Jennifer L Nielsen | The Evergreen State College (original) (raw)

Papers by Jennifer L Nielsen

Reviews in Fish Biology …, 2002

Fisheries, 1998

Standard methods used by biologists around the world for sampling fish populations and determinin... more Standard methods used by biologists around the world for sampling fish populations and determining fish and habitat relationships primarily involve electrofishing. With the recent listings of coastal salmon and steelhead as threatened or endangered, one must ask how electrofishinginduced injury to fish in rare populations relates to "take" under the U.S. Endangered Species Act. Issues related to electrofishing are under discussion in California as federal and state agencies determine how to approach permitting for monitoring and research activities in rivers containing protected fish populations. Many problems have been discussed in the literature based on shortand long-term injury to individual fish from different forms of electrofishing. To date no standard approach for this technology exists that will allow effective surveys without probable injury to some portion of the fish population. How electrofishing injuries made at the individual fish level translate into population effects has not been adequately studied. In many areas of central and southern California, however, where the numbers of salmon and trout can be very small, and effective population size is frequently less than 25 breeding pairs, accumulated effects due to electrofishing may be significant. This paper reviews the electrofishing literature published during the last nine years. Based on this review and personal experience, I believe fisheries biologists frequently electrofish without considering potential harm or alternative methods. Therefore, I suggest the American Fisheries Society (AFS) develop a set of guidelines for least-invasive sampling methodologies, and adopt a policy on the ethical use of electrofishing for use by federal or state agencies to regulate all electrofishing activities in habitats containing wild fish. I believe other noninvasive study methods should be required in areas where it can be shown that electrofishing may significantly reduce a population's ability to persist.

"Risks of population extinction have been estimated using a variety of methods incorporating... more "Risks of population extinction have been estimated using a variety of methods incorporating information from different spatial and temporal scales. We briefly consider how several broad classes of extinction risk assessments, including population viability analysis, incidence functions, and ranking methods integrate information on different temporal and spatial scales. In many circumstances, data from surveys of neutral genetic variability within, and among, populations can provide information useful for assessing extinction risk. Patterns of genetic variability resulting from past and present ecological and demographic events, can indicate risks of extinction that are otherwise difficult to infer from ecological and demographic analyses alone. We provide examples of how patterns of neutral genetic variability, both within, and among populations, can be used to corroborate and complement extinction risk assessments."

Fisheries Oceanography, 2003

The importance of interspecific competition as a mechanism regulating population abundance in off... more The importance of interspecific competition as a mechanism regulating population abundance in off- shore marine communities is largely unknown. We evaluated offshore competition between Asian pink salmon and Bristol Bay (Alaska) sockeye salmon, which intermingle in the North Pacific Ocean and Bering Sea, using the unique biennial abundance cycle of Asian pink salmon from 1955 to 2000. Sockeye salmon growth

Transactions of the American Fisheries Society, 1988

Page 1. Transactions of the American Fisheries Society 117:322-335. 1988 «-': Copyri... more Page 1. Transactions of the American Fisheries Society 117:322-335. 1988 «-': Copyright by the American Fisheries Society 1988 Summer Production of Coho Salmon Stocked in Mount St. Helens Streams 3-6 Years after the 1980 Eruption ...

Transactions of the American Fisheries Society, 1988

... hydraulics of small stream channels, the distribution and abundance of juvenile coho salmon O... more ... hydraulics of small stream channels, the distribution and abundance of juvenile coho salmon Oncorhynchus kisutch, juvenile steelhead Salmo ... Some morphological variation among the stocks from different river systems (Taylor and McPhail 1985a) probably was obscured as a ...

Transactions of the American Fisheries Society, 2007

Molecular genetic methods were used to quantify natural hybridization between rainbow trout Oncor... more Molecular genetic methods were used to quantify natural hybridization between rainbow trout Oncorhynchus mykiss or steelhead (anadromous rainbow trout) and coastal cutthroat trout O. clarkii clarkii collected in the Copper River delta, Southeast Alaska. Eleven locations were sampled to determine the extent of hybridization and the distribution of hybrids. Four diagnostic nuclear microsatellite loci and four speciesspecific simple sequence repeat markers were used in combination with restriction fragment length polymorphism analyses of NADH dehydrogenase 5/6 (ND5/6) mitochondrial DNA (mtDNA) to investigate the genetic structure of trout from both species and identify putative interspecific hybrids. Hybrids were found in 7 of the 11 streams sampled in the Copper River delta, the extent of hybridization across all streams varying from 0% to 58%. Hybrid trout distribution appeared to be nonrandom, most individuals of mixed taxonomic ancestry being detected in streams containing rainbow trout rather than in streams containing coastal cutthroat trout. Genotypic disequilibrium was observed among microsatellite loci in populations with high levels of hybridization. We found no significant correlation between unique stream channel process groups and the number of hybrid fish sampled. Eighty-eight percent of fish identified as first-generation hybrids (F 1 ) in two populations contained coastal cutthroat trout mtDNA, suggesting directionality in hybridization. However, dominance of coastal cutthroat trout mtDNA was not observed at a third location containing F 1 hybrids, indicating that interspecific mating behavior varied among locations. Backcrossed individuals were found in drainages lacking F 1 hybrids and in populations previously thought to contain a single species. The extent and distribution of backcrossed individuals suggested that at least some hybrids are reproductively viable and backcrossed hybrid offspring move throughout the system.

Transactions of the American Fisheries Society, 2010

Here we compare the body shape of juvenile (age-0) sockeye salmon Oncorhynchus nerka that rear in... more Here we compare the body shape of juvenile (age-0) sockeye salmon Oncorhynchus nerka that rear in lakes (lake type) with that of those that rear in rivers (riverine) and relate rearing habitat to morphology and ecology. The two habitats present different swimming challenges with respect to water flow, foraging strategy, habitat complexity, and predation level. We present morphological data from three riverine and three lake-type populations in southwest Alaska. Using multivariate analyses conducted via geometric morphometrics, we determine population-and habitat-specific body shape. As predicted, riverine sockeye salmon have a more robust body shape, whereas lake-type sockeye salmon have a more streamlined body shape. In particular, we found differences in caudal peduncle depth (riverine deeper), eye size (riverine larger), and overall body depth (riverine deeper). One lake-type population did not follow the predicted pattern, exhibiting an overall exaggerated riverine body shape. Differences between the habitats in terms of predation, complexity, and foraging ecology are probably drivers of these differences. Allometry differed between life history types, suggesting that there are habitat-specific developmental differences.

Transactions of the American Fisheries Society, 1994

Thermal stratification occurred in pools of three rivers in northern California when inflow of co... more Thermal stratification occurred in pools of three rivers in northern California when inflow of cold water was sufficiently great or currents were sufficiently weak to prevent thorough mixing of water of contrasting temperatures. Surface water temperatures in such pools were commonly 3-9°C higher than those at the bottom. Cold water entered pools from tributaries, intergravel flow through river bars, and streamside subsurface sources. In Redwood and Rancheria Creeks, cold water was protected where gravel bars encroached into pools that were scoured along bedrock banks, creating isolated backwaters. Sixty-five percent of the juvenile steelhead Oncorhynchus mykiss found in the Rancheria Creek study reaches moved into adjacent stratified pools during periods of high ambient stream temperatures (23-28°C). Fish showed a decline in forage behavior and increased agonistic activity just before movement into stratified pools. In the Middle Fork Eel River, pools deeper than 3 m stratified when surface flow decreased to less than 1 m 3 /s. Summer-run steelhead adults were found in deep stratified pools on the Middle Fork Eel River throughout summer when midday ambient stream temperatures ranged from 26 to 29°C and coldwater pockets averaged 3.5°C cooler. Thermally stratified pools provided refuge habitat for significant numbers of young-of-the-year, yearling, and adult steelhead in marginal river habitats where stream temperatures reach upper incipient lethal levels.

Reviews in Fish Biology and Fisheries, 2011

outcomes, and (7) studies that cover a range of endpoints over ecologically relevant time periods.

Reviews in Fish Biology and Fisheries, 2004

Journal of Fish Biology, 2009

The hypothesis that growth in Pacific salmon Oncorhynchus spp. is dependent on previous growth wa... more The hypothesis that growth in Pacific salmon Oncorhynchus spp. is dependent on previous growth was tested using annual scale growth measurements of wild Chinook salmon Oncorhynchus tshawytscha returning to the Yukon and Kuskokwim Rivers, Alaska, from 1964 to 2004. Firstyear marine growth in individual O. tshawytscha was significantly correlated with growth in fresh water. Furthermore, growth during each of 3 or 4 years at sea was related to growth during the previous year. The magnitude of the growth response to the previous year's growth was greater when mean year-class growth during the previous year was relatively low. Length (eye to tail fork, L ETF ) of adult O. tshawytscha was correlated with cumulative scale growth after the first year at sea. Adult L ETF was also weakly correlated with scale growth that occurred during freshwater residence 4 to 5 years earlier, indicating the importance of growth in fresh water. Positive growth response to previous growth in O. tshawytscha was probably related to piscivorous diet and foraging benefits of large body size. Faster growth among O. tshawytscha year classes that initially grew slowly may reflect high mortality in slow growing fish and subsequent compensatory growth in survivors. Oncorhynchus tshawytscha in this study exhibited complex growth patterns showing a positive relationship with previous growth and a possible compensatory response to environmental factors affecting growth of the age class.

Environmental Biology of Fishes, 1998

Nucleotide sequences from the right-domain of salmonid mitochondrial DNA (mtDNA) control region f... more Nucleotide sequences from the right-domain of salmonid mitochondrial DNA (mtDNA) control region flanking the phenylalanine tRNA gene (tRNAPhe) were determined for 5 species and 14 subspecies of Oncorhynchus at the southern extent of their range. In all but one population, the right domain contained two 72 bp tandem repeats located between the tRNAPhe gene and the conserved sequence block CSB-3.

Environmental Biology of Fishes, 2000

Environmental Biology of Fishes, 2000

Environmental Biology of Fishes, 1996

Environmental Biology of Fishes, 2012

Increasing production of hatchery salmon over

Environmental Biology of Fishes, 2005

Identifying spawning behavior in Pacific halibut, Hippoglossus stenolepis, is particularly challe... more Identifying spawning behavior in Pacific halibut, Hippoglossus stenolepis, is particularly challenging because they occupy a deep, remote environment during the spawning season. To identify spawning events, a method is needed in which direct observation by humans is not employed. Spawning behavior of seven other flatfish species has been directly observed in their natural environment by investigators using SCUBA. All of these flatfish species display almost identical spawning behavior that follows a routine. Therefore, it is reasonable to believe that this spawning behavior occurs in other flatfish species, including Pacific halibut. As part of a larger study, we recaptured two Pacific halibut on which Pop-up Archival Transmitting (PAT) tags had been attached during the winter spawning season. Because the tags were physically retrieved, we were able to collect minute-by-minute depth records for 135 and 155 days. We used these depth data to tentatively identify spawning events. On seven separate occasions between 20 January 2001 and 9 February 2001, one fish displayed a conspicuous routine only seen during the spawning season of Pacific halibut and the routine parallels the actions of other spawning flatfish directly observed by humans using SCUBA. Therefore, we propose this routine represents spawning behavior in Pacific halibut. The second tagged fish did not display the conspicuous routine, thus challenging the assumption that Pacific halibut are annual spawners. PAT tags may prove to be a useful tool for identifying spawning events of Pacific halibut, and that knowledge may be used for improved management in the future.

Ecological Complexity, 2005

Many biological, hydrological, and geological processes are interactively linked in ecosystems. T... more Many biological, hydrological, and geological processes are interactively linked in ecosystems. These ecological phenomena normally vary within bounded ranges, but rapid, nonlinear changes to markedly different conditions can be triggered by even small differences if threshold values are exceeded. Intrinsic and extrinsic ecological thresholds can lead to effects that cascade among systems, precluding accurate modeling and prediction of system response to climate change. Ten case studies from North America illustrate how changes in climate can lead to rapid, threshold-type responses within ecological communities; the case studies also highlight the role of human activities that alter the rate or direction of system response to climate change. Understanding and anticipating nonlinear dynamics are important aspects of adaptation planning since responses of biological resources to changes in the physical climate system are not necessarily proportional and sometimes, as in the case of complex ecological systems, inherently nonlinear. Published by Elsevier B.V.

Reviews in Fish Biology …, 2002

Fisheries, 1998

Standard methods used by biologists around the world for sampling fish populations and determinin... more Standard methods used by biologists around the world for sampling fish populations and determining fish and habitat relationships primarily involve electrofishing. With the recent listings of coastal salmon and steelhead as threatened or endangered, one must ask how electrofishinginduced injury to fish in rare populations relates to "take" under the U.S. Endangered Species Act. Issues related to electrofishing are under discussion in California as federal and state agencies determine how to approach permitting for monitoring and research activities in rivers containing protected fish populations. Many problems have been discussed in the literature based on shortand long-term injury to individual fish from different forms of electrofishing. To date no standard approach for this technology exists that will allow effective surveys without probable injury to some portion of the fish population. How electrofishing injuries made at the individual fish level translate into population effects has not been adequately studied. In many areas of central and southern California, however, where the numbers of salmon and trout can be very small, and effective population size is frequently less than 25 breeding pairs, accumulated effects due to electrofishing may be significant. This paper reviews the electrofishing literature published during the last nine years. Based on this review and personal experience, I believe fisheries biologists frequently electrofish without considering potential harm or alternative methods. Therefore, I suggest the American Fisheries Society (AFS) develop a set of guidelines for least-invasive sampling methodologies, and adopt a policy on the ethical use of electrofishing for use by federal or state agencies to regulate all electrofishing activities in habitats containing wild fish. I believe other noninvasive study methods should be required in areas where it can be shown that electrofishing may significantly reduce a population's ability to persist.

"Risks of population extinction have been estimated using a variety of methods incorporating... more "Risks of population extinction have been estimated using a variety of methods incorporating information from different spatial and temporal scales. We briefly consider how several broad classes of extinction risk assessments, including population viability analysis, incidence functions, and ranking methods integrate information on different temporal and spatial scales. In many circumstances, data from surveys of neutral genetic variability within, and among, populations can provide information useful for assessing extinction risk. Patterns of genetic variability resulting from past and present ecological and demographic events, can indicate risks of extinction that are otherwise difficult to infer from ecological and demographic analyses alone. We provide examples of how patterns of neutral genetic variability, both within, and among populations, can be used to corroborate and complement extinction risk assessments."

Fisheries Oceanography, 2003

The importance of interspecific competition as a mechanism regulating population abundance in off... more The importance of interspecific competition as a mechanism regulating population abundance in off- shore marine communities is largely unknown. We evaluated offshore competition between Asian pink salmon and Bristol Bay (Alaska) sockeye salmon, which intermingle in the North Pacific Ocean and Bering Sea, using the unique biennial abundance cycle of Asian pink salmon from 1955 to 2000. Sockeye salmon growth

Transactions of the American Fisheries Society, 1988

Page 1. Transactions of the American Fisheries Society 117:322-335. 1988 «-': Copyri... more Page 1. Transactions of the American Fisheries Society 117:322-335. 1988 «-': Copyright by the American Fisheries Society 1988 Summer Production of Coho Salmon Stocked in Mount St. Helens Streams 3-6 Years after the 1980 Eruption ...

Transactions of the American Fisheries Society, 1988

... hydraulics of small stream channels, the distribution and abundance of juvenile coho salmon O... more ... hydraulics of small stream channels, the distribution and abundance of juvenile coho salmon Oncorhynchus kisutch, juvenile steelhead Salmo ... Some morphological variation among the stocks from different river systems (Taylor and McPhail 1985a) probably was obscured as a ...

Transactions of the American Fisheries Society, 2007

Molecular genetic methods were used to quantify natural hybridization between rainbow trout Oncor... more Molecular genetic methods were used to quantify natural hybridization between rainbow trout Oncorhynchus mykiss or steelhead (anadromous rainbow trout) and coastal cutthroat trout O. clarkii clarkii collected in the Copper River delta, Southeast Alaska. Eleven locations were sampled to determine the extent of hybridization and the distribution of hybrids. Four diagnostic nuclear microsatellite loci and four speciesspecific simple sequence repeat markers were used in combination with restriction fragment length polymorphism analyses of NADH dehydrogenase 5/6 (ND5/6) mitochondrial DNA (mtDNA) to investigate the genetic structure of trout from both species and identify putative interspecific hybrids. Hybrids were found in 7 of the 11 streams sampled in the Copper River delta, the extent of hybridization across all streams varying from 0% to 58%. Hybrid trout distribution appeared to be nonrandom, most individuals of mixed taxonomic ancestry being detected in streams containing rainbow trout rather than in streams containing coastal cutthroat trout. Genotypic disequilibrium was observed among microsatellite loci in populations with high levels of hybridization. We found no significant correlation between unique stream channel process groups and the number of hybrid fish sampled. Eighty-eight percent of fish identified as first-generation hybrids (F 1 ) in two populations contained coastal cutthroat trout mtDNA, suggesting directionality in hybridization. However, dominance of coastal cutthroat trout mtDNA was not observed at a third location containing F 1 hybrids, indicating that interspecific mating behavior varied among locations. Backcrossed individuals were found in drainages lacking F 1 hybrids and in populations previously thought to contain a single species. The extent and distribution of backcrossed individuals suggested that at least some hybrids are reproductively viable and backcrossed hybrid offspring move throughout the system.

Transactions of the American Fisheries Society, 2010

Here we compare the body shape of juvenile (age-0) sockeye salmon Oncorhynchus nerka that rear in... more Here we compare the body shape of juvenile (age-0) sockeye salmon Oncorhynchus nerka that rear in lakes (lake type) with that of those that rear in rivers (riverine) and relate rearing habitat to morphology and ecology. The two habitats present different swimming challenges with respect to water flow, foraging strategy, habitat complexity, and predation level. We present morphological data from three riverine and three lake-type populations in southwest Alaska. Using multivariate analyses conducted via geometric morphometrics, we determine population-and habitat-specific body shape. As predicted, riverine sockeye salmon have a more robust body shape, whereas lake-type sockeye salmon have a more streamlined body shape. In particular, we found differences in caudal peduncle depth (riverine deeper), eye size (riverine larger), and overall body depth (riverine deeper). One lake-type population did not follow the predicted pattern, exhibiting an overall exaggerated riverine body shape. Differences between the habitats in terms of predation, complexity, and foraging ecology are probably drivers of these differences. Allometry differed between life history types, suggesting that there are habitat-specific developmental differences.

Transactions of the American Fisheries Society, 1994

Thermal stratification occurred in pools of three rivers in northern California when inflow of co... more Thermal stratification occurred in pools of three rivers in northern California when inflow of cold water was sufficiently great or currents were sufficiently weak to prevent thorough mixing of water of contrasting temperatures. Surface water temperatures in such pools were commonly 3-9°C higher than those at the bottom. Cold water entered pools from tributaries, intergravel flow through river bars, and streamside subsurface sources. In Redwood and Rancheria Creeks, cold water was protected where gravel bars encroached into pools that were scoured along bedrock banks, creating isolated backwaters. Sixty-five percent of the juvenile steelhead Oncorhynchus mykiss found in the Rancheria Creek study reaches moved into adjacent stratified pools during periods of high ambient stream temperatures (23-28°C). Fish showed a decline in forage behavior and increased agonistic activity just before movement into stratified pools. In the Middle Fork Eel River, pools deeper than 3 m stratified when surface flow decreased to less than 1 m 3 /s. Summer-run steelhead adults were found in deep stratified pools on the Middle Fork Eel River throughout summer when midday ambient stream temperatures ranged from 26 to 29°C and coldwater pockets averaged 3.5°C cooler. Thermally stratified pools provided refuge habitat for significant numbers of young-of-the-year, yearling, and adult steelhead in marginal river habitats where stream temperatures reach upper incipient lethal levels.

Reviews in Fish Biology and Fisheries, 2011

outcomes, and (7) studies that cover a range of endpoints over ecologically relevant time periods.

Reviews in Fish Biology and Fisheries, 2004

Journal of Fish Biology, 2009

The hypothesis that growth in Pacific salmon Oncorhynchus spp. is dependent on previous growth wa... more The hypothesis that growth in Pacific salmon Oncorhynchus spp. is dependent on previous growth was tested using annual scale growth measurements of wild Chinook salmon Oncorhynchus tshawytscha returning to the Yukon and Kuskokwim Rivers, Alaska, from 1964 to 2004. Firstyear marine growth in individual O. tshawytscha was significantly correlated with growth in fresh water. Furthermore, growth during each of 3 or 4 years at sea was related to growth during the previous year. The magnitude of the growth response to the previous year's growth was greater when mean year-class growth during the previous year was relatively low. Length (eye to tail fork, L ETF ) of adult O. tshawytscha was correlated with cumulative scale growth after the first year at sea. Adult L ETF was also weakly correlated with scale growth that occurred during freshwater residence 4 to 5 years earlier, indicating the importance of growth in fresh water. Positive growth response to previous growth in O. tshawytscha was probably related to piscivorous diet and foraging benefits of large body size. Faster growth among O. tshawytscha year classes that initially grew slowly may reflect high mortality in slow growing fish and subsequent compensatory growth in survivors. Oncorhynchus tshawytscha in this study exhibited complex growth patterns showing a positive relationship with previous growth and a possible compensatory response to environmental factors affecting growth of the age class.

Environmental Biology of Fishes, 1998

Nucleotide sequences from the right-domain of salmonid mitochondrial DNA (mtDNA) control region f... more Nucleotide sequences from the right-domain of salmonid mitochondrial DNA (mtDNA) control region flanking the phenylalanine tRNA gene (tRNAPhe) were determined for 5 species and 14 subspecies of Oncorhynchus at the southern extent of their range. In all but one population, the right domain contained two 72 bp tandem repeats located between the tRNAPhe gene and the conserved sequence block CSB-3.

Environmental Biology of Fishes, 2000

Environmental Biology of Fishes, 2000

Environmental Biology of Fishes, 1996

Environmental Biology of Fishes, 2012

Increasing production of hatchery salmon over

Environmental Biology of Fishes, 2005

Identifying spawning behavior in Pacific halibut, Hippoglossus stenolepis, is particularly challe... more Identifying spawning behavior in Pacific halibut, Hippoglossus stenolepis, is particularly challenging because they occupy a deep, remote environment during the spawning season. To identify spawning events, a method is needed in which direct observation by humans is not employed. Spawning behavior of seven other flatfish species has been directly observed in their natural environment by investigators using SCUBA. All of these flatfish species display almost identical spawning behavior that follows a routine. Therefore, it is reasonable to believe that this spawning behavior occurs in other flatfish species, including Pacific halibut. As part of a larger study, we recaptured two Pacific halibut on which Pop-up Archival Transmitting (PAT) tags had been attached during the winter spawning season. Because the tags were physically retrieved, we were able to collect minute-by-minute depth records for 135 and 155 days. We used these depth data to tentatively identify spawning events. On seven separate occasions between 20 January 2001 and 9 February 2001, one fish displayed a conspicuous routine only seen during the spawning season of Pacific halibut and the routine parallels the actions of other spawning flatfish directly observed by humans using SCUBA. Therefore, we propose this routine represents spawning behavior in Pacific halibut. The second tagged fish did not display the conspicuous routine, thus challenging the assumption that Pacific halibut are annual spawners. PAT tags may prove to be a useful tool for identifying spawning events of Pacific halibut, and that knowledge may be used for improved management in the future.

Ecological Complexity, 2005

Many biological, hydrological, and geological processes are interactively linked in ecosystems. T... more Many biological, hydrological, and geological processes are interactively linked in ecosystems. These ecological phenomena normally vary within bounded ranges, but rapid, nonlinear changes to markedly different conditions can be triggered by even small differences if threshold values are exceeded. Intrinsic and extrinsic ecological thresholds can lead to effects that cascade among systems, precluding accurate modeling and prediction of system response to climate change. Ten case studies from North America illustrate how changes in climate can lead to rapid, threshold-type responses within ecological communities; the case studies also highlight the role of human activities that alter the rate or direction of system response to climate change. Understanding and anticipating nonlinear dynamics are important aspects of adaptation planning since responses of biological resources to changes in the physical climate system are not necessarily proportional and sometimes, as in the case of complex ecological systems, inherently nonlinear. Published by Elsevier B.V.