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J.L. Nielsen

Publications and source records attributed to J.L. Nielsen.

13 recordsLinked to original sources
USGS2011

Electronic tags and genetics explore variation in migrating steelhead kelts (oncorhynchus mykiss), Ninilchik river, Alaska

Acoustic and archival tags examined freshwater and marine migrations of postspawn steelhead kelts (Oncorhynchus mykiss) in the Ninilchik River, Alaska, USA. Postspawn steelhead were captured at a weir in 2002-2005. Scale analysis indicated multiple migratory life histories and spawning behaviors. Acoustic tags were implanted in 99 kelts (2002-2003), and an array of acoustic receivers calculated the average speed of outmigration, timing of saltwater entry, and duration of residency in the vicinity of the river mouth. Ocean migration data were recovered from two archival tags implanted in kelts in 2004 (one male and one female). Archival tags documented seasonal differences in maximum depth and behavior with both fish spending 97% of time at sea <6 m depth (day and night). All study fish were double tagged with passive integrated transponder (PIT) tags implanted in the body cavity. Less than 4% of PIT tags were retained in postspawn steelhead. Molecular genetics demonstrated no significant differences in genetic population structure across years or among spawning life history types, suggesting a genetically panmictic population with highly diverse life history characteristics in the Ninilchik River.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2009

Linking marine and freshwater growth in western Alaska Chinook salmon Oncorhynchus tshawytscha

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. First-year 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, LETF) of adult O. tshawytscha was correlated with cumulative scale growth after the first year at sea. Adult LETF 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.

Alaska↗
USGS2007

Revisiting evolutionary dead ends in sockeye salmon ( Oncorhynchus nerka ) life history

This study challenges recent hypotheses about sockeye salmon ( Oncorhynchus nerka ) colonization based on life history and broadens the pathways that investigators should consider when studying sockeye colonization of novel habitats. Most sockeye populations exhibit lake-type life histories. Riverine populations are thought to be more likely to stray from their natal stream to spawn and therefore colonize new habitat. We examined genetic relationships among five geographically proximate sockeye populations from the Aniakchak region of the Alaska Peninsula, Alaska. Specifically, we sought to determine if the genetic population structure was consistent with the hypothesis that a riverine population colonized a recently available upriver volcanic caldera lake, and whether recent volcanism led to genetic bottlenecks in these sockeye populations. Heterozygosity and allelic richness were not higher in the riverine population. Patterns of genetic divergence suggested that the geographically proximate riverine sockeye population did not colonize the lake; the caldera populations were more genetically divergent from the downstream riverine population ( F ST &ensp;=&ensp; 0.047) than a lake-type population in a different drainage ( F ST &ensp;=&ensp; 0.018). Our results did not suggest the presence of genetic bottlenecks in the caldera populations.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2005

Identifying spawning behavior in Pacific halibut ( Hippoglossus stenolepis ) using electronic tags

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.

Environmental Biology of Fishes↗
USGS2003

The importance of genetic verification for determination of Atlantic salmon in north Pacific waters

Genetic analyses of two unknown but putative Atlantic salmon Salmo salar captured in the Copper River drainage, Alaska, demonstrated the need for validation of morphologically unusual fishes. Mitochondrial DNA sequences (control region and cytochrome b) and data from two nuclear genes [first internal transcribed spacer (ITS-1) sequence and growth hormone (GH1) amplification product] indicated that the fish caught in fresh water on the Martin River was a coho salmon Oncorhynchus kisutch, while the other fish caught in the intertidal zone of the Copper River delta near Grass Island was an Atlantic salmon. Determination of unusual or cryptic fish based on limited physical characteristics and expected seasonal spawning run timing will add to the controversy over farmed Atlantic salmon and their potential effects on native Pacific species. It is clear that determination of all putative collections of Atlantic salmon found in Pacific waters requires validation. Due to uncertainty of fish identification in the field using plastic morphometric characters, it is recommended that genetic analyses be part of the validation process. ?? 2003 The Fisheries Society of the British Isles.

Journal of Fish Biology↗
USGS2003

Evidence of sexually dimorphic introgression in Pinaleno Mountain Apache trout

The high-elevation headwater streams of the Pinaleno Mountains support small populations of threatened Apache trout Oncorhynchus apache that were stocked following the chemical removal of nonnative salmonids in the 1960s. A fisheries survey to assess population composition, growth, and size structure confirmed angler reports of infrequent occurrences of Oncorhynchus spp. exhibiting the external morphological characteristics of both Apache trout and rainbow trout O. mykiss. Nonlethal tissue samples were collected from 50 individuals in the headwaters of each stream. Mitochondrial DNA (mtDNA) sequencing and amplification of nuclear microsatellite loci were used to determine the levels of genetic introgression by rainbow trout in Apache trout populations at these locations. Sexually dimorphic introgression from the spawning of male rainbow trout with female Apache trout was detected using mtDNA and microsatellites. Estimates of the degree of hybridization based on three microsatellite loci were 10-88%. The use of nonlethal DNA genetic analyses can supplement information obtained from standard survey methods and be useful in assessing the relative importance of small and sensitive populations with a history of nonnative introductions.

North American Journal of Fisheries Management↗
USGS2001

Microsatellite analyses of the trout of northwest Mexico

The trout of northwest Mexico represent an undescribed group of fish considered part of the Oncorhynchus mykiss (Pacific trout) complex of species and subspecies. Recent genetic studies have shown these fish to have important genetic diversity and a unique evolutionary history when compared to coastal rainbow trout. Increased levels of allelic diversity have been found in this species at the southern extent of its range. In this study we describe the trout in the Sierra Madre Occidental from the rios Yaqui, Mayo, Casas Grandes and de Bavispe, and their relationship to the more southern distribution of Mexican golden trout (O. chrysogaster) using 11 microsatellite loci. Microsatellite allelic diversity in Mexican trout was high with a mean of 6.6 alleles/locus, average heterozygosity = 0.35, and a mean Fst = 0.43 for all loci combined. Microsatellite data were congruent with previously published mtDNA results showing unique panmictic population structure in the Rio Yaqui trout that differs from Pacific coastal trout and Mexican golden trout. These data also add support for the theory of headwaters transfer of trout across the Continental Divide from tributaries of the Rio de Bavispe into the Rio Casas Grandes. Rio Mayo trout share a close genetic relationship to trout in Rio Yaqui, but sample sizes from the Rio Mayo prevent significant comparisons in this study. Microsatellite analyses show significant allelic frequency differences between Rio Yaqui trout and O. chrysogaster in Sinaloa and Durango Mexico, adding further support for a unique evolutionary status for this group of northwestern Mexican trout.

Genetica↗
USGS2000

Molecular analysis of population genetic structure and recolonization of rainbow trout following the Cantara spill

Mitochondrial DNA (mtDNA) sequence and allelic frequency data for 12 microsatellite loci were used to analyze population genetic structure and recolonization by rainbow trout, Oncorhynchus mykiss , following the 1991 Cantara spill on the upper Sacramento River, California. Genetic analyses were performed on 1,016 wild rainbow trout collected between 1993 and 1996 from the mainstem and in 8 tributaries. Wild trout genotypes were compared to genotypes for 79 Mount Shasta Hatchery rainbow trout. No genetic heterogeneity was found 2 years after the spill (1993) between tributary populations and geographically proximate mainstem fish, suggesting recolonization of the upper mainstem directly from adjacent tributaries. Trout collections made in 1996 showed significant year-class genetic variation for mtDNA and microsatellites when compared to fish from the same locations in 1993. Five years after the spill, mainstem populations appeared genetically mixed with no significant allelic frequency differences between mainstem populations and geographically proximate tributary trout. In our 1996 samples, we found no significant genetic differences due to season of capture (summer or fall) or sampling technique used to capture rainbow trout, with the exception of trout collected by electrofishing and hook and line near Prospect Avenue. Haplotype and allelic frequencies in wild rainbow trout populations captured in the upper Sacramento River and its tributaries were found to differ genetically from Mount Shasta Hatchery trout for both years, with the notable exception of trout collected in the lower mainstem river near Shasta Lake, where mtDNA and microsatellite data both suggested upstream colonization by hatchery fish from the reservoir. These data suggest that the chemical spill in the upper Sacramento River produced significant effects over time on the genetic population structure of rainbow trout throughout the entire upper river basin.

California↗
USGS1999

The evolutionary history of steelhead ( Oncorhynchus mykiss ) along the US Pacific Coast: Developing a conservation strategy using genetic diversity

Changes in genetic variation across a species range may indicate patterns of population structure resulting from past ecological and demographic events that are otherwise difficult to infer and thus provide insight into evolutionary development. Genetic data is used, drawn from 11 microsatellite loci amplified from anadromous steelhead ( Oncorhynchus mykiss ) sampled throughout its range in the eastern Pacific Ocean, to explore population structure at the southern edge in California. Steelhead populations in this region represent less than 10% of their reported historic abundance and survive in very small populations found in fragmented habitats. Genetic data derived from three independent molecular systems (allozymes, mtDNA, and microsatellites) have shown that the southernmost populations are characterized by a relatively high genetic diversity. Two hypothetical models supporting genetic population substructure such as observed were considered: (1) range expansion with founder-flush effects and subsequent population decline; (2) a second Pleistocene radiation from the Gulf of California. Using genetic and climatic data, a second Pleistocene refugium contributing to a southern ecotone seems more feasible. These data support strong conservation measures based on genetic diversity be developed to ensure the survival of this uniquely diverse gene pool.

ICES Journal of Marine Science↗
USGS1988

Channel hydraulics, habitat use, and body form of juvenile coho salmon, steelhead, and cutthroat trout in streams

Habitat use by juvenile coho salmon Oncorhynchus kisutch , steelhead Salmo gairdneri , and the coastal subspecies of cutthroat trout Salmo clarki clarki in small streams in western Washington was influenced by hydraulic characteristics of different types of channel units. Coho salmon preferred pools with average velocities less than 20 cm/s; very few fish were found in riffles with high current velocities. Steelhead occurred in riffles and also utilized deep pools with relatively high velocities along the center of the channel. Cutthroat trout were intermediate between coho salmon and steelhead in their use of swiftly flowing habitats. Variation in body shape and fin size among the three species generally fit the predicted morphologies that would be favored in different locations within the channel. Coho salmon possessed a deep, laterally compressed body with large median and paired fins. These features are believed to facilitate rapid turns and quick but transient burst swimming. Steelhead possessed a more cylindrical body shape with short median fins and relatively large paired fins, attributes that appear well adapted to holding a position in swift water. The cutthroat troutˈs lack of morphological adaptation to either fast or slow water may help to explain why this species is dominated by coho salmon and steelhead in areas of sympatry.

Transactions of the American Fisheries Society↗
USGS1988

Summer production of coho salmon stocked in Mount St. Helens streams 3-6 years after the 1980 eruption

We monitored habitat use and summer production of stocked underyearling coho salmon Oncorhynchus kisutch from 1983 to 1986 in three streams affected by the 1980 eruption of Mount St. Helens, Washington. Two streams were in the blast area and one was on a volcanic mudflow terrace, Midsummer water temperatures frequently exceeded presumed stressful thresholds and occasionally surpassed the incipient lethal limit. Temperatures at the study sites (up to 29.5°C) may have been the highest ever recorded in small streams in western Washington. In addition, there was relatively little submerged cover and limited pool habitat. Despite the severe conditions created by the eruption, production rates of stocked coho salmon at all sites ranged from 15.1 to 143.8 mg/m 2 ·d (2.3–21.6 g/m 2 over an average 150‐d summer period) and were equal to or greater than those measured in other streams of comparable size in the region. Coho salmon production in the streams was more strongly influenced by population biomass and density than by average individual growth rate. Production was also influenced by timing and average weight at stocking; larger fish stocked later in the summer had higher survival than smaller fish stocked earlier. Apparent summer mortality (true mortality plus emigration) may have been influenced by the presence of other salmonids. Coho salmon density at the end of summer was consistently lowest in the mudflow stream, the only site to have a large population of steelhead (anadromous rainbow trout Oncorhynchus mykiss , formerly Salmo gairdneri ). We suspected that an abundance of both terrestrial and aquatic food was partly responsible for the high summer production of stocked coho salmon in what was an otherwise hostile environment.

Washington↗