Thomas P. Quinn

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• Doctor of Philosophy
• Professor at University of Washington

Greater understanding of environmental effects to salmon survival during incubation can aid in prediction and facilitate population modeling at local and regional scales. Four basin-scale studies of Chinook salmon egg-to-fry survival were conducted between years 2009 and 2021 in spawning tributaries of the upper and middle Columbia River. Each of t...

Freshwater populations of typically marine species present unique opportunities to investigate biodiversity, evolutionary divergence, and the adaptive potential and niche width of species. A few pinniped species have populations that reside solely in freshwater. The harbour seals inhabiting Iliamna Lake, Alaska constitute one such population. Their...

The present study quantified the vertical and horizontal distribution of sub-adult Chinook salmon Oncorhynchus tshawytscha in nearshore marine environments. Depth-specific hook and line sampling was conducted along the Pacific Ocean coast of Washington, USA. Our analysis, based on 187 Chinook salmon from 1299 sampling deployments and 6616 hooks, re...

Background The large-scale seasonal migrations undertaken by many species require complex navigational and timing decisions. Animals migrating in groups might benefit from collective decision making, especially if the environment is noisy (i.e., has high degree of local variation rather than smooth gradients in, for example, salinity or temperature...

Background The large-scale seasonal migrations undertaken by many species require complex navigational and timing decisions. Animals migrating in groups might benefit from collective decision making, especially if the environment is noisy (i.e., has high degree of local variation rather than smooth gradients in, for example, salinity or temperature...

Sculpins (coastrange and slimy) and sticklebacks (ninespine and threespine) are widely distributed fishes cohabiting 2 south-central Alaskan lakes (Aleknagik and Iliamna), and all these species are parasitized by cryptic diphyllobothriidean cestodes in the genus Schistocephalus. The goal of this investigation was to test for host-specific parasitic...

Many ecosystems have been dramatically affected by non-native species, but not all such species have strong deleterious effects. American shad, Alosa sapidissima, a fish species native to the Atlantic coast of North America, was transplanted to the Pacific coast in the late nineteenth century and quickly colonized many US rivers. Their increased ab...

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,...

Anadromous salmonid species vary in their use of open ocean, coastal, and inland marine waters. To better understand this diversity in behavior and habitat use, 120 coastal cutthroat trout, Oncorhynchus clarkii clarkii, were caught in southern Puget Sound, Washington, USA, tagged with acoustic transmitters, and 95 were detected by a network of rece...

Synopsis Pacific salmon (Oncorhynchus spp.) hatch and feed in freshwater habitats, migrate to sea to mature, and return to spawn at natal sites. The final, riverine stages of the return migrations are mediated by chemical properties of the natal stream that they learned as juveniles. Like some other fish, salmon growth is asymptotic; they grow cont...

Anadromous brown trout (Salmo trutta) in the northeastern Atlantic Ocean, and coastal cutthroat trout (Oncorhynchus clarkii clarkii) in the northeastern Pacific Ocean, are analogs in many ways. Both species display similar patterns of complex life histories and behavioral flexibility, are iteroparous and facultatively anadromous and occupy nearshor...

Ecological models are used to understand where fishing vessels operate, improving fisheries management success. The ideal free distribution (IFD) predicts equalization of catch across locations in response to distributions of fish and competing vessels. We applied the IFD as a null model to investigate the movement and catch per vessel (CPUE) of th...

Many foraging models assume “perfect information” and “free movement” when describing predator foraging behavior, although this is rare in nature. Here, we quantified predation by brown bears (Ursus arctos Linnaeus, 1758) on adult sockeye salmon (Oncorhynchus nerka (Walbaum, 1792)) in a series of spatially proximate ponds that largely satisfied bot...

Abstract: The phenomenon of homing by salmonid fishes to natal sites for breeding is well established, but the chemicals in rivers that they learn as juveniles and identify as adults are not fully determined. Dissolved free amino acid (DFAA) profiles have been hypothesized to allow salmonids to distinguish their natal river from others nearby. To e...

Fisheries managers stock triploid (i.e., infertile, artificially produced) rainbow trout Oncorhynchus mykiss in North American lakes to support sport fisheries while minimizing the risk of genetic introgression between hatchery and wild trout. In Washington State, the Washington Department of Fish and Wildlife (WDFW) allocates approximately US $3 m...

The native fish biodiversity of Patagonia has been highly modified by a long history of salmonid introductions from the Northern Hemisphere for recreational fishing and aquaculture purposes. Coho salmon, Oncorhynchus kisutch, is the most recent salmonid established in Patagonia, first recorded in Chile in 2014 and 2019. In this work, we report for...

Long-term datasets can reveal otherwise undetectable ecological trends, illuminating the historical context of contemporary ecosystem states. We used two decades (1997–2019) of scientific trawling data from a subtidal, benthic site in Puget Sound, Washington, USA to test for gradual trends and sudden shifts in total sea star abundance across 11 spe...

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 distributi...

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 distrib...

Mobile species are particularly affected by artificial barriers in riverine ecosystems requiring large investments to restore connectivity. However, few large-scale studies have examined the long-term, broad-scale ecological outcomes of restoring connectivity for these species. In our study, which spanned 15 to 20 years depending on response, we qu...

Sockeye salmon, Oncorhynchus nerka, are anadromous, semelparous fish that breed in freshwater - typically in streams, and juveniles in most populations feed in lakes for one or two years, then migrate to sea to feed for two or three additional years, before returning to their natal sites to spawn and die. This species undergoes important changes in...

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, popul...

Homing is an essential aspect of the evolutionary ecology of salmon, and the final stages are guided by odors learned prior to migration from natal sites. Amino acids (AAs) have been hypothesized to provide olfactory information sufficient for homing. We sampled water from five tributaries to Lake Aleknagik, Alaska prior to and after the arrival of...

Grouping is ubiquitous across animal taxa and environments. Safety in numbers is perhaps the most cited reason for grouping, yet this fundamental tenet of ecological theory has rarely been tested in wild populations. We analyzed a multidecadal dataset of Pacific salmon at sea and found that individuals in larger groups had lower predation risk; wit...

Comparison of trends in Puget Sound Chinook salmon body size from a culturally unique recreational fishery and purse seine samples reveals the importance of differential migration in the analysis of body size trends.

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 va...

Partial migration in salmonids provides access to freshwater and marine feeding environments varying in productivity. To test the hypothesis that partial migration drives differences in growth and energy storage with differential consequences for females than males, we assigned Oncorhynchus mykiss sampled on the western Kamchatka Peninsula, Russia,...

The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to ada...

Diadromous fishes migrate between freshwater and marine habitats to complete their life cycle, a complexity that makes them vulnerable to the adverse effects of current and past human activities on land and in the oceans. Many North American species are critically endangered, and entire populations have been lost. Major factors driving declines inc...

Hair samples obtained from barbed wire can identify bears from DNA, assess trophic position from stable isotopes, and yield other data. For brown bears (Ursus arctos), a wire height of 50 cm has become standard protocol, but the efficacy of this height has not been evaluated. Here, we briefly review this protocol, and use data from wires across sma...

Each year, juveniles of eight salmonid species enter the Salish Sea — the inland marine waters between northwestern Washington, USA, and British Columbia, Canada. These species vary in the proportions remaining there and migrating to feed in the Pacific Ocean. Such differential migration affects their growth rates and exposure to habitat alteration...

Salmonid olfactory imprinting during the parr‐to‐smolt transformation (PST) is essential for successful homing to natal spawning sites years later by mature fish. However, in many species, juveniles may move away from spawning sites before the PST, yet home to the natal site as adults, indicating that there may be multiple imprinting windows. To te...

The timing of anadromous migrations varies greatly among species, reflecting foraging opportunities, predation risk, and physical factors in freshwater and marine habitats. We studied the timing of bull trout, Salvelinus. confluentus, migrations downstream into Puget Sound, Washington, and the return migration using data from a combination of traps...

Detection, pursuit, capture, and consumption of prey by predators may be time consuming or not, depending on predators and prey, and this time allocation affects other aspects of predator ecology. Pacific salmon contribute substantially to coastal brown bear (Ursus arctos) diets, with implications for predators, prey, and their ecosystem. Brown bea...

The remarkable ability of Pacific salmon (genus Oncorhynchus) to home to their natal stream to spawn has tended to obscure the fact that a small proportion of the spawners stray to non-natal streams. It is hypothesized that straying is an evolutionary alternative to homing and that these two life-history strategies are in dynamic equilibrium. Stray...

Brown bears Ursus arctos consume a wide range of organisms, including ungulates and plants, but Pacific salmon Oncorhynchus spp. are especially important to their diet where their ranges overlap. Although some brown bears minimize antagonistic encounters with other brown bears or infanticide by avoiding streams where salmon spawn, studies generally...

Many adult hatchery‐origin Pacific salmon return to their natal river but do not enter the hatchery, instead spawning in the river, where they can have detrimental genetic and ecological effects on naturally reproducing wild populations. This phenomenon is especially well documented in Elk River, Oregon Chinook Salmon, based on previous analyses of...

When barriers to migration are removed, anadromous fishes from other rivers may colonize accessible habitat, or landlocked forms of the species may resume anadromy if conditions allow. For example, two large hydroelectric dams on the Elwha River, in Washington, USA, were removed, between 2011 and 2014, to restore Pacific salmon populations after a...

Migration timing has evolved in many animals, allowing them to maximize breeding and feeding success by matching seasonal changes in abiotic conditions and resource pulses. These seasonal changes can shift with the climate, resulting in mismatches between migrations and resource availability unless the populations respond through phenotypic plastic...

Migrations affect the population dynamics, life history, evolution, and connections of animals to natural ecosystems and humans. Many species and populations display partial migration (some individuals migrate and some do not), and differential migration (migration distance varies). Partial migration is widely distributed in fishes but the term dif...

Apex predators play keystone roles in ecosystems through top-down control, but the effects of apex omnivores on ecosystems could be more varied because changes in the resource base alter their densities and reverberate through ecosystems in complex ways. In coastal temperate ecosystems throughout much of the Northern Hemisphere, anadromous salmon o...

Programs to control predatory fishes have succesfully increased the survival of imperiled prey fishes in some cases, but efficacy depends on the population dynamics and ecological interactions between the predators, prey, and the rest of the community. In California’s Sacramento‐San Joaquin Delta, extremely low survival of downstream‐migrating juve...

Freshwater colonization by threespine stickleback has led to divergence in morphology between ancestral marine and derived freshwater populations, making them ideal for studying natural selection on phenotypes. In an open brackish–freshwater system, we previously discovered two genetically distinct stickleback populations that also differ in geomet...

Scavenging, an underappreciated mechanism of prey consumption for many predators, can contribute substantially to nutritional intake. Facultative scavengers such as brown bears (Ursus arctos Linnaeus, 1758) may both kill and scavenge Pacific salmon (genus Oncorhynchus Suckley, 1861), though the extent of scavenging and factors affecting this behavi...

The eggs of salmonid fishes are an important food source for many aquatic predators that detect eggs using olfaction. Moreover, chemicals from eggs and ovarian fluid aid sperm cells in detecting and locating eggs for fertilization, and ovarian fluid is attractive to conspecific males. Thus chemicals from eggs and ovarian fluid may facilitate reprod...

Median timing of reproduction in salmonid populations is generally consistent among years, reflecting long-term patterns of natural selection from characteristics of the local environment. However, altered selection from factors related to climate change or human intervention might shift timing over generations, with implications for the population...

Context Non-invasive sampling methods are widely used by ecologists to collect animal hair, images, tissue or signs. Sampling devices are imperfect, and collection success may vary over time owing to behavioural changes in study organisms or other factors. If collection success decreases, the utility of non-invasive sampling devices for longitudina...

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 ha...

Studies of the movements and abundance of predators can reveal their ecological roles and facilitate their conservation. These studies rely increasingly on noninvasive methods such as hair collection and camera traps. Insights from hair sampling, however, may be compromised if collection devices elicit avoidance behavior. To determine the extent to...

Many wildlife studies use noninvasive survey methods such as barbed wire to obtain hair samples for DNA analysis. If laboratory costs preclude processing all samples, it may be important to know a priori which samples are most likely to yield useful DNA. It may also be helpful to know whether apparently poor‐quality samples will yield useable DNA,...

Ecosystem‐based management requires consideration of overlapping resource use between humans and other consumers. Pacific salmon are an important resource for both fisheries and populations of wildlife around the Pacific rim, including coastal brown bears (Ursus arctos); salmon consumption has been positively linked to bear density, body size, and...

Pacific salmon acquire most of their biomass in the ocean before returning to spawn and die in coastal streams and lakes, thus providing subsidies of marine-derived nitrogen (MDN) to freshwater and terrestrial ecosystems. Recent declines in salmon abundance have raised questions of whether managers should mitigate for losses of salmon MDN subsidies...

We examined individual variation and the role of sex on the movements of the reef manta ray Mobula alfredi. Specifically, we analysed several movement metrics using 6 years of nightly observations (1 January 2009–31 December 2014) of 118 individually identifiable manta rays at two discrete but spatially proximate sites, locally known as Manta Heave...

The movements of maturing Pacific salmon (Oncorhynchus spp.) from marine waters into rivers pose challenges for their physiology, especially in basins affected by human structures and increasing temperatures. This study determined the thermal regimes experienced by maturing Chinook salmon (O. tshawytscha) entering the Lake Washington basin in weste...

Induced triploidy typically causes sterility in teleost fishes, and has therefore been proposed as a tool to manage genetic risks that farmed and hatchery-produced salmon pose to wild populations. Application of this technology for aquaculture has been challenged by inferior growth, survivorship and, in the case of free-ranging anadromous salmonids...

Alternative ecotypes of diverse animal taxa exhibit distinct, habitat-specific phenotypes. Rainbow trout (Oncorhynchus mykiss), a salmonid fish, exhibits stream-resident (fluvial), lake-migrant (adfluvial) and ocean-migrant (anadromous) ecotypes throughout its range. We investigated the coloration, and morphology associated with swimming performanc...

Studies of parallel evolution are seldom able to disentangle the influence of cryptic environmental variation from that of evolutionary history; whereas the unique life history of pink salmon (Oncorhynchus gorbuscha) presents an opportunity to do so. All pink salmon mature at age two and die after breeding. Hence, pink salmon bred in even years are...

Salmonid fishes may reside within or migrate between stream and lake habitats, or undergo anadromous migrations between freshwater and the ocean. While the degree of anadromy of salmonids has been thoroughly compared, no analogous review has examined the degree of lake use. To assess the extent of reliance on lake habitat in this family, we conside...

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 luciu...

In the original publication, the following disclaimer statement included in the first page should be ignored.

Selective consumption of prey by predators, observed in many animals, is often attributed to optimal foraging. Consistent with this idea, brown bears (Ursus arctos) often exhibit partial consumption, feeding exclusively on lipid-rich tissues of Pacific salmon (Oncorhynchus spp.), and discarding remains. However, bears also kill and abandon salmon w...

Migratory behaviour patterns in animals are controlled by a complex genetic architecture. Rainbow trout (Oncorhynchus mykiss) is a salmonid fish that spawns in streams but exhibits three primary life history pathways: stream‐resident (fluvial), lake‐migrant (adfluvial) and ocean‐migrant (anadromous). Previous studies examining fluvial and anadromou...

Migration of fishes between habitats influences population dynamics and ecological interactions. Some “partially migratory” populations include both migratory and non-migratory individuals, adding complexity to these dynamics. For partially migratory fishes with diadromous life histories, freshwater and marine habitats can differ greatly in availab...

Median bull trout Salvelinus confluentus breeding was 2 weeks earlier in a cool stream than in a proximate warmer stream, aligning with expectations for salmonids, followed by emergence timing calculated to be 6 weeks later in the cool stream than the warm stream. This pattern is consistent with both site‐specific adaptation and thermal spawning th...

The timing of breeding migration and reproduction links generations and substantially influences individual fitness. In salmonid fishes, such phenological events (seasonal return to fresh water and spawning) vary among populations but are consistent among years, indicating local adaptation in these traits to prevailing environmental conditions. Cha...

The tendencies of salmon and trout to spawn in proximity to their natal site and follow the parental timing of breeding are fundamental to their population structure, and also affect the performance of enhancement facilities. Specifically, understanding how parental spawning date and offspring release location affect the timing and place of breedin...

Studies of parallel or convergent evolution (the repeated, independent evolution of similar traits in similar habitats) rarely explicitly quantify the extent of parallelism (i.e., variation in the direction and/or magnitude of divergence) between the sexes; instead they often investigate both sexes together or exclude one sex. However, differences...

Biological invasions provide opportunities to examine contemporary evolutionary processes in novel environments. American shad, an anadromous fish native to the Atlantic Coast of North America, was introduced to California in 1871 and established spawning populations along the Pacific Coast that may provide insights into the dynamics of dispersal,...

Estuaries are used by anadromous fishes, either as the definitive marine habitat or as transition habitat as they move to fully marine waters, and extent of estuary use may vary with habitat conditions and fish attributes. Bull trout (Salvelinus confluentus) are commonly fluvial or adfluvial, though anadromous populations also exist. However, littl...

The cover image, by Peter M. Kiffney et al., is based on the original article Spatiotemporal patterns of mountain whitefish (Prosopium williamsoni) in response to a restoration of longitudinal connectivity, DOI: 10.1111/eff.12413.

As they return to spawn and die in their natal streams, anadromous, semelparous fishes such as Pacific salmon import marine‐derived nutrients to otherwise nutrient‐poor freshwater and riparian ecosystems. Diverse organisms exploit this resource, and previous studies have indicated that riparian tree growth may be enhanced by such marine‐derived nut...

There are three main themes in this self-reflective essay, and I hope they are thought-provoking without being pretentious. The first is the topic of scientific specialization. How do we steer a course between being a dilettante on one hand, dabbling in everything without making major contributions in any field, and on the other hand being a specia...

• Survival of post‐larval and juvenile organisms can depend on multiple seasonally‐fluctuating features, including thermal conditions and food availability. Alterations in the phenology of either consumers or their prey might decouple trophic relationships and reduce consumer growth and survival, and this potential for mismatches is especially pron...

Does disturbance increase or decrease parasite transmission among wildlife hosts? Ecologists cannot answer this controversial question, in part because few historical datasets rigorously document parasite abundance. Without such a baseline, it is difficult to determine whether contemporary ecosystems are experiencing elevated parasite burdens. Here...

The interaction between brown bears (Ursus arctos) and Pacific salmon (Oncorhynchus spp.) is important to the population dynamics of both species and a celebrated example of consumer‐mediated nutrient transport. Yet, much of the site‐specific information we have about the bears in this relationship comes from observations at a few highly visible bu...

To examine the role of longitudinal connectivity on the spatial and temporal dynamics of mountain whitefish (Prosopium williamsoni), we quantified movement and population dynamics following installation of the Landsburg Dam fishway, Cedar River, WA, USA. Mountain whitefish is widely distributed, poorly studied and not the focus of restoration. Befo...

Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non‐native populations. Yet, our understanding of how artificial (human‐mediated) and natural dispersal pathways of non‐native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the wide...