Search

Search Results

• 1. [Article] Beyond dichotomous life histories in partially migrating populations: cessation of anadromy in a long-lived fish

  This is the publisher’s final pdf. The published article is copyrighted by Ecological Society of America and can be found at: http://www.esajournals.org/loi/ecol

  Citation × Citation Citation Abstract Copy Title: Beyond dichotomous life histories in partially migrating populations: cessation of anadromy in a long-lived fish Author: Miller, Jessica A., Bond, Morgan H. This is the publisher’s final pdf. The published article is copyrighted by Ecological Society of America and can be found at: http://www.esajournals.org/loi/ecol Title: Beyond dichotomous life histories in partially migrating populations: cessation of anadromy in a long-lived fish Author: Miller, Jessica A., Bond, Morgan H. This is the publisher’s final pdf. The published article is copyrighted by Ecological Society of America and can be found at: http://www.esajournals.org/loi/ecol Close

• 2. [Article] Variation in the timing of coho salmon (Oncorhynchus kisutch) migration and spawning relative to river discharge and temperature

  Coho salmon (Oncorhynchus kisutch) migration and spawning are unique components of the salmon life cycle because they require synchrony of behavior with other individuals as well as with acceptable fluvial ...

  Citation × Citation Citation Abstract Copy Title: Variation in the timing of coho salmon (Oncorhynchus kisutch) migration and spawning relative to river discharge and temperature Author: LovellFord, Rachel Coho salmon (Oncorhynchus kisutch) migration and spawning are unique components of the salmon life cycle because they require synchrony of behavior with other individuals as well as with acceptable fluvial conditions. As with other organisms that exhibit group mating behavior, it is likely that environmental cues trigger coho salmon movement to spawning grounds. These cues may also provide usable habitat for migration and spawning. River discharge, temperature, and length of day have long been assumed to be the environmental cues which trigger migration and spawning of coho salmon as coho return within the same season each year to spawn. Hatchery studies have also shown that the timing of reproductive behavior is heritable. If this heritability is determined by the fluvial conditions of the spawning grounds, then a predictable relationship should exist between reproductive behavior and the hydrologic and thermal regimes. Surprisingly, no defensible correlations between discharge thresholds and spawning or migrating activity have been identified for naturally reproducing coho salmon. Thermal, velocity, and depth limitations have been identified for coho salmon, but these values have not been examined in combination or within the context of a hydrologic and thermal regime. This study compares interannual patterns in the timing of coho mid-river migration in the North Umqua (180 km up river from the estuary) and the initiation of spawn timing in the Smith River basins (Oregon) with river discharge and water temperature data to ascertain whether these behaviors are driven by fluvial conditions. Additionally, we used this data to identify the window over which most migration and spawning takes place in our test systems. On the North Umpqua, coho salmon mid-river migration initiated (first 5% of migrants) after summer peak temperatures and following a threshold average daily temperature of 18 C°, but before fall storm events occurred. In most years, approximately 75% of the migrating coho salmon have moved past the Winchester Dam before fall storms initiated and when discharge remained less than the 11 year average for the month of November, more similar to summer than winter flow levels. Additionally, characteristic lengths and numbers of peaks within the distribution of annual migrations were attributable to the generational cohort that the migration belonged to despite the similarity in population size across all years. These patterns in the distribution of generational cohorts suggest an inherited timing response as well as highlight cohorts which may contain diminished sub-populations. The initiation of coho salmon spawning appears limited both by a thermal threshold of 12 C° in all basins, as well as by a minimal discharge threshold, which is unique to each stream. Continued spawning activity occurs as discharge remains elevated from fall levels. It is also notable that there was no statistical difference in the date of the initiation of spawning within each basin in a given year or across years at a given site. Together, these studies highlight the important role that the coho salmon genome plays in reproductive timing as well as the ways that fluvial thresholds limit reproductive behavior in time. Coho have survived because of their genome has been resilient when faced with environmental change. Future work should consider variability in fluvial conditions relative to coho salmon phenotypic plasticity over time. Coho salmon phenotypic plasticity will determine whether the rate of change of the hydrologic and thermal regimes important to coho salmon survival outpaces the coho’s ability to adapt. This study contributed to this future work by establishing baseline relationships between the behavior of a threatened species and measurable environmental thresholds. Title: Variation in the timing of coho salmon (Oncorhynchus kisutch) migration and spawning relative to river discharge and temperature Author: LovellFord, Rachel Coho salmon (Oncorhynchus kisutch) migration and spawning are unique components of the salmon life cycle because they require synchrony of behavior with other individuals as well as with acceptable fluvial conditions. As with other organisms that exhibit group mating behavior, it is likely that environmental cues trigger coho salmon movement to spawning grounds. These cues may also provide usable habitat for migration and spawning. River discharge, temperature, and length of day have long been assumed to be the environmental cues which trigger migration and spawning of coho salmon as coho return within the same season each year to spawn. Hatchery studies have also shown that the timing of reproductive behavior is heritable. If this heritability is determined by the fluvial conditions of the spawning grounds, then a predictable relationship should exist between reproductive behavior and the hydrologic and thermal regimes. Surprisingly, no defensible correlations between discharge thresholds and spawning or migrating activity have been identified for naturally reproducing coho salmon. Thermal, velocity, and depth limitations have been identified for coho salmon, but these values have not been examined in combination or within the context of a hydrologic and thermal regime. This study compares interannual patterns in the timing of coho mid-river migration in the North Umqua (180 km up river from the estuary) and the initiation of spawn timing in the Smith River basins (Oregon) with river discharge and water temperature data to ascertain whether these behaviors are driven by fluvial conditions. Additionally, we used this data to identify the window over which most migration and spawning takes place in our test systems. On the North Umpqua, coho salmon mid-river migration initiated (first 5% of migrants) after summer peak temperatures and following a threshold average daily temperature of 18 C°, but before fall storm events occurred. In most years, approximately 75% of the migrating coho salmon have moved past the Winchester Dam before fall storms initiated and when discharge remained less than the 11 year average for the month of November, more similar to summer than winter flow levels. Additionally, characteristic lengths and numbers of peaks within the distribution of annual migrations were attributable to the generational cohort that the migration belonged to despite the similarity in population size across all years. These patterns in the distribution of generational cohorts suggest an inherited timing response as well as highlight cohorts which may contain diminished sub-populations. The initiation of coho salmon spawning appears limited both by a thermal threshold of 12 C° in all basins, as well as by a minimal discharge threshold, which is unique to each stream. Continued spawning activity occurs as discharge remains elevated from fall levels. It is also notable that there was no statistical difference in the date of the initiation of spawning within each basin in a given year or across years at a given site. Together, these studies highlight the important role that the coho salmon genome plays in reproductive timing as well as the ways that fluvial thresholds limit reproductive behavior in time. Coho have survived because of their genome has been resilient when faced with environmental change. Future work should consider variability in fluvial conditions relative to coho salmon phenotypic plasticity over time. Coho salmon phenotypic plasticity will determine whether the rate of change of the hydrologic and thermal regimes important to coho salmon survival outpaces the coho’s ability to adapt. This study contributed to this future work by establishing baseline relationships between the behavior of a threatened species and measurable environmental thresholds. Close

• 3. [Article] Effects of estuarine circulation patterns and stress on the migratory behavior of juvenile salmonids (Oncorhynchus sp.)

  For the first objective of this thesis, we attempt to understand the role of water flow and directionality in determining steelhead (Oncorhynchus mykiss) and spring/summer and fall Chinook (O. tschawytscha) ...

  Citation × Citation Citation Abstract Copy Title: Effects of estuarine circulation patterns and stress on the migratory behavior of juvenile salmonids (Oncorhynchus sp.) Author: Truelove, Nathan Kobun For the first objective of this thesis, we attempt to understand the role of water flow and directionality in determining steelhead (Oncorhynchus mykiss) and spring/summer and fall Chinook (O. tschawytscha) migration patterns within the Columbia River Estuary and plume by integrating recent advances in biotelemetry and environmental observation and forecasting systems (EOFS). The underlying methodology included analysis of the spatial and temporal movements of juvenile outmigrant salmonids with hydrological data from the CORIE modeling system (http://www.ccalmr.ogi.edu/CORIE). The CORIE modeling system, an EOFS for the Columbia River and nearshore environment, integrates a real-time sensor network, data management system and advanced 3-dimensional numerical models. Numerical simulations of key physical variables (water level, velocities, and directionality) were generated for the precise time and location that individual juvenile salmonids implanted with radio transmitters were present in the Columbia River Estuary. Five general behavioral trends were evident from these simulations: i) passive movement (drifting) during ebb tides, ii) active swimming with the current during ebb tides, iii) active swimming against the current during flood tides, iv) active swimming cross current during flood tides, and v) passive drifting during flood tide. Direction of water flow had a significant effect on fish velocity. All fish types showed a positive relationship between fish velocity and simulated drifter velocity with outgoing water flow. During slack water flow (< 0.25 m/s), this relationship was only observed in barged fall Chinook. With incoming water flow, spring/summer and fall Chinook fish types showed no relationship, whereas steelhead did. Analysis over a three-year period suggested that data from the CORIE modeling system corresponded well with juvenile salmonid migratory behavior and that the model may be a useful tool for evaluating the impact of different hydrological regimes on fish movement. The secondary objective of this thesis evaluated the effects of both acute and chronic crowding stressors on the migratory behavior of hatchery reared juvenile steelhead released into Abernathy Creek, a tributary of the Columbia River Estuary, Washington. The acute stress treatment consisted of surgical implantation of a NanoTag radio transmitter (Lotek Wireless, Canada), followed by 6 hours of crowding immediately prior to release. The chronic stress treatment consisted of surgical implantation of a PIT-tag (Digital Angel Corporation), 36 days of acclimation, followed by 3 weeks of crowding in low water conditions prior to release. Short-term migratory success of steelhead that received the acute stress treatment was determined by radio telemetry. Numbers of migrating fish that received experimental stress treatments and their speed was determined by both mobile radio telemetry and stationary PIT-tag and radio-tag interrogation systems already established on Abernathy Creek. Acute and chronic stress treatments both significantly delayed migration by 2 to 10 days, respectively, compared to controls. Furthermore, the acute stress treatment significantly decreased the both the rate of migration and numbers of juvenile steelhead that successfully migrated out of Abernathy creek. Title: Effects of estuarine circulation patterns and stress on the migratory behavior of juvenile salmonids (Oncorhynchus sp.) Author: Truelove, Nathan Kobun For the first objective of this thesis, we attempt to understand the role of water flow and directionality in determining steelhead (Oncorhynchus mykiss) and spring/summer and fall Chinook (O. tschawytscha) migration patterns within the Columbia River Estuary and plume by integrating recent advances in biotelemetry and environmental observation and forecasting systems (EOFS). The underlying methodology included analysis of the spatial and temporal movements of juvenile outmigrant salmonids with hydrological data from the CORIE modeling system (http://www.ccalmr.ogi.edu/CORIE). The CORIE modeling system, an EOFS for the Columbia River and nearshore environment, integrates a real-time sensor network, data management system and advanced 3-dimensional numerical models. Numerical simulations of key physical variables (water level, velocities, and directionality) were generated for the precise time and location that individual juvenile salmonids implanted with radio transmitters were present in the Columbia River Estuary. Five general behavioral trends were evident from these simulations: i) passive movement (drifting) during ebb tides, ii) active swimming with the current during ebb tides, iii) active swimming against the current during flood tides, iv) active swimming cross current during flood tides, and v) passive drifting during flood tide. Direction of water flow had a significant effect on fish velocity. All fish types showed a positive relationship between fish velocity and simulated drifter velocity with outgoing water flow. During slack water flow (< 0.25 m/s), this relationship was only observed in barged fall Chinook. With incoming water flow, spring/summer and fall Chinook fish types showed no relationship, whereas steelhead did. Analysis over a three-year period suggested that data from the CORIE modeling system corresponded well with juvenile salmonid migratory behavior and that the model may be a useful tool for evaluating the impact of different hydrological regimes on fish movement. The secondary objective of this thesis evaluated the effects of both acute and chronic crowding stressors on the migratory behavior of hatchery reared juvenile steelhead released into Abernathy Creek, a tributary of the Columbia River Estuary, Washington. The acute stress treatment consisted of surgical implantation of a NanoTag radio transmitter (Lotek Wireless, Canada), followed by 6 hours of crowding immediately prior to release. The chronic stress treatment consisted of surgical implantation of a PIT-tag (Digital Angel Corporation), 36 days of acclimation, followed by 3 weeks of crowding in low water conditions prior to release. Short-term migratory success of steelhead that received the acute stress treatment was determined by radio telemetry. Numbers of migrating fish that received experimental stress treatments and their speed was determined by both mobile radio telemetry and stationary PIT-tag and radio-tag interrogation systems already established on Abernathy Creek. Acute and chronic stress treatments both significantly delayed migration by 2 to 10 days, respectively, compared to controls. Furthermore, the acute stress treatment significantly decreased the both the rate of migration and numbers of juvenile steelhead that successfully migrated out of Abernathy creek. Close

• 4. [Article] Long-distance migration of prey synchronizes demographic rates of top predators across broad spatial scales

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the author(s) and ...

  Citation × Citation Citation Abstract Copy Title: Long-distance migration of prey synchronizes demographic rates of top predators across broad spatial scales Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. J. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the author(s) and published by John Wiley & Sons, Inc. on behalf of Ecological Society of America. It can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%292150-8925/ Title: Long-distance migration of prey synchronizes demographic rates of top predators across broad spatial scales Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. J. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the author(s) and published by John Wiley & Sons, Inc. on behalf of Ecological Society of America. It can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%292150-8925/ Close

• 5. [Article] WardLongDistanceMigration.pdf

  Citation × Citation Citation Abstract Copy Title: WardLongDistanceMigration.pdf Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. J. Title: WardLongDistanceMigration.pdf Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. J. Close

• 6. [Article] WardLongDistanceMigrationAppendixS1.pdf

  Citation × Citation Citation Abstract Copy Title: WardLongDistanceMigrationAppendixS1.pdf Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. J. Title: WardLongDistanceMigrationAppendixS1.pdf Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. J. Close

• 7. [Article] Juvenile coho salmon movement and migration through tide gates

  Tidal marshlands in the upper estuary ecotone provide essential habitat for juvenile salmonids. In this environment, salmonids grow rapidly and acclimate to saltwater. Worldwide, tidal marshes have been ...

  Citation × Citation Citation Abstract Copy Title: Juvenile coho salmon movement and migration through tide gates Author: Bass, Arthur Langer Tidal marshlands in the upper estuary ecotone provide essential habitat for juvenile salmonids. In this environment, salmonids grow rapidly and acclimate to saltwater. Worldwide, tidal marshes have been diked and drained to provide agricultural and residential land. Tide gates are one-way doors integrated into dike systems that prevent saltwater flooding and allow upland drainage to the estuary during low tide. By preventing tidal exchange, tide gates have significant upstream effects on water temperature and chemistry, plant and animal community structure, and geomorphology. Since they are closed most of the day and may be difficult to pass when open, tide gates may act as fish passage barriers for juvenile salmonids. They may also affect juvenile salmon migration timing by altering environmental variables that influence emigration rate in upstream habitats. We conducted our research in Coos Bay, one of the many Oregon estuaries with extensive use of tide gates. We studied three streams, one with a top-hinged tide gate, one with a side-hinged gate, and one without any tide gates that acted as our reference site. Our study species was coho salmon, Oncorhynchus kisutch, which may encounter tide gates both in the subyearling and smolt life stages in our study streams. Our objectives were to: 1) quantify upstream and downstream fish passage occurrence at all three sites, 2) determine whether juvenile coho salmon passage is associated with a specific range of gate conditions, and 3) identify any associations between coho smolt emigration rate and environmental variables that are influenced by tide gates. We installed stationary passive integrated transponder (PIT) antennae around both tide gates and a tidal channel in the non-gated stream to record the movement of PIT tagged juvenile coho salmon. Coho salmon smolts passed upstream most frequently at the non-gated channel (48% of all smolts detected at the array), next the side-hinged gate (28%), and lastly, the top-hinged gate (3%). Juvenile coho salmon passed more frequently at a specific range of gate angles and tailwater depths at both top hinged and side-hinged tide gates. Smolts passed downstream more frequently at greater gate angles and tailwater depths than available on average at both tide gates. Subyearlings passed upstream more frequently during small gate angles and a narrow range of tailwater depths at the top-hinged gate but did not pass more frequently under a particular range of conditions at the side-hinged gate. At the top-hinged gate, conditions favorable for subyearling upstream passage occurred towards the end of the gate open period and therefore subyearlings were severely limited in their opportunities for passage. At multiple sites, emigration rate was associated with environmental variables that may be altered by tide gates. Increases in water temperature were associated with an increasing likelihood of smolt emigration at multiple sites. At a tide gate that allowed upstream estuarine influence, increasing salinity was associated with a decreasing likelihood of emigration. Our results suggest that tide gates may interfere with salmonid movement and migration by creating physical barriers to fish passage and potentially influencing migratory timing by altering environmental variables. When installing or retrofitting tide gates, these factors should be taken into consideration since a tide gate's design may determine the severity of its effects on salmonids. Our work should be considered a case study and the findings should not be assumed to be transferable due to the great diversity of tide gate installations in use. We recommend further research, including a more in depth analysis of the affects of tide gates on subyearling coho salmon and an investigation of piscivorous predator exploitation of tide gates. Title: Juvenile coho salmon movement and migration through tide gates Author: Bass, Arthur Langer Tidal marshlands in the upper estuary ecotone provide essential habitat for juvenile salmonids. In this environment, salmonids grow rapidly and acclimate to saltwater. Worldwide, tidal marshes have been diked and drained to provide agricultural and residential land. Tide gates are one-way doors integrated into dike systems that prevent saltwater flooding and allow upland drainage to the estuary during low tide. By preventing tidal exchange, tide gates have significant upstream effects on water temperature and chemistry, plant and animal community structure, and geomorphology. Since they are closed most of the day and may be difficult to pass when open, tide gates may act as fish passage barriers for juvenile salmonids. They may also affect juvenile salmon migration timing by altering environmental variables that influence emigration rate in upstream habitats. We conducted our research in Coos Bay, one of the many Oregon estuaries with extensive use of tide gates. We studied three streams, one with a top-hinged tide gate, one with a side-hinged gate, and one without any tide gates that acted as our reference site. Our study species was coho salmon, Oncorhynchus kisutch, which may encounter tide gates both in the subyearling and smolt life stages in our study streams. Our objectives were to: 1) quantify upstream and downstream fish passage occurrence at all three sites, 2) determine whether juvenile coho salmon passage is associated with a specific range of gate conditions, and 3) identify any associations between coho smolt emigration rate and environmental variables that are influenced by tide gates. We installed stationary passive integrated transponder (PIT) antennae around both tide gates and a tidal channel in the non-gated stream to record the movement of PIT tagged juvenile coho salmon. Coho salmon smolts passed upstream most frequently at the non-gated channel (48% of all smolts detected at the array), next the side-hinged gate (28%), and lastly, the top-hinged gate (3%). Juvenile coho salmon passed more frequently at a specific range of gate angles and tailwater depths at both top hinged and side-hinged tide gates. Smolts passed downstream more frequently at greater gate angles and tailwater depths than available on average at both tide gates. Subyearlings passed upstream more frequently during small gate angles and a narrow range of tailwater depths at the top-hinged gate but did not pass more frequently under a particular range of conditions at the side-hinged gate. At the top-hinged gate, conditions favorable for subyearling upstream passage occurred towards the end of the gate open period and therefore subyearlings were severely limited in their opportunities for passage. At multiple sites, emigration rate was associated with environmental variables that may be altered by tide gates. Increases in water temperature were associated with an increasing likelihood of smolt emigration at multiple sites. At a tide gate that allowed upstream estuarine influence, increasing salinity was associated with a decreasing likelihood of emigration. Our results suggest that tide gates may interfere with salmonid movement and migration by creating physical barriers to fish passage and potentially influencing migratory timing by altering environmental variables. When installing or retrofitting tide gates, these factors should be taken into consideration since a tide gate's design may determine the severity of its effects on salmonids. Our work should be considered a case study and the findings should not be assumed to be transferable due to the great diversity of tide gate installations in use. We recommend further research, including a more in depth analysis of the affects of tide gates on subyearling coho salmon and an investigation of piscivorous predator exploitation of tide gates. Close

• 8. [Article] Genomics of migration : from marine distributions of salmonids to mechanisms of olfactory and magnetic cue perception for natal homing

  Substantial scientific investment has been directed towards understanding factors that influence distribution patterns and animals' remarkable ability for precise orientation and navigation, yet fundamental ...

  Citation × Citation Citation Abstract Copy Title: Genomics of migration : from marine distributions of salmonids to mechanisms of olfactory and magnetic cue perception for natal homing Author: Bellinger, M. Renee Substantial scientific investment has been directed towards understanding factors that influence distribution patterns and animals' remarkable ability for precise orientation and navigation, yet fundamental gaps in our knowledge remain. In my dissertation, I applied emerging genetic technologies to conduct a top-down and bottom-up investigation of animal movement and cue perception. First, in partnership with Project CROOS and the California Salmon Genetic Stock Identification project, stock-specific, marine migratory distributions of Chinook salmon (Oncorhynchus tshawytscha) were characterized for five consecutive months (2010) over 1000 km of coastline. A statistical model was developed to provide measures of relative stockspecific abundance, insights into broad factors that influence migratory distribution, and for fisheries management applications. For the second component of my dissertation, I studied specialized olfactory cells of salmonids that are proposed to contain nanometer-sized magnetite crystals that interact with earth strength magnetic fields to transduce them into neural signals. The transcriptome profiles of candidate magnetoreceptor and non-magnetic cells isolated from olfactory rosette tissue, whole olfactory rosettes, and blood and muscle tissue were characterized from ~661 million Illumina RNA-seq reads. A total of 1,006 differentially expressed genes were identified in the magnetic cell sample type. Results, consistent with having identified genes involved in magnetite crystal formation in fish, were used to develop a genetic model of magnetic sensory perception. Finally, to provide insights into olfaction-based homing that takes place in freshwater, the olfactory repertoire of salmonids was inferred from the Rainbow trout (O. mykiss) genome and compared to that of 15 other teleosts and the jawless fish, sea lamprey (Petromyzon marinus), an ancient species. The abundance and diversity of trace amine-associated and V2R-like genes suggests that these classes of chemoreceptors have biological importance. These findings have relevance for resolving if salmon and other marine organisms imprint on magnetic fields, and contribute to our understanding of how magnetic sense, olfaction, and genetic programming are involved in migratory distributions. Title: Genomics of migration : from marine distributions of salmonids to mechanisms of olfactory and magnetic cue perception for natal homing Author: Bellinger, M. Renee Substantial scientific investment has been directed towards understanding factors that influence distribution patterns and animals' remarkable ability for precise orientation and navigation, yet fundamental gaps in our knowledge remain. In my dissertation, I applied emerging genetic technologies to conduct a top-down and bottom-up investigation of animal movement and cue perception. First, in partnership with Project CROOS and the California Salmon Genetic Stock Identification project, stock-specific, marine migratory distributions of Chinook salmon (Oncorhynchus tshawytscha) were characterized for five consecutive months (2010) over 1000 km of coastline. A statistical model was developed to provide measures of relative stockspecific abundance, insights into broad factors that influence migratory distribution, and for fisheries management applications. For the second component of my dissertation, I studied specialized olfactory cells of salmonids that are proposed to contain nanometer-sized magnetite crystals that interact with earth strength magnetic fields to transduce them into neural signals. The transcriptome profiles of candidate magnetoreceptor and non-magnetic cells isolated from olfactory rosette tissue, whole olfactory rosettes, and blood and muscle tissue were characterized from ~661 million Illumina RNA-seq reads. A total of 1,006 differentially expressed genes were identified in the magnetic cell sample type. Results, consistent with having identified genes involved in magnetite crystal formation in fish, were used to develop a genetic model of magnetic sensory perception. Finally, to provide insights into olfaction-based homing that takes place in freshwater, the olfactory repertoire of salmonids was inferred from the Rainbow trout (O. mykiss) genome and compared to that of 15 other teleosts and the jawless fish, sea lamprey (Petromyzon marinus), an ancient species. The abundance and diversity of trace amine-associated and V2R-like genes suggests that these classes of chemoreceptors have biological importance. These findings have relevance for resolving if salmon and other marine organisms imprint on magnetic fields, and contribute to our understanding of how magnetic sense, olfaction, and genetic programming are involved in migratory distributions. Close

• 9. [Article] Life histories of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River estuary as inferred from scale and otolith microchemistry

  Despite evidence that juvenile Chinook salmon (Oncorhynchus tshawytscha) utilize North Pacific estuaries for growth and salinity acclimation, research in the Columbia River estuary has lead to opposing ...

  Citation × Citation Citation Abstract Copy Title: Life histories of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River estuary as inferred from scale and otolith microchemistry Author: Campbell, Lance A. Despite evidence that juvenile Chinook salmon (Oncorhynchus tshawytscha) utilize North Pacific estuaries for growth and salinity acclimation, research in the Columbia River estuary has lead to opposing hypotheses about the estuary’s importance as a salmon rearing environment. Many contemporary tagging studies indicate that salmon residency within the estuary is short (< 1 week) and that mortality of estuarine migrants is a significant impediment to recovery of depressed salmon stocks. On the other hand, life history interpretations from fish scales collected early in the twentieth century suggest that juvenile Chinook salmon reared extensively in the estuary, leading some to hypothesize that life history variation has been constrained by anthropogenic changes in the Columbia River basin. To test these hypotheses we first validated previous methods of life history interpretation by comparing the results of otolith chemistry, scale chemistry, and scale morphology from juvenile salmon collected during monthly beach seine surveys in 2003. Although scale and otolith chemistry were strongly correlated, and scale chemistry was an accurate indicator of salt-water entry, scale morphometric characteristics did not coincide consistently with the time of salmon entry into brackish water. We measured Strontium 86 and Calcium 43 in salmon otoliths collected in the lower Columbia River estuary in 2003-05 to quantify the period of salt-water residency of juvenile salmon and to back-calculate their size at salt-water entry. The estimated salt-water residency of juvenile Chinook ranged from 0-176 days with a mean residence time of 54, 67 and 30 days in 2003, 2004 and 2005, respectively. Chinook salmon that resided in salt water for more than 30 days comprised 55, 51 and 30% of the total estuary beach seine collections during each of these years. Forty to fifty percent of Chinook salmon had entered the saline portion of the estuary at a fork length < 60 mm. Furthermore we found a negative relationship between the size and time of entry with residency, where smaller earlier migrants on average resided for longer periods then larger late migrants. Peak migration times occurred in May, and 90% of the outmigration was completed by August 30 in all years. This pattern is substantially truncated relative to the results of a 1914-1916 salmon life-history survey, which showed that the historical outmigration period lasted well into the fall and was characterized by late pulses of new recruits into the lower estuary. Nonetheless, recent otolith results indicate that subyearling Chinook salmon use the saline portion of the estuary in a high proportion and for extended periods of time in contrast to short residency times reported by contemporary tagging and marking studies. Title: Life histories of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River estuary as inferred from scale and otolith microchemistry Author: Campbell, Lance A. Despite evidence that juvenile Chinook salmon (Oncorhynchus tshawytscha) utilize North Pacific estuaries for growth and salinity acclimation, research in the Columbia River estuary has lead to opposing hypotheses about the estuary’s importance as a salmon rearing environment. Many contemporary tagging studies indicate that salmon residency within the estuary is short (< 1 week) and that mortality of estuarine migrants is a significant impediment to recovery of depressed salmon stocks. On the other hand, life history interpretations from fish scales collected early in the twentieth century suggest that juvenile Chinook salmon reared extensively in the estuary, leading some to hypothesize that life history variation has been constrained by anthropogenic changes in the Columbia River basin. To test these hypotheses we first validated previous methods of life history interpretation by comparing the results of otolith chemistry, scale chemistry, and scale morphology from juvenile salmon collected during monthly beach seine surveys in 2003. Although scale and otolith chemistry were strongly correlated, and scale chemistry was an accurate indicator of salt-water entry, scale morphometric characteristics did not coincide consistently with the time of salmon entry into brackish water. We measured Strontium 86 and Calcium 43 in salmon otoliths collected in the lower Columbia River estuary in 2003-05 to quantify the period of salt-water residency of juvenile salmon and to back-calculate their size at salt-water entry. The estimated salt-water residency of juvenile Chinook ranged from 0-176 days with a mean residence time of 54, 67 and 30 days in 2003, 2004 and 2005, respectively. Chinook salmon that resided in salt water for more than 30 days comprised 55, 51 and 30% of the total estuary beach seine collections during each of these years. Forty to fifty percent of Chinook salmon had entered the saline portion of the estuary at a fork length < 60 mm. Furthermore we found a negative relationship between the size and time of entry with residency, where smaller earlier migrants on average resided for longer periods then larger late migrants. Peak migration times occurred in May, and 90% of the outmigration was completed by August 30 in all years. This pattern is substantially truncated relative to the results of a 1914-1916 salmon life-history survey, which showed that the historical outmigration period lasted well into the fall and was characterized by late pulses of new recruits into the lower estuary. Nonetheless, recent otolith results indicate that subyearling Chinook salmon use the saline portion of the estuary in a high proportion and for extended periods of time in contrast to short residency times reported by contemporary tagging and marking studies. Close

• 10. [Article] Tags Versus Genetics : Identifying Which Tool Provides the Best Information about Chinook Salmon (Oncorhynchus tshawytscha) Distributions in the California Current

  The movement of Chinook salmon through space and time, across political boundaries, and through fisheries, creates one of the most complex marine resource management problems in the world. Information ...

  Citation × Citation Citation Abstract Copy Title: Tags Versus Genetics : Identifying Which Tool Provides the Best Information about Chinook Salmon (Oncorhynchus tshawytscha) Distributions in the California Current Author: Flaherty, Ryan James The movement of Chinook salmon through space and time, across political boundaries, and through fisheries, creates one of the most complex marine resource management problems in the world. Information garnered from the recovery of coded-wire tags (CWTs) has been used since the 1970s to direct management decisions. Growing concern surrounding the quality and limitations of CWT data spurred interest in technologies that may improve stock specific information for Chinook salmon. Genetic stock identification (GSI) is one of the rapidly growing technologies with significant potential for generating information that could be used in addition to CWT data to improve salmon management. This is the first study to explicitly compare the capabilities of CWT and GSI data to identify stock-specific distribution patterns of Chinook salmon. Our results demonstrate that GSI data are a powerful tool that can be used to investigate stock-specific Chinook distributions at refined space-time scales that cannot be investigated with traditionally reported CWT data. Additionally, we found that, at coarse space-time scales, CWT and GSI data provide similar stock distribution information, lending support to the critical assumption that CWT data reflect the distribution patterns of the untagged fish they are intended to represent. As a by-product of this comparison, we describe the distribution and migration patterns of the Chinook stocks most commonly encountered in the commercial fishery off the coasts of Oregon and California. GSI and other 21st century genetics-based tools have potential to play a critical role in improving salmon management regimes of the future. Title: Tags Versus Genetics : Identifying Which Tool Provides the Best Information about Chinook Salmon (Oncorhynchus tshawytscha) Distributions in the California Current Author: Flaherty, Ryan James The movement of Chinook salmon through space and time, across political boundaries, and through fisheries, creates one of the most complex marine resource management problems in the world. Information garnered from the recovery of coded-wire tags (CWTs) has been used since the 1970s to direct management decisions. Growing concern surrounding the quality and limitations of CWT data spurred interest in technologies that may improve stock specific information for Chinook salmon. Genetic stock identification (GSI) is one of the rapidly growing technologies with significant potential for generating information that could be used in addition to CWT data to improve salmon management. This is the first study to explicitly compare the capabilities of CWT and GSI data to identify stock-specific distribution patterns of Chinook salmon. Our results demonstrate that GSI data are a powerful tool that can be used to investigate stock-specific Chinook distributions at refined space-time scales that cannot be investigated with traditionally reported CWT data. Additionally, we found that, at coarse space-time scales, CWT and GSI data provide similar stock distribution information, lending support to the critical assumption that CWT data reflect the distribution patterns of the untagged fish they are intended to represent. As a by-product of this comparison, we describe the distribution and migration patterns of the Chinook stocks most commonly encountered in the commercial fishery off the coasts of Oregon and California. GSI and other 21st century genetics-based tools have potential to play a critical role in improving salmon management regimes of the future. Close