporal scales

Developing fast, cost-effective assessments of wild animal abundance is an important goal for many researchers, and environmental DNA (eDNA) holds much promise for this purpose. However, the quantitative relationship between species abundance and the amount of DNA present in the environment is likely to vary substantially among taxa and with ecological context. Here, we report a strong quantitative relationship between eDNA concentration and the abundance of spawning sockeye salmon in a small stream in Alaska, USA, where we took temporally- and spatially-replicated samples during the spawning period. This high-resolution dataset suggests that (1) eDNA concentrations vary significantly day-to-day, and likely within hours, in the context of the dynamic biological event of a salmon spawning season; (2) eDNA, as detected by species-specific quantitative PCR probes, seems to be conserved over short distances (tens of meters) in running water, but degrade quickly over larger scales (ca. 1.5 km); and (3) factors other than the mere presence of live, individual fish — such as location within the stream, live/dead ratio, and water temperature — can affect the eDNA-biomass correlation in space or time. A multivariate model incorporating both biotic and abiotic variables accounted for over 75% of the eDNA variance observed, suggesting that where a system is well-characterized, it may be possible to predict species' abundance from eDNA surveys, although we underscore that species- and system-specific variables are likely to limit the generality of any given quantitative model. Nevertheless, these findings provide an important step toward quantitative applications of eDNA in conservation and management.

Alaska↗

USGS2017

Thermal adaptation and phenotypic plasticity in a warming world: Insights from common garden experiments on Alaskan sockeye salmon

An important unresolved question is how populations of coldwater-dependent fishes will respond to rapidly warming water temperatures. For example, the culturally and economically important group, Pacific salmon ( Oncorhynchus spp.), experience site-specific thermal regimes during early development that could be disrupted by warming. To test for thermal local adaptation and heritable phenotypic plasticity in Pacific salmon embryos, we measured the developmental rate, survival, and body size at hatching in two populations of sockeye salmon ( Oncorhynchus nerka ) that overlap in timing of spawning but incubate in contrasting natural thermal regimes. Using a split half-sibling design, we exposed embryos of 10 families from each of two populations to variable and constant thermal regimes. These represented both experienced temperatures by each population, and predicted temperatures under plausible future conditions based on a warming scenario from the downscaled global climate model (MIROC A1B scenario). We did not find evidence of thermal local adaptation during the embryonic stage for developmental rate or survival. Within treatments, populations hatched within 1 day of each other, on average, and among treatments, did not differ in survival in response to temperature. We did detect plasticity to temperature; embryos developed 2.5 times longer (189 days) in the coolest regime compared to the warmest regime (74 days). We also detected variation in developmental rates among families within and among temperature regimes, indicating heritable plasticity. Families exhibited a strong positive relationship between thermal variability and phenotypic variability in developmental rate but body length and mass at hatching were largely insensitive to temperature. Overall, our results indicated a lack of thermal local adaptation, but a presence of plasticity in populations experiencing contrasting conditions, as well as family-specific heritable plasticity that could facilitate adaptive change.

Global Change Biology↗

USGS2016

Recovery of sockeye salmon in the Elwha River, Washington, after dam removal: Dependence of smolt production on the resumption of anadromy by landlocked kokanee

Pacific salmon Oncorhynchus spp. are adept at colonizing habitat that has been reopened to anadromous passage. Sockeye Salmon O. nerka are unique in that most populations require lakes to fulfill their life history. Thus, for Sockeye Salmon to colonize a system, projects like dam removals must provide access to lakes. However, if the lakes contain landlocked kokanee (lacustrine Sockeye Salmon), the recovery of Sockeye Salmon could be mediated by interactions between the two life history forms and the processes associated with the resumption of anadromy. Our objective was to evaluate the extent to which estimates of Sockeye Salmon smolt production and recovery are sensitive to the resumption of anadromy by kokanee after dam removal. We informed the analysis based on the abiotic and biotic features of Lake Sutherland, which was recently opened to passage after dam removal on the Elwha River, Washington. We first developed maximum expectations for the smolt-producing capacity of Lake Sutherland by using two predictive models developed from Sockeye Salmon populations in Alaska and British Columbia: one model was based on the mean seasonal biomass of macrozooplankton, and the other was based on the euphotic zone volume of the lake. We then constructed a bioenergetics-based simulation model to evaluate how the capacity of Lake Sutherland to rear yearling smolts could change with varying degrees of anadromy among O. nerka fry. We demonstrated that (1) the smolt-producing capacity of a nursery lake for juvenile Sockeye Salmon changes in nonlinear ways with changes in smolt growth, mortality, and the extent to which kokanee resume anadromy after dam removal; (2) kokanee populations may be robust to changes in abundance after dam removal, particularly if lakes are located higher in the watershed on tributaries separate from where dams were removed; and (3) the productivity of newly establishing Sockeye Salmon can vary considerably depending on whether the population becomes rearing limited or is recruitment limited and depending on how adult escapement is managed.

Washington↗

USGS2016

Influence of species, size and relative abundance on the outcomes of competitive interactions between brook trout and juvenile coho salmon

Resource competition between animals is influenced by a number of factors including the species, size and relative abundance of competing individuals. Stream-dwelling animals often experience variably available food resources, and some employ territorial behaviors to increase their access to food. We investigated the factors that affect dominance between resident, non-native brook trout and recolonizing juvenile coho salmon in the Elwha River, WA, USA, to see if brook trout are likely to disrupt coho salmon recolonization via interference competition. During dyadic laboratory feeding trials, we hypothesized that fish size, not species, would determine which individuals consumed the most food items, and that species would have no effect. We found that species, not size, played a significant role in dominance; coho salmon won 95% of trials, even when only 52% the length of their brook trout competitors. As the pairs of competing fish spent more time together during a trial sequence, coho salmon began to consume more food, and brook trout began to lose more, suggesting that the results of early trials influenced fish performance later. In group trials, we hypothesized that group composition and species would not influence fish foraging success. In single species groups, coho salmon consumed more than brook trout, but the ranges overlapped. Brook trout consumption remained constant through all treatments, but coho salmon consumed more food in treatments with fewer coho salmon, suggesting that coho salmon experienced more intra- than inter-specific competition and that brook trout do not pose a substantial challenge. Based on our results, we think it is unlikely that competition from brook trout will disrupt Elwha River recolonization by coho salmon.

Washington↗

USGS2007

An evaluation of the effects of conservation and fishery enhancement hatcheries on wild populations of salmon

The historical, political and scientific aspects of salmon hatchery programmes designed to enhance fishery production, or to recover endangered populations, are reviewed. We start by pointing out that the establishment of hatcheries has been a political response to societal demands for harvest and conservation; given this social context, we then critically examined the levels of activity, the biological risks, and the economic analysis associated with salmon hatchery programmes. A rigorous analysis of the impacts of hatchery programmes was hindered by the lack of standardized data on release sizes and survival rates at all ecological scales, and since hatchery programme objectives are rarely defined, it was also difficult to measure their effectiveness at meeting release objectives. Debates on the genetic effects of hatchery programmes on wild fish have been dominated by whether correct management practices can reduce negative outcomes, but we noted that there has been an absence of programmatic research approaches addressing this important issue. Competitive interactions between hatchery and wild fish were observed to be complex, but studies researching approaches to reduce these interactions at all ecological scales during the entire salmon life history have been rare, and thus are not typically considered in hatchery management. Harvesting of salmon released from fishery enhancement hatcheries likely impacts vulnerable wild populations; managers have responded to this problem by mass marking hatchery fish, so that fishing effort can be directed towards hatchery populations. However, we noted that the effectiveness of this approach is dependant on accurate marking and production of hatchery fish with high survival rates, and it is not yet clear whether selective fishing will prevent overharvest of wild populations. Finally, research demonstrating disease transmission from hatchery fish to wild populations was observed to be equivocal; evidence in this area has been constrained by the lack of effective approaches to studying the fate of pathogens in the wild. We then reviewed several approaches to studying the economic consequences of hatchery activities intended to inform the social decisions surrounding programmes, but recognized that placing monetary value on conservation efforts or on hatcheries that mitigate cultural groups’ loss of historical harvest opportunities may complicate these analyses. We noted that economic issues have rarely been included in decision making on hatchery programmes. We end by identifying existing major knowledge gaps, which, if filled, could contribute towards a fuller understanding of the role that hatchery programmes could play in meeting divergent goals. However, we also recognized that many management recommendations arising from such research may involve trade-offs between different risks, and that decisions about these trade-offs must occur within a social context. Hatcheries have played an important role in sustaining some highly endangered populations, and it is possible that reform of practices will lead to an increase in the number of successful programmes. However, a serious appraisal of the role of hatcheries in meeting broader needs is urgently warranted and should take place at the scientific, but more effectively, at the societal level.

Advances in Marine Biology↗

USGS1995

Critical thermal maxima of coho salmon ( Oncorhynchus kisutch ) fry under field and laboratory acclimation regimes

Juvenile coho salmon ( Oncorhynchus kisutch ) from three populations in Washington State were captured in the field and tested for critical thermal maximum (CTM). Tolerances varied among the populations (mean CTMs were 28.21, 29.13, and 29.23 °C) and exceeded published data from some laboratory tests. The population from a relatively cool stream had a lower CTM than the two populations from warmer streams. However, after the salmon had been in the laboratory for 3 months under constant, common temperature regimes, the CTMs no longer differed, indicating that the population-specific differences resulted from different acclimation regimes rather than from genetic adaptation.

Washington↗