Kathleen G O'Malley

Kathleen G O'Malley
Oregon State University | OSU · Department of Fisheries and Wildlife

About

49
Publications
6,667
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709
Citations
Citations since 2016
24 Research Items
344 Citations
20162017201820192020202120220102030405060
20162017201820192020202120220102030405060
20162017201820192020202120220102030405060
20162017201820192020202120220102030405060

Publications

Publications (49)
Article
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...
Article
Full-text available
Teleost fish are the most diverse group of vertebrates and provide opportunities to study the evolution of sex determination (SD) systems. Using genomic and functional analyses, we identified a male-specific duplication of anti-Müllerian hormone (amh) gene as the male master sex-determining (MSD) gene in Sebastes schlegelii. By resequencing 10 male...
Article
Full-text available
Albacore (Thunnus alalunga) support an economically valuable global fishery, but surprisingly little is known about the population structure of this highly migratory species. Physical tagging data suggest that Albacore from the North and South Pacific Ocean are separate stocks, but results from previous genetic studies did not support this two stoc...
Article
Genetic methods can guide and improve management of recreational mixed‐stock fisheries by informing stock‐specific estimates of harvest. We applied genetic stock identification and parentage‐based tagging to a recreational Chinook Salmon Oncorhynchus tshawytscha fishery in the Columbia River to illustrate the value of genetic analysis in management...
Article
Full-text available
The phenotypic identification of sex in Sebastes rockfish is difficult and often impractical from a management perspective, and the genetic basis of sex determination in the genus is currently uncertain. We tested a previously developed sex identification polymerase chain reaction restriction fragment length polymorphism (PCR–RFLP) assay in eight s...
Article
Full-text available
The California Current Ecosystem (CCE) is a dynamic marine ecosystem from which many socioeconomically important fisheries species are harvested. Here, a genotyping-by-sequencing (GBS) approach was used to examine genomic variation in an early life stage (megalopae) of the Dungeness crab (Cancer magister), which constitutes the most valuable single...
Article
Full-text available
Little is known about intraspecific variation within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50‐km2 area off the Oregon coas...
Article
Full-text available
The Arctic will be especially affected by climate change, resulting in altered seasonal timing. Anadromous Arctic char (Salvelinus alpinus) is strongly influenced by sea surface temperature (SST) delimiting time periods available for foraging in the sea. Recent studies of salmonid species have shown variation at phenology‐related loci associated wi...
Article
Full-text available
Reintroductions are widely implemented as a means of reestablishing wild populations and genetic parentage methods can be used in concert with these efforts to monitor and evaluate efficacy. In addition to understanding demographic outcomes, reconstructed pedigrees, when combined with phenotypic data, can provide insight into the adaptive potential...
Article
Full-text available
Arctic freshwater ecosystems have been profoundly affected by climate change. Given that the Arctic charr (Salvelinus alpinus) is often the only fish species inhabiting these ecosystems, it represents a valuable model for studying the impacts of climate change on species life‐history diversity and adaptability. Using a genotyping‐by‐sequencing appr...
Article
Full-text available
Using a combination of population- and individual-based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200 km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population ge...
Article
Full-text available
Limited approaches exist for studying population connectivity in widely dispersing marine benthic invertebrates. Genetic techniques can provide important insights toward identifying recruitment trajectories. Here, 10 microsatellite loci were used to examine connectivity among Oregon Dungeness crabs (Cancer magister, Dana, 1852) in the California Cu...
Article
Full-text available
Understanding connectivity of marine organisms is necessary for determining the appropriate scale of conservation and management strategies. For species that inhabit both the coastal ocean and partially enclosed water bodies (i.e., estuaries or fjords), this information is even more critical since estuaries and fjords are often characterized by hyd...
Article
Full-text available
Dams contribute to declines in fish abundance, in part, by blocking access to historical habitat. When fish ladders are infeasible, fish can be trapped below a dam and transported above to provide access to habitat. However, this conservation strategy has received little attention in the literature, and many questions regarding efficacy remain unan...
Article
Full-text available
Dams, utilized for hydroelectric or flood control purposes, obstruct organism dispersal and have contributed to the decline of many migratory fish populations. For threatened Chinook salmon (Oncorhynchus tshawytscha) from the Willamette River Basin in Oregon, human-assisted reintroductions are being used to facilitate dispersal to historical habita...
Data
Full-text available
Dams have contributed to the decline of migratory fishes by blocking access to historical habitat. The active transport (trap and haul) of migratory fish species above existing dams can sometimes support population recovery when the use of fish ladders or dam removal is infeasible. However, little is known about the efficacy of trap and haul conser...
Article
Full-text available
Reintroductions are used to reestablish populations to historical habitats from which they were extirpated. The long-term success of these efforts will depend on genetic diversity and the ability of reintroduced individuals to adapt to ecological change. We examined variation at circadian clock (OtsClock1b and OmyFbxw11) and reproductive timing (Ot...
Article
Full-text available
Dams have contributed to the decline of migratory fishes by blocking access to historical habitat. The active transport (trap and haul) of migratory fish species above existing dams can sometimes support population recovery when the use of fish ladders or dam removal is infeasible. However, little is known about the efficacy of trap and haul conser...
Article
Major histocompatibility complex (MHC) and immune-relevant gene markers were used to evaluate differences in reproductive success (RS) among naturally spawning coho salmon Oncorhynchus kisutch mate pairs involving an alternative male reproductive phenotype, known as jacks. These mate pairs included both hatchery-reared and wild origin fish such tha...
Conference Paper
Many fish species have been negatively affected by the construction of high head dams because they alter temperature and flow regimes, as well as, impede fish migration. In recent years, managers have begun to reintroduce salmonids above dams in an effort to mitigate these effects. This strategy has been adopted on the South Fork McKenzie River, Or...
Article
Full-text available
Hatcheries support fisheries and aid in the recovery of endangered wild populations. Evidence for reduced reproductive success (RS) in wild-spawning hatchery-reared salmon compared with that in wild-born fish invites questions about the impact on subsequent generations. Immune gene-dependent mate preference is one mechanism known to influence salmo...
Article
Full-text available
The application of DNA-based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life-history differences. Accurate and efficient identification of the most likely origin for salmon...
Article
Full-text available
Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorh...
Article
Given their large sizes, early running multisea-winter (MSW) Atlantic salmon, Salmo salar L., often termed spring fish, are particularly prized by anglers; hence, there is likely to be great management interest in this component of the run. Indeed overexploitation by anglers may have been one of the factors contributing to the long-term declines in...
Article
Full-text available
We examined the distribution of Umpqua Chub Oregonichthys kalawatseti, an endemic, vulnerable minnow in western Oregon, and whether six ecological populations (based on distribution patterns) had sufficient genetic cohesion to be considered evolutionary populations. We also evaluated the influence of Holocene geological events and recent nonnative...
Conference Paper
It has been shown that hatchery fish have lower reproductive success (RS) than wild fish when breeding in the wild and that there is a carry-over effect from hatchery bred fish to subsequent generations of wild populations. One causal mechanism that has been suggested to result in reproductive differences between wild and hatchery fish and also amo...
Article
Full-text available
Seasonal timing of life-history events is often under strong natural selection. The Clock gene is a central component of an endogenous circadian clock that senses changes in photoperiod (day length) and mediates seasonal behaviours. Among Pacific salmonids (Oncorhynchus spp.), seasonal timing of migration and breeding is influenced by photoperiod....
Article
Full-text available
In most organisms, an internal circadian clock coordinates the expression of biological rhythms and enables individuals to anticipate and respond to the seasonally changing environment. There is remarkable conservation of function in the molecular machinery underlying this circadian clock across taxa with 4 canonical proteins interacting to form an...
Article
Full-text available
A critical seasonal event for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which adults migrate from the ocean to breed in freshwater. We investigated whether allelic variation at the circadian rhythm genes, OtsClock1a and OtsClock1b, underlies genetic control of migration timing among 42 populations in North America. We iden...
Article
Full-text available
Circadian rhythms underlie diverse life functions ranging from cellular activities to behavior. Multiple clock genes play a central role in the generation of these rhythms. We partially characterized two copies of the Clock gene from Chinook salmon (Oncorhynchus tshawytscha), OtsClock1a and OtsClock1b. The 6,460 bp OtsClock1a sequence contains 16 e...
Article
Local adaptation is a dynamic process driven by selection that can vary both in space and time. One important temporal adaptation for migratory animals is the time at which individuals return to breeding sites. Chinook salmon (Oncorhynchus tshawytscha) are excellent subjects for studying the genetic basis of temporal adaptation because their high s...
Article
Development of nine polymorphic microsatellites from a genomic library of hybrid striped bass (female Morone chrysops × male Morone saxatilus) DNA is described. Breeding of hybrid striped bass for aquaculture is based largely on breeding wild fish. Molecular markers such as microsatellites will be useful tools for developing broodstock, estimating...
Article
Full-text available
We incorporated 69 microsatellite loci into an existing data set of 132 markers to test for quantitative trait loci (QTLs) affecting spawning date and body weight in a backcross between two outbred strains of rainbow trout (Oncorhynchus mykiss). Twenty-six linkage groups were identified and synteny of duplicated microsatellite markers was used to c...
Article
Thirty-eight nuclear-encoded microsatellites were isolated from the marine fish Sciaenops ocellatus (red drum). The species is of economic importance in the southeastern United States, and declines in abundance have led to augmentation of the ‘wild’ fishery with hatchery-raised fingerlings. The microsatellites will be useful for studies designed to...

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Projects

Projects (3)
Archived project
Investigation of genetic population structure and otolith shape variation in the deacon rockfish (Sebastes diaconus), followed by an a study testing a genetic sex identification assay for the Sebastes rockfish genus
Project
This project aims to investigate whether vulnerability to angling is a heritable trait in hatchery steelhead.
Project
This meta-project aims to investigate processes affecting the diversity, distribution and abundance of spring-run Chinook salmon in Oregon's upper Willamette River