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• 1051. [Article] Influence of Soft Wheat Characteristics on Quality of Batter-based Products

  Wheat is a globally traded staple crop. Wheat is important in human diets because of its agronomic adaptability, physical characteristics, functionality for the production of leavened products and nutritional ...

  Citation × Citation Citation Abstract Copy Title: Influence of Soft Wheat Characteristics on Quality of Batter-based Products Author: Fajardo Centeno, Carlos A. Wheat is a globally traded staple crop. Wheat is important in human diets because of its agronomic adaptability, physical characteristics, functionality for the production of leavened products and nutritional value. Two significant characteristics make wheat an important staple food-crop. First, the proteins present in wheat endosperm have attributes that enable gas retention after the proteins are hydrated and mechanically worked during dough production. Second, a wider variety of products can be made out of wheat compared to other cereals. Wheat quality is defined in terms of suitability for specific end-uses. This is important for breeders, farmers, flour millers, and food producers and consumers. In the U.S. Pacific Northwest (PNW) climatic conditions favor production of soft wheat. Three soft wheat types are planted in the PNW, soft white winter (SWW), soft white spring (SWS), and club (CLUB). Batter-based products are important applications for soft wheats and include a wide range of products such as pancakes and waffles, cakes, and coatings. Pancakes are produced from fluid batters using a single step mixing process and contain sugar concentrations < 30% in their formulations. Cakes are complex food systems where their classification is based on mixing process to produce the batters and the sugar-flour ratio concentrations in their formulations. This dissertation is focused on the functionality, analysis, and selection of soft wheat quality traits that affect end-product performance and also developing a methodology to rapidly predict cake quality. The first study (Chapter 3) was concerned with the functionality of SWW wheats in pancake making. The aim of this study was to observe the differences in genotype and protein concentration on batter flow and pancake making performance of a collection of SWW wheats. Two formulations were used in the study: one based on Finnie et al (2006) called "old" and another based on the AACC-I Approved Method 10-80.01 called "new". The "new" lean formulation had an improved ability to distinguish the performance of different flours compared with the “old” as a result of wider range of pancake diameters. This study showed that pancake making performance would not be optimized by conventional superior high-quality soft wheat flours with soft kernel texture, high break flour yield, and low water-, carbonate-, and sucrose SRCs. From our results it appears that for unchlorinated flours, at least for thicker pancakes, the most appropriate flour would have higher water and sucrose SRCs and be grown under management conditions conductive to higher protein. The second study (Chapter 4) was a meta-analysis of data collected by the USDA Western Wheat Quality Laboratory (Pullman, WA). This study was done to advance understanding soft wheat quality traits that differentially affect sugar-snap cookie diameter (CODI) and Japanese sponge cake (SC) volume (CAVOL). Principal component analysis (PCA) and partial least square (PLS) regression models were used to obtain useful actionable information from the data. The overall data showed that break flour yield (BKFY) was the single most important trait positively associated with both CAVOL and CODI. SWW wheats showed CVs > 10% for kernel hardness (SKHRD), grain and flour protein concentrations, ash, sucrose-, and lactic acid SRCs. These observations suggested that hardness, protein, ash, and the two SRCs were more sensitive to G&E effects than were the end-product traits that had CVs < 10%. The third study (Chapter 5) was built on the second study by adding two additional quality tests, oxidative gelation capacity (PeakOXI) and median particle size, to the potential prediction of CODI and CAVOL. Similar to the second study, BKFY was the single most important trait positively associated with both CAVOL and CODI. Virtual selection of SWWs based on either BKFY or SKHRD alone showed (in both the second and third studies) that using these enabled a gain of 134 mL for CAVOL and 0.6 cm for CODI using SKHRD and 122 mL for CAVOL and 0.58 cm for CODI using BKFY (Chapter 5). PeakOXI was significantly correlated with CODI but not with CAVOL. This contrasted with our hypothesis that PeakOXI would affect both products similarly. Notably 13 SWW samples had PeakOXI values higher than 800 cP. PeakOXI values this high have never been observed in soft wheats prior to this study. This is a valuable genetic resource for further studies that may lead to ways to better exploit oxidative gelation. The fourth study (Chapter 6) expanded the concepts in previous studies and included the use of a test to measure cake-batter viscosity in an attempt to predict cake quality. This study investigated the relationships between wheat quality traits, cake batters, and cake making quality in three cake types: SC, layer cake (LC), and pound cake (PoC). This study differed from the studies in Chapters 4 and 5 and was similar to Chapter 3 as the samples were fewer but specifically chosen to span the entire range of typical SWW quality. In this study we also developed a viscosity-based method to predict SC and LC quality that takes only eight minutes. This could be useful for screening or selection for cake quality in soft wheat breeding programs. In SC, there were no significant differences in cake quality traits between varieties. However, SC volume had a strong negative association with PeakOXI. For LC, the variety Tubbs, with harder kernel and higher absorption characteristics, had the largest LC volume. In contrast to SC, LC volume was significantly and positively associated with PeakOXI. In PoC, Kaseburg, with the highest protein content, had the largest cake volume. PoC was significantly and positively associated with flour protein concentration suggesting that flour proteins were important for larger volumes and confirming other observations in the literature. In contrast to LC and SC, PoC was not significantly associated with PeakOXI. The overall impact of the studies reported is: - For pancakes, the most important soft wheat trait is flour protein concentration. Water-, and sucrose SRCs were potentially useful parameters for predicting pancake quality. - For SC and sugar-snap cookies, break flour yield was the most important single trait in predicting higher SC volumes and larger cookie diameters. Therefore, selection in soft wheat breeding should be focused on kernel hardness and break flour yields as primary factors. Title: Influence of Soft Wheat Characteristics on Quality of Batter-based Products Author: Fajardo Centeno, Carlos A. Wheat is a globally traded staple crop. Wheat is important in human diets because of its agronomic adaptability, physical characteristics, functionality for the production of leavened products and nutritional value. Two significant characteristics make wheat an important staple food-crop. First, the proteins present in wheat endosperm have attributes that enable gas retention after the proteins are hydrated and mechanically worked during dough production. Second, a wider variety of products can be made out of wheat compared to other cereals. Wheat quality is defined in terms of suitability for specific end-uses. This is important for breeders, farmers, flour millers, and food producers and consumers. In the U.S. Pacific Northwest (PNW) climatic conditions favor production of soft wheat. Three soft wheat types are planted in the PNW, soft white winter (SWW), soft white spring (SWS), and club (CLUB). Batter-based products are important applications for soft wheats and include a wide range of products such as pancakes and waffles, cakes, and coatings. Pancakes are produced from fluid batters using a single step mixing process and contain sugar concentrations < 30% in their formulations. Cakes are complex food systems where their classification is based on mixing process to produce the batters and the sugar-flour ratio concentrations in their formulations. This dissertation is focused on the functionality, analysis, and selection of soft wheat quality traits that affect end-product performance and also developing a methodology to rapidly predict cake quality. The first study (Chapter 3) was concerned with the functionality of SWW wheats in pancake making. The aim of this study was to observe the differences in genotype and protein concentration on batter flow and pancake making performance of a collection of SWW wheats. Two formulations were used in the study: one based on Finnie et al (2006) called "old" and another based on the AACC-I Approved Method 10-80.01 called "new". The "new" lean formulation had an improved ability to distinguish the performance of different flours compared with the “old” as a result of wider range of pancake diameters. This study showed that pancake making performance would not be optimized by conventional superior high-quality soft wheat flours with soft kernel texture, high break flour yield, and low water-, carbonate-, and sucrose SRCs. From our results it appears that for unchlorinated flours, at least for thicker pancakes, the most appropriate flour would have higher water and sucrose SRCs and be grown under management conditions conductive to higher protein. The second study (Chapter 4) was a meta-analysis of data collected by the USDA Western Wheat Quality Laboratory (Pullman, WA). This study was done to advance understanding soft wheat quality traits that differentially affect sugar-snap cookie diameter (CODI) and Japanese sponge cake (SC) volume (CAVOL). Principal component analysis (PCA) and partial least square (PLS) regression models were used to obtain useful actionable information from the data. The overall data showed that break flour yield (BKFY) was the single most important trait positively associated with both CAVOL and CODI. SWW wheats showed CVs > 10% for kernel hardness (SKHRD), grain and flour protein concentrations, ash, sucrose-, and lactic acid SRCs. These observations suggested that hardness, protein, ash, and the two SRCs were more sensitive to G&E effects than were the end-product traits that had CVs < 10%. The third study (Chapter 5) was built on the second study by adding two additional quality tests, oxidative gelation capacity (PeakOXI) and median particle size, to the potential prediction of CODI and CAVOL. Similar to the second study, BKFY was the single most important trait positively associated with both CAVOL and CODI. Virtual selection of SWWs based on either BKFY or SKHRD alone showed (in both the second and third studies) that using these enabled a gain of 134 mL for CAVOL and 0.6 cm for CODI using SKHRD and 122 mL for CAVOL and 0.58 cm for CODI using BKFY (Chapter 5). PeakOXI was significantly correlated with CODI but not with CAVOL. This contrasted with our hypothesis that PeakOXI would affect both products similarly. Notably 13 SWW samples had PeakOXI values higher than 800 cP. PeakOXI values this high have never been observed in soft wheats prior to this study. This is a valuable genetic resource for further studies that may lead to ways to better exploit oxidative gelation. The fourth study (Chapter 6) expanded the concepts in previous studies and included the use of a test to measure cake-batter viscosity in an attempt to predict cake quality. This study investigated the relationships between wheat quality traits, cake batters, and cake making quality in three cake types: SC, layer cake (LC), and pound cake (PoC). This study differed from the studies in Chapters 4 and 5 and was similar to Chapter 3 as the samples were fewer but specifically chosen to span the entire range of typical SWW quality. In this study we also developed a viscosity-based method to predict SC and LC quality that takes only eight minutes. This could be useful for screening or selection for cake quality in soft wheat breeding programs. In SC, there were no significant differences in cake quality traits between varieties. However, SC volume had a strong negative association with PeakOXI. For LC, the variety Tubbs, with harder kernel and higher absorption characteristics, had the largest LC volume. In contrast to SC, LC volume was significantly and positively associated with PeakOXI. In PoC, Kaseburg, with the highest protein content, had the largest cake volume. PoC was significantly and positively associated with flour protein concentration suggesting that flour proteins were important for larger volumes and confirming other observations in the literature. In contrast to LC and SC, PoC was not significantly associated with PeakOXI. The overall impact of the studies reported is: - For pancakes, the most important soft wheat trait is flour protein concentration. Water-, and sucrose SRCs were potentially useful parameters for predicting pancake quality. - For SC and sugar-snap cookies, break flour yield was the most important single trait in predicting higher SC volumes and larger cookie diameters. Therefore, selection in soft wheat breeding should be focused on kernel hardness and break flour yields as primary factors. Close

• 1052. [Article] Linking Habitat and Benthic Invertebrate Species Distributions in Areas of Potential Renewable Energy Development

  While the coastal waters of western North America hold great promise for wind and wave energy development, many concerns have been raised about the potential environmental impacts of the installation of ...

  Citation × Citation Citation Abstract Copy Title: Linking Habitat and Benthic Invertebrate Species Distributions in Areas of Potential Renewable Energy Development Author: Henkel, Sarah K., Goldfinger, Chris While the coastal waters of western North America hold great promise for wind and wave energy development, many concerns have been raised about the potential environmental impacts of the installation of these devices and their complex mooring systems. Here I focus on characterizing benthic habitats and biological communities in offshore sedimentary and reef habitats where wind and wave energy facilities could be located. While little is known about species-habitat relationships and community processes in the depths and substrate types targeted for offshore renewable energy installation, an understanding of the natural dynamics of these systems is of utmost importance if we hope to forecast changes that might be brought about by wind and wave development. Since May 2010 we have conducted surveys of benthic habitats from northern California to Washington using a variety of techniques, providing baseline data on habitats and species potentially affected by wind and wave development, identifying species-habitat relationships, and quantifying spatial and temporal trends in species abundances and distributions. The first step in identifying and evaluating benthic communities is sonar mapping to determine depth and substrate types. In summer 2010 and 2011 six new offshore sites were mapped by the Seafloor Mapping and Plate Tectonics Lab at OSU using high-resolution multi-beam sonar and acoustic backscatter. In addition to the backscatter, Shipek grabs were taken in soft-bottom areas to collect sediment samples, which were run through a laser particle size analyzer (LDPSA) to determine actual grain size. Mapping began at the federal jurisdiction line and extended 9 – 12 miles offshore. Oregon and California have undertaken extensive mapping of state waters, so many areas have been mapped inshore of these sites as well. In summer 2011 and 2012, we visited 8 sites (6 newly mapped sites, one previously mapped, and one unmapped site) to collect a total of 153 cores using a 0.1 m2 box-corer. A sub-sample of sediment was collected from the corer and analyzed using the LDPSA; the rest was sieved through 1 mm mesh and all infaunal organisms were counted and identified. At each box core sampling station, CTD casts were conducted to obtain physical data describing the overlying water column for further habitat characterization. Unique infaunal invertebrate assemblages were found in sedimentary habitats at each of the Pacific Northwest shelf sites. Thus for renewable energy siting, it does not appear that baseline surveys conducted at one site can necessarily serve as a proxy for distant sites. However, some general trends were detected. Significantly different invertebrate assemblages were found in different depth ranges with a break at approximately 80 to 90 m depth; deeper sites exhibited greater diversity. Shallower sites had greater spatial heterogeneity in infaunal invertebrate assemblages than deeper sites; thus as monitoring protocols are developed we recommend that shallower sites be sampled more extensively in order to adequately characterize those communities. Molluscs seemed to be the most responsive to substrate type, with different assemblages found in pure sand, slightly muddy sand, and mostly silt/clay. In addition to sampling of sedimentary habitat, we conducted limited surveys of offshore reef habitats. Although it is unlikely that devices would be installed in these areas, reefs may be crossed by electrical cables, and changes in sediment transport due to ocean energy extraction or alterations of flow around large device arrays could lead to community impacts. The aim of this study was to describe baseline relationships between macroinvertebrate communities and habitat features against which to measure potential future impacts and to develop tools to predict community compositions of unsampled areas in the region based on substrate features. To date we have analyzed submersible dive video from three sites conducted in the mid-1990s. In the summers of 2011 and 2012, we visited these previously surveyed sites with an ROV. Analysis of submersible and ROV surveys indicated that two major substratum groups held different macroinvertebrate assemblages: moderate to high-relief rocky habitats and low-relief fine sediment habitats. The majority of macroinvertebrate taxa were associated with high-relief rocks; these taxa were further differentiated between flat and ridge rock habitats. Low-relief fine sediment habitat was most often associated with motile invertebrates. Within this habitat it appeared that fine-sediment substrata mixed with mud, boulders, or gravel each yield unique macro-invertebrate associations versus those found on uniformly mud or sand substrata. Latitude also was correlated with variation in macroinvertebrate assemblages. A major challenge will be detecting effects of wind and wave energy installations above the inherent natural variability in these systems. Decadal scale shifts in the California Current affect this ecosystem, with warm regimes and associated declines in planktonic production resulting in degradation of benthic community. On shorter timescales El Niño events can cause major, short-term disturbances. Off the Oregon coast, summer hypoxia events can have dramatic effects on benthic communities, and ocean acidification is an increasing concern. Thus, evaluation of this ecosystem must be made in the context of seasonal and climatic trends. Prior to installation of device arrays, baseline sampling is usually required as part of the permitting process. However, one-time sampling will not capture the variability of the system in a given area, and developers and regulators typically are not able to make the investment (in time or money) to repeatedly survey an area before development. Funding agencies rarely support long-term monitoring studies. Thus, finding support for repeated field sampling across time and space is especially challenging. The biggest issue facing wind and wave energy developers in the environmental arena is the high level of uncertainty regarding environmental effects. Without a substantial understanding of the natural dynamics of a system, it will be difficult to reduce that uncertainty. Title: Linking Habitat and Benthic Invertebrate Species Distributions in Areas of Potential Renewable Energy Development Author: Henkel, Sarah K., Goldfinger, Chris While the coastal waters of western North America hold great promise for wind and wave energy development, many concerns have been raised about the potential environmental impacts of the installation of these devices and their complex mooring systems. Here I focus on characterizing benthic habitats and biological communities in offshore sedimentary and reef habitats where wind and wave energy facilities could be located. While little is known about species-habitat relationships and community processes in the depths and substrate types targeted for offshore renewable energy installation, an understanding of the natural dynamics of these systems is of utmost importance if we hope to forecast changes that might be brought about by wind and wave development. Since May 2010 we have conducted surveys of benthic habitats from northern California to Washington using a variety of techniques, providing baseline data on habitats and species potentially affected by wind and wave development, identifying species-habitat relationships, and quantifying spatial and temporal trends in species abundances and distributions. The first step in identifying and evaluating benthic communities is sonar mapping to determine depth and substrate types. In summer 2010 and 2011 six new offshore sites were mapped by the Seafloor Mapping and Plate Tectonics Lab at OSU using high-resolution multi-beam sonar and acoustic backscatter. In addition to the backscatter, Shipek grabs were taken in soft-bottom areas to collect sediment samples, which were run through a laser particle size analyzer (LDPSA) to determine actual grain size. Mapping began at the federal jurisdiction line and extended 9 – 12 miles offshore. Oregon and California have undertaken extensive mapping of state waters, so many areas have been mapped inshore of these sites as well. In summer 2011 and 2012, we visited 8 sites (6 newly mapped sites, one previously mapped, and one unmapped site) to collect a total of 153 cores using a 0.1 m2 box-corer. A sub-sample of sediment was collected from the corer and analyzed using the LDPSA; the rest was sieved through 1 mm mesh and all infaunal organisms were counted and identified. At each box core sampling station, CTD casts were conducted to obtain physical data describing the overlying water column for further habitat characterization. Unique infaunal invertebrate assemblages were found in sedimentary habitats at each of the Pacific Northwest shelf sites. Thus for renewable energy siting, it does not appear that baseline surveys conducted at one site can necessarily serve as a proxy for distant sites. However, some general trends were detected. Significantly different invertebrate assemblages were found in different depth ranges with a break at approximately 80 to 90 m depth; deeper sites exhibited greater diversity. Shallower sites had greater spatial heterogeneity in infaunal invertebrate assemblages than deeper sites; thus as monitoring protocols are developed we recommend that shallower sites be sampled more extensively in order to adequately characterize those communities. Molluscs seemed to be the most responsive to substrate type, with different assemblages found in pure sand, slightly muddy sand, and mostly silt/clay. In addition to sampling of sedimentary habitat, we conducted limited surveys of offshore reef habitats. Although it is unlikely that devices would be installed in these areas, reefs may be crossed by electrical cables, and changes in sediment transport due to ocean energy extraction or alterations of flow around large device arrays could lead to community impacts. The aim of this study was to describe baseline relationships between macroinvertebrate communities and habitat features against which to measure potential future impacts and to develop tools to predict community compositions of unsampled areas in the region based on substrate features. To date we have analyzed submersible dive video from three sites conducted in the mid-1990s. In the summers of 2011 and 2012, we visited these previously surveyed sites with an ROV. Analysis of submersible and ROV surveys indicated that two major substratum groups held different macroinvertebrate assemblages: moderate to high-relief rocky habitats and low-relief fine sediment habitats. The majority of macroinvertebrate taxa were associated with high-relief rocks; these taxa were further differentiated between flat and ridge rock habitats. Low-relief fine sediment habitat was most often associated with motile invertebrates. Within this habitat it appeared that fine-sediment substrata mixed with mud, boulders, or gravel each yield unique macro-invertebrate associations versus those found on uniformly mud or sand substrata. Latitude also was correlated with variation in macroinvertebrate assemblages. A major challenge will be detecting effects of wind and wave energy installations above the inherent natural variability in these systems. Decadal scale shifts in the California Current affect this ecosystem, with warm regimes and associated declines in planktonic production resulting in degradation of benthic community. On shorter timescales El Niño events can cause major, short-term disturbances. Off the Oregon coast, summer hypoxia events can have dramatic effects on benthic communities, and ocean acidification is an increasing concern. Thus, evaluation of this ecosystem must be made in the context of seasonal and climatic trends. Prior to installation of device arrays, baseline sampling is usually required as part of the permitting process. However, one-time sampling will not capture the variability of the system in a given area, and developers and regulators typically are not able to make the investment (in time or money) to repeatedly survey an area before development. Funding agencies rarely support long-term monitoring studies. Thus, finding support for repeated field sampling across time and space is especially challenging. The biggest issue facing wind and wave energy developers in the environmental arena is the high level of uncertainty regarding environmental effects. Without a substantial understanding of the natural dynamics of a system, it will be difficult to reduce that uncertainty. Close

• 1053. [Article] Tidal influence on downstream fining in gravel-bed rivers

  This research examines the downstream fining phenomenon as it operates in coastal gravel-bed rivers of Oregon. Downstream fining is a change in bed composition toward smaller sediment sizes in the downstream ...

  Citation × Citation Citation Abstract Copy Title: Tidal influence on downstream fining in gravel-bed rivers Author: Coles, Derron Rafiq This research examines the downstream fining phenomenon as it operates in coastal gravel-bed rivers of Oregon. Downstream fining is a change in bed composition toward smaller sediment sizes in the downstream direction. Changes in stream flow discharge and channel slope affect the rate of bed-load transport, thereby altering the downstream fining regime. This research focuses on ascertaining the rate of downstream fining and the characterization of tidal influence on bed-load transport in the lower-river reaches. For this purpose, a combination of physical and numerical analysis techniques were used. Variations of particle size distributions and specific gravity values were assessed along the main channel. Numerical analysis techniques included a MATLAB program for simulating bed-load transport as affected by tide. The numerical model developed for this investigation, TIMM (Tidally Influenced Movement Model) uses physically based excess shear stress as the underlying mechanism. Namely, an undulating water surface is applied to Shields criterion for incipient motion and bed-load transport. The Generalized Stream Tube model for Alluvial River Simulation version 2.1 (GSTARS 2.1), developed by the Bureau of Reclamation, was used to validate conclusions drawn from field data analyses. The five rivers of the Tillamook Basin were the sites of field data collection. The Tillamook Basin is located approximately 60 miles (96.6 kilometers) west of Portland, Oregon and 60 miles (96.6 kilometers) south of the Columbia River mouth at the Pacific Ocean. The basin has a total area of 570 square miles (1476 square kilometers) including Tillamook Bay, which is the second largest estuary in Oregon. All rivers empty into the Tillamook Bay. From north to south, the rivers are the Miami, Kilchis, Wilson, Trask and Tillamook. The Kilchis River was the primary field research site and the other four rivers allowed expansion of field research for added understanding of downstream fining. Bulk sampling of the armor and sub-armor layer of the Kilchis River was completed for five sidebars along the river, from river mile 0 to river mile 14 (0 - 22.5 km). Photo frame sampling was carried out for the armor layer of sidebars along the four additional rivers. In total, 21 sampling locations with 141 individual sampling points were used for the particle size analyses. Assessment of longitudinal variation in specific gravity of bed particles by size fraction was performed for all five rivers. Particle size analyses showed a distinct downstream fining trend. Kilchis River surface particle sizes decreased from 216 mm at river mile 14 (22.5 km) to 10 mm at river mile 0. Miami River surface particle sizes decreased from 43 mm at river mile 9 to 29 mm at river mile 1.5 (2.4 km). Wilson River surface particle sizes decreased from 51 mm at river mile 27 to 23 mm at river mile 0. Trask River surface particle sizes decreased from 55 mm at river mile 18 to 26 mm at river mile 4 (6.4 km). Diminution coefficients (rates of size reduction) were found to be 0.55 km⁻¹ for the armor layer and 0.48 km⁻¹ for the sub-armor layer of the Kilchis River. The R-squared values for the armor and sub-armor coefficients are 0.92 and 0.99, respectively. Results of regression analyses performed for the photo frame sampling data were 0.02, 0.03, and 0.04 km⁻¹ for the Miami, Wilson, and Trask Rivers, respectively. R-squared values of 0.19, 0.78, and 0.81, respectively. Diminution coefficients reported for all rivers were far outside the value reported for abrasion-dominated systems (0.089 km⁻¹), yet were within the range of diminution coefficients reported for selective sorting-dominated systems (0.001 to 0.05 km⁻¹). Average specific gravities for bed material were 2.78, 2.68, 2.73, 2.56, and 2.76 for the Miami, Kilchis, Wilson, Trask, and Tillamook Rivers, respectively. Simulations of sediment transport within the tidal portion of the Kilchis River (river mile 0 to 3 or 0 to 4.8 km) using TIMM at moderate river streamflow above the threshold for transport of material showed that tidal influence causes distinct deposition zones during periods of high, low, and moderate tide levels. Depositional zones were found to propagate downstream with increases in river discharge, such that at elevated river stage the location of depositional zones associated with tide levels were undistinguishable. It can be concluded that tide has a significant influence at flows below, and moderately above the threshold for transport. Simulations of a simplified version of the Kilchis River using GSTARS 2.1 produced comparable results to the TIMM simulations. GSTARS 2.1 was run using three scenarios, 1) a uniform bed and incoming sediment supply set at 7.9 mm, 2) a mixed bed with mean sediment diameter of 7.9 mm and coarser incoming sediment supply, and 3) a mixed bed with mean sediment diameter of 7.9 mm and finer incoming sediment supply. Each scenario had output data that show maximum deposition in the zone of tidal influence. The location of head of tide for the simplified Kilchis River was found to occur at river mile 5 instead of river mile 3 used for the head of tide in TIMM simulations. GSTARS 2.1 simulations showed that variations in particle size distribution of incoming sediment supply influence rates of downstream fining. An incoming sediment supply that had a coarser particle size distribution than the particle size distribution of the bed resulted in an observable increase in deposition of large particle sizes in the upstream reaches; however, there was no observable increase in deposition of large particle sizes in downstream reaches. An incoming sediment supply that had a finer particle size distribution than the particle size distribution of the bed resulted in an observable increase in deposition of smaller particles in the downstream reaches, with no observable increase in deposition of smaller sizes in the upstream reaches. Therefore, simulations show evidence that sediment supply of particles coarser than the bed causes increased rates of fining in reaches near the sediment source. Key contributions of this research are in the categories of methodology, numerical analysis, and basic understanding of the fate and transport of sediment in the zone of tidal influence. It has been shown that particle size data, collected in detail on sidebars, can be used in conjunction with specific gravity data to categorize in-stream particles based on probable origin and type. Characterization of sediment transport in the zone of tidal influence using numerical models showed the tide cycle influences the downstream fining trend in lower reaches by shifting the zone of deposition farther upstream than would the case without tidal influence, with a net effect of increasing the rate of downstream fining. Moreover, tidal influence was found to have an inverse relationship with water discharge. Finally, it was shown that numerical modeling of river reaches in the tidal zone should include consideration of tidal fluctuations in order to predict erosion and depositional areas more accurately. Title: Tidal influence on downstream fining in gravel-bed rivers Author: Coles, Derron Rafiq This research examines the downstream fining phenomenon as it operates in coastal gravel-bed rivers of Oregon. Downstream fining is a change in bed composition toward smaller sediment sizes in the downstream direction. Changes in stream flow discharge and channel slope affect the rate of bed-load transport, thereby altering the downstream fining regime. This research focuses on ascertaining the rate of downstream fining and the characterization of tidal influence on bed-load transport in the lower-river reaches. For this purpose, a combination of physical and numerical analysis techniques were used. Variations of particle size distributions and specific gravity values were assessed along the main channel. Numerical analysis techniques included a MATLAB program for simulating bed-load transport as affected by tide. The numerical model developed for this investigation, TIMM (Tidally Influenced Movement Model) uses physically based excess shear stress as the underlying mechanism. Namely, an undulating water surface is applied to Shields criterion for incipient motion and bed-load transport. The Generalized Stream Tube model for Alluvial River Simulation version 2.1 (GSTARS 2.1), developed by the Bureau of Reclamation, was used to validate conclusions drawn from field data analyses. The five rivers of the Tillamook Basin were the sites of field data collection. The Tillamook Basin is located approximately 60 miles (96.6 kilometers) west of Portland, Oregon and 60 miles (96.6 kilometers) south of the Columbia River mouth at the Pacific Ocean. The basin has a total area of 570 square miles (1476 square kilometers) including Tillamook Bay, which is the second largest estuary in Oregon. All rivers empty into the Tillamook Bay. From north to south, the rivers are the Miami, Kilchis, Wilson, Trask and Tillamook. The Kilchis River was the primary field research site and the other four rivers allowed expansion of field research for added understanding of downstream fining. Bulk sampling of the armor and sub-armor layer of the Kilchis River was completed for five sidebars along the river, from river mile 0 to river mile 14 (0 - 22.5 km). Photo frame sampling was carried out for the armor layer of sidebars along the four additional rivers. In total, 21 sampling locations with 141 individual sampling points were used for the particle size analyses. Assessment of longitudinal variation in specific gravity of bed particles by size fraction was performed for all five rivers. Particle size analyses showed a distinct downstream fining trend. Kilchis River surface particle sizes decreased from 216 mm at river mile 14 (22.5 km) to 10 mm at river mile 0. Miami River surface particle sizes decreased from 43 mm at river mile 9 to 29 mm at river mile 1.5 (2.4 km). Wilson River surface particle sizes decreased from 51 mm at river mile 27 to 23 mm at river mile 0. Trask River surface particle sizes decreased from 55 mm at river mile 18 to 26 mm at river mile 4 (6.4 km). Diminution coefficients (rates of size reduction) were found to be 0.55 km⁻¹ for the armor layer and 0.48 km⁻¹ for the sub-armor layer of the Kilchis River. The R-squared values for the armor and sub-armor coefficients are 0.92 and 0.99, respectively. Results of regression analyses performed for the photo frame sampling data were 0.02, 0.03, and 0.04 km⁻¹ for the Miami, Wilson, and Trask Rivers, respectively. R-squared values of 0.19, 0.78, and 0.81, respectively. Diminution coefficients reported for all rivers were far outside the value reported for abrasion-dominated systems (0.089 km⁻¹), yet were within the range of diminution coefficients reported for selective sorting-dominated systems (0.001 to 0.05 km⁻¹). Average specific gravities for bed material were 2.78, 2.68, 2.73, 2.56, and 2.76 for the Miami, Kilchis, Wilson, Trask, and Tillamook Rivers, respectively. Simulations of sediment transport within the tidal portion of the Kilchis River (river mile 0 to 3 or 0 to 4.8 km) using TIMM at moderate river streamflow above the threshold for transport of material showed that tidal influence causes distinct deposition zones during periods of high, low, and moderate tide levels. Depositional zones were found to propagate downstream with increases in river discharge, such that at elevated river stage the location of depositional zones associated with tide levels were undistinguishable. It can be concluded that tide has a significant influence at flows below, and moderately above the threshold for transport. Simulations of a simplified version of the Kilchis River using GSTARS 2.1 produced comparable results to the TIMM simulations. GSTARS 2.1 was run using three scenarios, 1) a uniform bed and incoming sediment supply set at 7.9 mm, 2) a mixed bed with mean sediment diameter of 7.9 mm and coarser incoming sediment supply, and 3) a mixed bed with mean sediment diameter of 7.9 mm and finer incoming sediment supply. Each scenario had output data that show maximum deposition in the zone of tidal influence. The location of head of tide for the simplified Kilchis River was found to occur at river mile 5 instead of river mile 3 used for the head of tide in TIMM simulations. GSTARS 2.1 simulations showed that variations in particle size distribution of incoming sediment supply influence rates of downstream fining. An incoming sediment supply that had a coarser particle size distribution than the particle size distribution of the bed resulted in an observable increase in deposition of large particle sizes in the upstream reaches; however, there was no observable increase in deposition of large particle sizes in downstream reaches. An incoming sediment supply that had a finer particle size distribution than the particle size distribution of the bed resulted in an observable increase in deposition of smaller particles in the downstream reaches, with no observable increase in deposition of smaller sizes in the upstream reaches. Therefore, simulations show evidence that sediment supply of particles coarser than the bed causes increased rates of fining in reaches near the sediment source. Key contributions of this research are in the categories of methodology, numerical analysis, and basic understanding of the fate and transport of sediment in the zone of tidal influence. It has been shown that particle size data, collected in detail on sidebars, can be used in conjunction with specific gravity data to categorize in-stream particles based on probable origin and type. Characterization of sediment transport in the zone of tidal influence using numerical models showed the tide cycle influences the downstream fining trend in lower reaches by shifting the zone of deposition farther upstream than would the case without tidal influence, with a net effect of increasing the rate of downstream fining. Moreover, tidal influence was found to have an inverse relationship with water discharge. Finally, it was shown that numerical modeling of river reaches in the tidal zone should include consideration of tidal fluctuations in order to predict erosion and depositional areas more accurately. Close

• 1054. [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

• 1055. [Article] Petrology and geochemistry of the Emigrant Pass volcanics, Nevada : implications for a magmatic-hydrothermal origin of the Carlin gold deposits

  The Emigrant Pass volcanics (EPV) are a 38.3 to 36.4 Ma calc-alkaline volcanic center that erupted andesite and dacite, and a late series of felsic dikes along the south flank of the Carlin gold district ...

  Citation × Citation Citation Abstract Copy Title: Petrology and geochemistry of the Emigrant Pass volcanics, Nevada : implications for a magmatic-hydrothermal origin of the Carlin gold deposits Author: Johnson, Curtis L. (Curtis Lawrence) The Emigrant Pass volcanics (EPV) are a 38.3 to 36.4 Ma calc-alkaline volcanic center that erupted andesite and dacite, and a late series of felsic dikes along the south flank of the Carlin gold district in north-central Nevada. The EPV includes dacite and rhyolite porphyry dikes indistinguishable from porphyry dikes associated with mineralization within the district. The volcanic rocks likely represent eruptive equivalents of deeper, unexposed Eocene plutons that may be the source of heat, fluids, and metals of Carlin-type gold deposits. New petrologic and geochemical data of the EPV are presented to test this hypothesis. The EPV are exposed over a 30 x 15 km area, have an estimated volume of 100 to >200 km³ and are divided into the early Primeaux lavas (38.1-38.3 Ma), the Mack Creek lavas and related intrusions (37.1-38.4 Ma), and late eruptive and hypabyssal rocks (Henry and Faulds, 1999). The Primeaux lavas are a >500 m thick sequence of pyroxene and hornblende andesite to dacite lavas and intrusions; minor pyroxene, hornblende and biotite dikes; and volcanic conglomerates. The Mack Creek lavas are a 180 m thick succession of porphyritic dacite lava flows, domes, and intrusions. Late small-volume units include the Bob Creek basaltic andesite to andesite lava (37.7 Ma) and rhyolitic to dacitic dikes (36.4-36.7 Ma). Primeaux andesite crystallized early clinopyroxene, orthopyroxene, plagioclase, and late hornblende, which suggests moderate water contents (~3 wt.%). Mack Creek dacite and late rhyolite-dacite dikes crystallized hornblende and biotite early, attesting to high water contents (>4 wt.%). Early Primeaux andesites contain abundant magnetite and sparse ilmenite, whereas Mack Creek dacites and late rhyolite-dacite dikes contain magnetite and local titanite. This mineralogy is consistent with the evolution of magmas from early moderately oxidized conditions to late strongly oxidized conditions (fO2 ≥ NNO+2) similar to porphyry copper magmas (Dilles, 1987). Carlin plagioclase-biotite-hornblende dacite porphyry dikes associated with gold ores yielded four new LA-ICP-MS U/Pb zircon ages (36.7±1.8, 38.8±1.7, 39.2±1.6, 39.4±1.5 Ma), overlapping in age with the earliest EPV eruptions. Two additional U/Pb zircon ages were obtained on a coarsely porphyritic dacite lava of the Mack Creek sequence (37.10±0.54 Ma), and a porphyritic dacite lava (148.2±2.3 Ma) likely of the Frenchie Creek Volcanics at the southern terminus of the EPV. All analyzed Carlin porphyries contain zircons with EuN/EuN* versus Hf arrays and EuN/EuN* > 0.4 similar to porphyry copper plutons (Dilles et al., 2015) and the 36 Ma Battle Mountain granodiorite porphyry associated with Cu(Au) ores (Farmer, 2013). Abundant partially melted granite xenoliths in EPV rocks indicate assimilation of crust during magma generation, whereas incompletely mixed magmas with differing mineralogy along with abundantly sieved plagioclase and resorbed amphibole indicate magma mixing processes. The andesites and dacites have high-K to shoshonitic compositions similar to subduction-related arc magmas. Whereas most major elements display simple linear correlations with silica, interpreted to indicate mixing, the MgO and Cr of most samples abruptly decrease with increased silica consistent with crystal fractionation. Dacites of the Mack Creek have elevated MgO and Cr compared to Primeaux andesites and Bob Creek basaltic-andesites, consistent with mixing of primitive basaltic andesite or andesite with rhyolite. Enrichment in Rb, Ba, and Cs indicate crustal additions compared to average arc magmas, whereas elevated V/Sc (1.4-17.3; Mean: 8.9) and Sr/Y (16.6-49.6; Mean: 36.1) ratios are similar to mineralizing porphyry Cu (Au) magmas (Loucks, 2014). Hornblende compositions from four samples are bimodal and include both low-Al and high-Al amphiboles now commonly recognized in arc suites (Aucanquilcha, Chile: Walker et al., 2013; Yanacocha, Peru: Chambefort et al., 2013). Using the Ridolfi et al. (2010) formulation, the low-Al hornblende crystallized at 820-890°C and 100-250 MPa (4-10 km depth), whereas high-Al amphibole crystallized at about 900-980°C and possibly greater depths. Electron microprobe studies of magmatic sulfide inclusions indicate monosulfide solid solution (MSS, pyrrhotite at low temperatures) was the dominant magmatic sulfide species with minor (n=4 of 119 analyses) intermediate solid solution (ISS, chalcopyrite at low temperatures). Sulfide contents decrease systematically as the magmas evolved from andesite-dacite-rhyolite, supporting the observation of increasing oxidation state and magmatic sulfate/sulfide ratio. Additionally, all phases of the EPV are highly depleted in whole rock Cu (<10ppm), suggesting Cu was efficiently removed during volatile exsolution at depth or alternatively was sequestered in magmatic sulfide at depth. Experimental studies of Au partitioning in intermediate composition melts indicate that the predominance of MSS over sulfide liquid or ISS is a prerequisite for forming Au-rich melts as MSS preferentially incorporates Cu over Au, thereby further enriching the Au/Cu ratio of the remaining melt (Muntean et al., 2011; Botcharnikov et al., 2013; Yi and Audetat, 2013). Muntean and others (2011) proposed a magmatic-hydrothermal fluid and metal source of the Carlin gold deposits and suggested source magmas were fundamentally enriched in Au relative to Cu as a result of MSS fractionation over ISS or sulfide liquid, which is supported by these new data on EPV magmatic sulfide inclusions. Title: Petrology and geochemistry of the Emigrant Pass volcanics, Nevada : implications for a magmatic-hydrothermal origin of the Carlin gold deposits Author: Johnson, Curtis L. (Curtis Lawrence) The Emigrant Pass volcanics (EPV) are a 38.3 to 36.4 Ma calc-alkaline volcanic center that erupted andesite and dacite, and a late series of felsic dikes along the south flank of the Carlin gold district in north-central Nevada. The EPV includes dacite and rhyolite porphyry dikes indistinguishable from porphyry dikes associated with mineralization within the district. The volcanic rocks likely represent eruptive equivalents of deeper, unexposed Eocene plutons that may be the source of heat, fluids, and metals of Carlin-type gold deposits. New petrologic and geochemical data of the EPV are presented to test this hypothesis. The EPV are exposed over a 30 x 15 km area, have an estimated volume of 100 to >200 km³ and are divided into the early Primeaux lavas (38.1-38.3 Ma), the Mack Creek lavas and related intrusions (37.1-38.4 Ma), and late eruptive and hypabyssal rocks (Henry and Faulds, 1999). The Primeaux lavas are a >500 m thick sequence of pyroxene and hornblende andesite to dacite lavas and intrusions; minor pyroxene, hornblende and biotite dikes; and volcanic conglomerates. The Mack Creek lavas are a 180 m thick succession of porphyritic dacite lava flows, domes, and intrusions. Late small-volume units include the Bob Creek basaltic andesite to andesite lava (37.7 Ma) and rhyolitic to dacitic dikes (36.4-36.7 Ma). Primeaux andesite crystallized early clinopyroxene, orthopyroxene, plagioclase, and late hornblende, which suggests moderate water contents (~3 wt.%). Mack Creek dacite and late rhyolite-dacite dikes crystallized hornblende and biotite early, attesting to high water contents (>4 wt.%). Early Primeaux andesites contain abundant magnetite and sparse ilmenite, whereas Mack Creek dacites and late rhyolite-dacite dikes contain magnetite and local titanite. This mineralogy is consistent with the evolution of magmas from early moderately oxidized conditions to late strongly oxidized conditions (fO2 ≥ NNO+2) similar to porphyry copper magmas (Dilles, 1987). Carlin plagioclase-biotite-hornblende dacite porphyry dikes associated with gold ores yielded four new LA-ICP-MS U/Pb zircon ages (36.7±1.8, 38.8±1.7, 39.2±1.6, 39.4±1.5 Ma), overlapping in age with the earliest EPV eruptions. Two additional U/Pb zircon ages were obtained on a coarsely porphyritic dacite lava of the Mack Creek sequence (37.10±0.54 Ma), and a porphyritic dacite lava (148.2±2.3 Ma) likely of the Frenchie Creek Volcanics at the southern terminus of the EPV. All analyzed Carlin porphyries contain zircons with EuN/EuN* versus Hf arrays and EuN/EuN* > 0.4 similar to porphyry copper plutons (Dilles et al., 2015) and the 36 Ma Battle Mountain granodiorite porphyry associated with Cu(Au) ores (Farmer, 2013). Abundant partially melted granite xenoliths in EPV rocks indicate assimilation of crust during magma generation, whereas incompletely mixed magmas with differing mineralogy along with abundantly sieved plagioclase and resorbed amphibole indicate magma mixing processes. The andesites and dacites have high-K to shoshonitic compositions similar to subduction-related arc magmas. Whereas most major elements display simple linear correlations with silica, interpreted to indicate mixing, the MgO and Cr of most samples abruptly decrease with increased silica consistent with crystal fractionation. Dacites of the Mack Creek have elevated MgO and Cr compared to Primeaux andesites and Bob Creek basaltic-andesites, consistent with mixing of primitive basaltic andesite or andesite with rhyolite. Enrichment in Rb, Ba, and Cs indicate crustal additions compared to average arc magmas, whereas elevated V/Sc (1.4-17.3; Mean: 8.9) and Sr/Y (16.6-49.6; Mean: 36.1) ratios are similar to mineralizing porphyry Cu (Au) magmas (Loucks, 2014). Hornblende compositions from four samples are bimodal and include both low-Al and high-Al amphiboles now commonly recognized in arc suites (Aucanquilcha, Chile: Walker et al., 2013; Yanacocha, Peru: Chambefort et al., 2013). Using the Ridolfi et al. (2010) formulation, the low-Al hornblende crystallized at 820-890°C and 100-250 MPa (4-10 km depth), whereas high-Al amphibole crystallized at about 900-980°C and possibly greater depths. Electron microprobe studies of magmatic sulfide inclusions indicate monosulfide solid solution (MSS, pyrrhotite at low temperatures) was the dominant magmatic sulfide species with minor (n=4 of 119 analyses) intermediate solid solution (ISS, chalcopyrite at low temperatures). Sulfide contents decrease systematically as the magmas evolved from andesite-dacite-rhyolite, supporting the observation of increasing oxidation state and magmatic sulfate/sulfide ratio. Additionally, all phases of the EPV are highly depleted in whole rock Cu (<10ppm), suggesting Cu was efficiently removed during volatile exsolution at depth or alternatively was sequestered in magmatic sulfide at depth. Experimental studies of Au partitioning in intermediate composition melts indicate that the predominance of MSS over sulfide liquid or ISS is a prerequisite for forming Au-rich melts as MSS preferentially incorporates Cu over Au, thereby further enriching the Au/Cu ratio of the remaining melt (Muntean et al., 2011; Botcharnikov et al., 2013; Yi and Audetat, 2013). Muntean and others (2011) proposed a magmatic-hydrothermal fluid and metal source of the Carlin gold deposits and suggested source magmas were fundamentally enriched in Au relative to Cu as a result of MSS fractionation over ISS or sulfide liquid, which is supported by these new data on EPV magmatic sulfide inclusions. Close

• 1056. [Article] Physical-Environmental Effects of Wave and Offshore Wind Energy Extraction: A Synthesis of Recent Oceanographic Research

  The ocean deployment of arrays of Wave Energy Converters (WEC arrays) appears likely in the near future, and deployment of offshore wind turbines has already started. These technologies tap into a potential ...

  Citation × Citation Citation Abstract Copy Title: Physical-Environmental Effects of Wave and Offshore Wind Energy Extraction: A Synthesis of Recent Oceanographic Research Author: Özkan-Haller, Tuba, Haller, Merrick C. The ocean deployment of arrays of Wave Energy Converters (WEC arrays) appears likely in the near future, and deployment of offshore wind turbines has already started. These technologies tap into a potential renewable energy resource but also involve complex systems with uncertain environmental consequences that will likely scale with the size of their ocean footprint. This synthesis talk will concentrate on the potential physical effects of these array technologies. Both WEC arrays and offshore wind farms consist of sizable structures placed in the water column; hence, their mere presence is a potential environmental stressor. Possible effects on the physical environment include wave scattering and wave shadowing; added drag on the coastal current field; modifications to sediment transport (by way of the aforementioned changes to the wave and current forcing); and changes to local sediment characteristics (due to anchors and pilings). In many ways, these effects are similar to those caused by other ocean structures that have been studied for some time (e.g., offshore platforms). However, there are additional potential effects of WECs and wind turbines that require further attention. For example, extraction of wave energy by WECs could have additional environmental consequences. Similarly, offshore wind farms can alter the local wind field, in turn altering locally-generated waves. We will address effects due to wave or wind installations on the wave field, on local ocean circulation, and on sediment transport characteristics. Because WECs partially extract and scatter incident wave energy, they cause significant modifications in the near-field. In fact, if device performance can be optimized at field scales, then by definition the near-field effects will be maximized, i.e., if energy extraction is maximized the potential physical effects of WECs are also maximized. Over the past decade a sizable number of studies have applied theoretical principles using varying assumptions and simplifications to the problem of WEC-wave interactions. Some of these assumptions (e.g., “optimal” motions, monochromatic wave conditions, etc.) have now been shown to be unrealistic, and there has been a convergence toward classes of models that appear to produce reasonable estimates. While recent model studies have managed to bound the problem, significant uncertainties remain. The primary cause for the remaining uncertainties is the lack of observational studies, particularly data sets that provide spatial information about the wave field in the vicinity of in situ devices. Nonetheless, a few studies have undertaken scaled laboratory testing, and these data sets are beginning to lend confidence to the available numerical model results and shed light on the dominant processes. Once near-field effects are understood, far-field effects can be assessed. Far-field effects influence the wave field near beaches, which, in turn, influences the sand transport processes that govern the morphodynamics of the beach face. Fortunately, hydrodynamic modelling of large-scale wave propagation processes in the absence of structures is highly advanced, i.e., if given accurate incident wave conditions in the lee of an installation and bathymetry for the model domain, models can well-simulate local wave conditions, wave-driven currents and sediment transport patterns. Therefore, once near-field WEC/wave dynamics are understood, expanding our understanding to the far-field will be relatively straightforward. Nonetheless, observational studies of far-field beach modifications shoreward of an installation will help to further solidify our understanding of beach behaviour. Offshore wind farms can also potentially influence the local wind field around them. Previous studies of such modifications at land-based wind farm installations serve as a reasonable basis for predictions offshore . Any changes to offshore winds will also influence the local wave field, especially where local winds are the dominant source of waves. Such effects will be minimal near coasts where the local wave climate is dominated by incident swells generated at large distances (e.g., the U.S. West Coast). In contrast, locally generated waves are a more important component of the wave climate on the East Coast of the U.S Modification to ocean currents by an array of structures can be assessed by considering the additional frictional effects (“form” drag) caused of the array. If the drag caused by a dense of array of structures is large, circulation will be altered, which might result in reduced current velocities or the diversion of currents toward an area of less drag. Note that ocean currents already experience drag due to bottom friction; hence, the question hinges on the relative magnitude of the drag induced by structures versus the pre-existing frictional drag. Finally, any near-field modifications to the wave and circulation field (due to either WEC arrays or wind farms) will necessarily result in changes in sediment transport. Any local reduction in flow velocities can result in a reduction of the sediment carrying capacity of circulation leading to sediment accumulation at the site. Small-scale modification to a current will also likely cause bumps and holes around the pilings or anchors. These effects are similar to those observed around existing offshore structures and pilings, and can be accounted for in the design of the structures. Far-field modification of waves and associated changes in wave-induced currents can also result in changes in sediment transport patterns near beaches. Although some recent studies exist, questions regarding far-field effects on beaches are still relatively poorly addressed. Title: Physical-Environmental Effects of Wave and Offshore Wind Energy Extraction: A Synthesis of Recent Oceanographic Research Author: Özkan-Haller, Tuba, Haller, Merrick C. The ocean deployment of arrays of Wave Energy Converters (WEC arrays) appears likely in the near future, and deployment of offshore wind turbines has already started. These technologies tap into a potential renewable energy resource but also involve complex systems with uncertain environmental consequences that will likely scale with the size of their ocean footprint. This synthesis talk will concentrate on the potential physical effects of these array technologies. Both WEC arrays and offshore wind farms consist of sizable structures placed in the water column; hence, their mere presence is a potential environmental stressor. Possible effects on the physical environment include wave scattering and wave shadowing; added drag on the coastal current field; modifications to sediment transport (by way of the aforementioned changes to the wave and current forcing); and changes to local sediment characteristics (due to anchors and pilings). In many ways, these effects are similar to those caused by other ocean structures that have been studied for some time (e.g., offshore platforms). However, there are additional potential effects of WECs and wind turbines that require further attention. For example, extraction of wave energy by WECs could have additional environmental consequences. Similarly, offshore wind farms can alter the local wind field, in turn altering locally-generated waves. We will address effects due to wave or wind installations on the wave field, on local ocean circulation, and on sediment transport characteristics. Because WECs partially extract and scatter incident wave energy, they cause significant modifications in the near-field. In fact, if device performance can be optimized at field scales, then by definition the near-field effects will be maximized, i.e., if energy extraction is maximized the potential physical effects of WECs are also maximized. Over the past decade a sizable number of studies have applied theoretical principles using varying assumptions and simplifications to the problem of WEC-wave interactions. Some of these assumptions (e.g., “optimal” motions, monochromatic wave conditions, etc.) have now been shown to be unrealistic, and there has been a convergence toward classes of models that appear to produce reasonable estimates. While recent model studies have managed to bound the problem, significant uncertainties remain. The primary cause for the remaining uncertainties is the lack of observational studies, particularly data sets that provide spatial information about the wave field in the vicinity of in situ devices. Nonetheless, a few studies have undertaken scaled laboratory testing, and these data sets are beginning to lend confidence to the available numerical model results and shed light on the dominant processes. Once near-field effects are understood, far-field effects can be assessed. Far-field effects influence the wave field near beaches, which, in turn, influences the sand transport processes that govern the morphodynamics of the beach face. Fortunately, hydrodynamic modelling of large-scale wave propagation processes in the absence of structures is highly advanced, i.e., if given accurate incident wave conditions in the lee of an installation and bathymetry for the model domain, models can well-simulate local wave conditions, wave-driven currents and sediment transport patterns. Therefore, once near-field WEC/wave dynamics are understood, expanding our understanding to the far-field will be relatively straightforward. Nonetheless, observational studies of far-field beach modifications shoreward of an installation will help to further solidify our understanding of beach behaviour. Offshore wind farms can also potentially influence the local wind field around them. Previous studies of such modifications at land-based wind farm installations serve as a reasonable basis for predictions offshore . Any changes to offshore winds will also influence the local wave field, especially where local winds are the dominant source of waves. Such effects will be minimal near coasts where the local wave climate is dominated by incident swells generated at large distances (e.g., the U.S. West Coast). In contrast, locally generated waves are a more important component of the wave climate on the East Coast of the U.S Modification to ocean currents by an array of structures can be assessed by considering the additional frictional effects (“form” drag) caused of the array. If the drag caused by a dense of array of structures is large, circulation will be altered, which might result in reduced current velocities or the diversion of currents toward an area of less drag. Note that ocean currents already experience drag due to bottom friction; hence, the question hinges on the relative magnitude of the drag induced by structures versus the pre-existing frictional drag. Finally, any near-field modifications to the wave and circulation field (due to either WEC arrays or wind farms) will necessarily result in changes in sediment transport. Any local reduction in flow velocities can result in a reduction of the sediment carrying capacity of circulation leading to sediment accumulation at the site. Small-scale modification to a current will also likely cause bumps and holes around the pilings or anchors. These effects are similar to those observed around existing offshore structures and pilings, and can be accounted for in the design of the structures. Far-field modification of waves and associated changes in wave-induced currents can also result in changes in sediment transport patterns near beaches. Although some recent studies exist, questions regarding far-field effects on beaches are still relatively poorly addressed. Close

• 1057. [Article] Linkages among land use, riparian zones, and uptake and transformation of nitrate in stream ecosystems

  Land use alters the physical and biological structure of stream ecosystems and potentially alters their capacity to process nitrogen (N), an essential nutrient that has nearly doubled in abundance on the ...

  Citation × Citation Citation Abstract Copy Title: Linkages among land use, riparian zones, and uptake and transformation of nitrate in stream ecosystems Author: Sobota, Daniel J. Land use alters the physical and biological structure of stream ecosystems and potentially alters their capacity to process nitrogen (N), an essential nutrient that has nearly doubled in abundance on the biosphere during the past century from human activities. In this dissertation, I quantified uptake and transformation of nitrate (NO₃⁻) in small (≤ third-order) streams and related these dynamics to aquatic ecosystem processes, including primary production and organic matter decomposition, and attributes of riparian zone structure and vegetation composition. I also analyze patterns of stream NO₃⁻ processing among three classes of adjacent land use practices (forest, agriculture, and urban). In Chapter 2, ambient rates of NO₃⁻ uptake and transformation were measured with 24-hr releases of ¹⁵N-labeled NO₃⁻ in nine stream reaches in the Willamette River Basin of western Oregon during summer low flow (July – August). Three reaches each were surrounded by forested, agricultural or urban land use. After standardizing reaches to a 500-m length, I estimated that ≥ 20% of tracer ¹⁵NO₃⁻ was taken up by detrital and autotrophic biomass in eight of the reaches. In the remaining stream, which had the largest discharge (120 L s⁻¹) in this study, only 8% of the tracer was taken up in 500 m. Tracer labeling of detritus and autotrophic biomass and a positive correlation (rs=0.81) of uptake with gross primary production suggested that assimilation was the dominant uptake pathway in all streams. Denitrification, dissimilatory reduction of NO₃⁻ to N₂ and N₂O gases, composed 3 – 15% of ¹⁵N budgets over 500 m in two agricultural reaches and in one urban reach dominated by large slowly-turning over pools. However, denitrification was below detection limit at five of the remaining six reaches. This study showed that pathways of stream NO₃⁻ uptake and transformation differed among streams adjacent to three diverse land use practices. In Chapter 3, I quantified effects of substrate nutritional quality and inorganic N loading (as NO₃⁻) on wood breakdown in western Oregon streams. Short-term (< 2 month) breakdown rates of wood substrates of high nutritional quality (Alnus rubra; red alder) and low quality (Pseudotsuga menziesii; Douglas-fir) increased with dissolved inorganic N (11 to 111 mg N L⁻¹) across six streams (p = 0.04), but this relationship was confounded with concurrent increases in stream temperature. Across the six streams, breakdown rates of red alder were consistently double that of Douglas-fir. A longer-term study (313 d) in a coniferous forest Oregon Cascades stream suggested effects of increased NO₃⁻ availability on wood breakdown became evident after cellulose and lignin components of woody tissues began to decompose (> 4 months of incubation). Average breakdown rates substrates enriched with NO₃⁻ were higher than those incubated in low NO₃⁻ conditions, but this difference was not statistically significant. However, microbial biofilm respiration rates and activity of two enzymes involved in the breakdown of woody tissues (beta-glucosidase and phenol oxidase) on red alder had significantly greater responses to NO₃⁻ additions than on Douglas-fir after four months of incubation in the stream. Results suggest that increases in N loading to streams bordered by riparian forests with fast-growing deciduous species could increase wood breakdown rates. On the other hand, increases to N loading may have a smaller effect on wood breakdown in streams surrounded by long-lived coniferous species. In Chapter 4, I quantified patterns of stream channel and riparian zone attributes for 72 streams equally distributed among forests or grasslands, agriculture, and urban land use practices on from eight major North American regions. I also related these patterns to stream NO₃⁻ uptake determined from ¹⁵NO₃⁻ tracer releases. Agricultural and urban streams had a simplified channel structure (low width-to-depth ratio, low variation in stream depth, and high stream banks) relative to forest or grassland streams. Agricultural and urban streams also had a significantly smaller median sediment diameter (D₅₀) and fraction of benthic sediments composed by silt than in forest and grassland streams. Overstory canopy cover over the channel and in the riparian zone was lowest for agricultural streams but did not significantly differ between forest or grassland streams and urban streams. A multiple regression model showed that stream NO₃⁻ uptake decreased with increasing canopy cover, but also increased with abundance of silt in benthic sediments. This suggested NO₃⁻ uptake was strongly influenced by in-stream primary production and extent of anoxic environments (conducive for denitrification). A multiple regression model for fractional NO₃⁻ uptake by denitrification further supported the concept that extent of anoxic environments influenced overall NO₃⁻ uptake in streams. Through these studies, I demonstrated that attributes of riparian zone structure and vegetation composition can strongly influence NO₃⁻ uptake and transformation in stream ecosystems by controlling organic matter dynamics. I also have shown that riparian zone attributes vary significantly among three different land use types (forest or grassland, agriculture, and urban). Similarly, pathways of NO₃⁻ uptake and effects of NO₃⁻ on wood breakdown did or were expected to differ among different land use types / riparian zone characteristics. However, other factors besides riparian attributes, particularly level of nutrient loading, alteration of stream channel physical structure, and basin position of the stream, must be considered in concert when evaluating effects of land use on riparian zone and stream ecosystem structure and function. Title: Linkages among land use, riparian zones, and uptake and transformation of nitrate in stream ecosystems Author: Sobota, Daniel J. Land use alters the physical and biological structure of stream ecosystems and potentially alters their capacity to process nitrogen (N), an essential nutrient that has nearly doubled in abundance on the biosphere during the past century from human activities. In this dissertation, I quantified uptake and transformation of nitrate (NO₃⁻) in small (≤ third-order) streams and related these dynamics to aquatic ecosystem processes, including primary production and organic matter decomposition, and attributes of riparian zone structure and vegetation composition. I also analyze patterns of stream NO₃⁻ processing among three classes of adjacent land use practices (forest, agriculture, and urban). In Chapter 2, ambient rates of NO₃⁻ uptake and transformation were measured with 24-hr releases of ¹⁵N-labeled NO₃⁻ in nine stream reaches in the Willamette River Basin of western Oregon during summer low flow (July – August). Three reaches each were surrounded by forested, agricultural or urban land use. After standardizing reaches to a 500-m length, I estimated that ≥ 20% of tracer ¹⁵NO₃⁻ was taken up by detrital and autotrophic biomass in eight of the reaches. In the remaining stream, which had the largest discharge (120 L s⁻¹) in this study, only 8% of the tracer was taken up in 500 m. Tracer labeling of detritus and autotrophic biomass and a positive correlation (rs=0.81) of uptake with gross primary production suggested that assimilation was the dominant uptake pathway in all streams. Denitrification, dissimilatory reduction of NO₃⁻ to N₂ and N₂O gases, composed 3 – 15% of ¹⁵N budgets over 500 m in two agricultural reaches and in one urban reach dominated by large slowly-turning over pools. However, denitrification was below detection limit at five of the remaining six reaches. This study showed that pathways of stream NO₃⁻ uptake and transformation differed among streams adjacent to three diverse land use practices. In Chapter 3, I quantified effects of substrate nutritional quality and inorganic N loading (as NO₃⁻) on wood breakdown in western Oregon streams. Short-term (< 2 month) breakdown rates of wood substrates of high nutritional quality (Alnus rubra; red alder) and low quality (Pseudotsuga menziesii; Douglas-fir) increased with dissolved inorganic N (11 to 111 mg N L⁻¹) across six streams (p = 0.04), but this relationship was confounded with concurrent increases in stream temperature. Across the six streams, breakdown rates of red alder were consistently double that of Douglas-fir. A longer-term study (313 d) in a coniferous forest Oregon Cascades stream suggested effects of increased NO₃⁻ availability on wood breakdown became evident after cellulose and lignin components of woody tissues began to decompose (> 4 months of incubation). Average breakdown rates substrates enriched with NO₃⁻ were higher than those incubated in low NO₃⁻ conditions, but this difference was not statistically significant. However, microbial biofilm respiration rates and activity of two enzymes involved in the breakdown of woody tissues (beta-glucosidase and phenol oxidase) on red alder had significantly greater responses to NO₃⁻ additions than on Douglas-fir after four months of incubation in the stream. Results suggest that increases in N loading to streams bordered by riparian forests with fast-growing deciduous species could increase wood breakdown rates. On the other hand, increases to N loading may have a smaller effect on wood breakdown in streams surrounded by long-lived coniferous species. In Chapter 4, I quantified patterns of stream channel and riparian zone attributes for 72 streams equally distributed among forests or grasslands, agriculture, and urban land use practices on from eight major North American regions. I also related these patterns to stream NO₃⁻ uptake determined from ¹⁵NO₃⁻ tracer releases. Agricultural and urban streams had a simplified channel structure (low width-to-depth ratio, low variation in stream depth, and high stream banks) relative to forest or grassland streams. Agricultural and urban streams also had a significantly smaller median sediment diameter (D₅₀) and fraction of benthic sediments composed by silt than in forest and grassland streams. Overstory canopy cover over the channel and in the riparian zone was lowest for agricultural streams but did not significantly differ between forest or grassland streams and urban streams. A multiple regression model showed that stream NO₃⁻ uptake decreased with increasing canopy cover, but also increased with abundance of silt in benthic sediments. This suggested NO₃⁻ uptake was strongly influenced by in-stream primary production and extent of anoxic environments (conducive for denitrification). A multiple regression model for fractional NO₃⁻ uptake by denitrification further supported the concept that extent of anoxic environments influenced overall NO₃⁻ uptake in streams. Through these studies, I demonstrated that attributes of riparian zone structure and vegetation composition can strongly influence NO₃⁻ uptake and transformation in stream ecosystems by controlling organic matter dynamics. I also have shown that riparian zone attributes vary significantly among three different land use types (forest or grassland, agriculture, and urban). Similarly, pathways of NO₃⁻ uptake and effects of NO₃⁻ on wood breakdown did or were expected to differ among different land use types / riparian zone characteristics. However, other factors besides riparian attributes, particularly level of nutrient loading, alteration of stream channel physical structure, and basin position of the stream, must be considered in concert when evaluating effects of land use on riparian zone and stream ecosystem structure and function. Close

• 1058. [Article] All in a DNA's work : conservation genetics and monitoring of the New Zealand endemic Maui's and Hector's dolphins

  The critically endangered Maui's dolphin (Cephalorhynchus hectori maui) and the endangered Hector's dolphin (C. h. hectori) are endemic to the coastal waters of New Zealand, where their primary threat ...

  Citation × Citation Citation Abstract Copy Title: All in a DNA's work : conservation genetics and monitoring of the New Zealand endemic Maui's and Hector's dolphins Author: Hamner, Rebecca Marie The critically endangered Maui's dolphin (Cephalorhynchus hectori maui) and the endangered Hector's dolphin (C. h. hectori) are endemic to the coastal waters of New Zealand, where their primary threat is fisheries-related mortality. The Maui's dolphin is among the most critically endangered cetaceans in the world, with its remnant population primarily concentrated in approximately 140 km along the central west coast of New Zealand's North Island. Its closely related sister subspecies, the Hector's dolphin, is more abundant and offers a useful comparison for studying the Maui's dolphin. My work used genetic tools to examine demographic and genetic parameters relevant for conservation considerations regarding Maui's and Hector's dolphins, as well as to build upon past genetic baselines for the purpose of long-term genetic monitoring of these subspecies. Three genetic datasets formed the basis for most analyses: (1) Maui's 01-07, including 54 Maui's dolphin individuals sampled between 2001 and 2007 (n = 70 biopsies, 12 beachcast); (2) Maui's 10-11, including 40 Maui's dolphin individuals sampled in 2010 and 2011 (n = 69 biopsies, 1 beachcast); and (3) Hector's CB11-12, including 148 Hector's dolphin individuals sampled in Cloudy Bay in 2011 and 2012 (n = 263 biopsies). Microsatellite genotypes were used to identify individuals for a genotype recapture abundance estimate of individuals age 1⁺ (N₁₊) and for the estimation of effective population size (N[subscript e]). Both populations exhibited a high N[subscript e] relative to N₁₊, consistent with expectations given their life history characteristics and the limited data available for other dolphin species. The abundance of Maui's dolphins was confirmed to be very low, Maui's 10-11 N₁₊ = 55 (95% CL = 48 - 69), and as expected, it had much lower linkage disequilibrium N[subscript e] (61, 95% CL = 29 - 338) than Hector's CB11-12 (N[subscript e] = 207, 95% CL = 127 - 447; N₁₊ = 272, 95% CL = 236 - 323). The slightly higher Ne/N₁₊ ratio of the Maui's dolphin compared to the Hector's dolphin is consistent with a recent decline in the Maui's dolphin. Although the point estimates of both N[subscript e] and N₁₊ decreased between the two Maui's dolphin datasets (Maui's 01-07: N[subscript e] = 74, 95% CL = 37 - 318; N₁₊ = 69, 95% CL = 38 - 125), the confidence intervals widely overlapped. Maui's 10-11 had significantly fewer alleles (average 4 alleles/locus) and lower heterozygosity (H₀ = 0.316, H[subscript e] = 0.319) than Hector's CB11-12 (average 7 alleles/locus, H₀ = 0.500, H[subscript e] = 0.495; all P <0.001). Interestingly, one microsatellite locus (PPHO104) had anomalously high diversity (31 to 63 alleles) in both Hector's and Maui's dolphins and appears to be influenced by diversifying selection. The observed and expected heterozygosity, internal relatedness, and F[subscript IS] of Maui's dolphins all showed patterns consistent with a decline of the subspecies, although none differed significantly over the short time interval between the two datasets collected in 2001-07 and 2010-11. The lack of significant decline in any of the parameters analyzed for Maui's dolphins is not surprising given the low power to detect a low to moderate decline over the short interval (<1 generation) between the two sampling periods. Compared to minimum viable effective population sizes proposed to guide management decisions, the Maui's dolphin has declined below the recommended threshold of N[subscript e] = 50, recently increased to N[subscript e] ≥100, thought to be necessary to avoid inbreeding depression in the short term (5 generations, ~65.2 years for Maui's and Hector's dolphins). Additionally, both the Maui's dolphin and Cloudy Bay Hector's dolphin populations are below the recommended threshold of N[subscript e] = 500, recently increased to N[subscript e] ≥1000, thought to be necessary to preserve long-term evolutionary potential. This is less of a concern for the Cloudy Bay Hector's population, which is thought to maintain gene flow with neighboring populations. However, for the small, isolated Maui's dolphin population, inbreeding depression is likely to be an increasing concern. Furthermore, each Maui's dolphin individual holds a disproportionate amount of the total genetic variation of the subspecies and would represent a disproportionately large demographic and genetic loss if it died before realizing its reproductive potential in the population. There is, however, potential for genetic restoration by interbreeding with Hector's dolphins, as genetic monitoring of Maui's dolphins revealed the first contemporary dispersal of four (two living females, one dead female, one dead male) Hector's dolphins into the Maui's dolphin distribution. Two Hector's dolphins (one dead female neonate, one living male) were also sampled along the North Island's southwest coast, outside the presumed range of either subspecies. Together, these records provide evidence of long-distance dispersal by Hector's dolphins (≥400 km) and the possibility of an unsampled Hector's dolphin population along the southwest coast of the North Island or northern South Island. These results highlight the value of genetic monitoring for subspecies lacking distinctive physical appearances, as such discoveries are not detected by other means but have important conservation implications. Although the Maui's dolphin is critically endangered, it is not necessarily doomed to extinction. The subspecies appears to be maintaining an equal sex ratio and connectivity within its remnant range, and the highly diverse locus PPHO104 could potentially offer clues to an inbreeding avoidance mechanism. If Maui's dolphins interbreed with the recently identified Hector's dolphin immigrants, it could provide genetic restoration, enhancing chances of long-term survival of the Maui's dolphin. Continued genetic monitoring and examination of recovered carcasses for phenotypic signs of inbreeding are important for gauging genetic threats to the survival of Maui's dolphins, as well as determining if any Hector's dolphin populations appear to be declining toward the critically endangered state of the Maui's dolphin. The results of this work contributed to the decision by the New Zealand Department of Conservation and Ministry for Primary Industries to conduct an updated risk assessment for Maui's dolphins and accelerate the review of the Maui's Dolphin Threat Management Plan. Consequently, commercial and recreational set net restrictions were extended slightly to reduce entanglement risk to Maui's dolphins utilizing the southern part of their distribution, as well as any Hector's dolphins that disperse north into that area. The results related to the population of Hector's dolphins in Cloudy Bay provide information that will contribute to the upcoming review of the Hector's dolphin component of the Threat Management Plan. Title: All in a DNA's work : conservation genetics and monitoring of the New Zealand endemic Maui's and Hector's dolphins Author: Hamner, Rebecca Marie The critically endangered Maui's dolphin (Cephalorhynchus hectori maui) and the endangered Hector's dolphin (C. h. hectori) are endemic to the coastal waters of New Zealand, where their primary threat is fisheries-related mortality. The Maui's dolphin is among the most critically endangered cetaceans in the world, with its remnant population primarily concentrated in approximately 140 km along the central west coast of New Zealand's North Island. Its closely related sister subspecies, the Hector's dolphin, is more abundant and offers a useful comparison for studying the Maui's dolphin. My work used genetic tools to examine demographic and genetic parameters relevant for conservation considerations regarding Maui's and Hector's dolphins, as well as to build upon past genetic baselines for the purpose of long-term genetic monitoring of these subspecies. Three genetic datasets formed the basis for most analyses: (1) Maui's 01-07, including 54 Maui's dolphin individuals sampled between 2001 and 2007 (n = 70 biopsies, 12 beachcast); (2) Maui's 10-11, including 40 Maui's dolphin individuals sampled in 2010 and 2011 (n = 69 biopsies, 1 beachcast); and (3) Hector's CB11-12, including 148 Hector's dolphin individuals sampled in Cloudy Bay in 2011 and 2012 (n = 263 biopsies). Microsatellite genotypes were used to identify individuals for a genotype recapture abundance estimate of individuals age 1⁺ (N₁₊) and for the estimation of effective population size (N[subscript e]). Both populations exhibited a high N[subscript e] relative to N₁₊, consistent with expectations given their life history characteristics and the limited data available for other dolphin species. The abundance of Maui's dolphins was confirmed to be very low, Maui's 10-11 N₁₊ = 55 (95% CL = 48 - 69), and as expected, it had much lower linkage disequilibrium N[subscript e] (61, 95% CL = 29 - 338) than Hector's CB11-12 (N[subscript e] = 207, 95% CL = 127 - 447; N₁₊ = 272, 95% CL = 236 - 323). The slightly higher Ne/N₁₊ ratio of the Maui's dolphin compared to the Hector's dolphin is consistent with a recent decline in the Maui's dolphin. Although the point estimates of both N[subscript e] and N₁₊ decreased between the two Maui's dolphin datasets (Maui's 01-07: N[subscript e] = 74, 95% CL = 37 - 318; N₁₊ = 69, 95% CL = 38 - 125), the confidence intervals widely overlapped. Maui's 10-11 had significantly fewer alleles (average 4 alleles/locus) and lower heterozygosity (H₀ = 0.316, H[subscript e] = 0.319) than Hector's CB11-12 (average 7 alleles/locus, H₀ = 0.500, H[subscript e] = 0.495; all P <0.001). Interestingly, one microsatellite locus (PPHO104) had anomalously high diversity (31 to 63 alleles) in both Hector's and Maui's dolphins and appears to be influenced by diversifying selection. The observed and expected heterozygosity, internal relatedness, and F[subscript IS] of Maui's dolphins all showed patterns consistent with a decline of the subspecies, although none differed significantly over the short time interval between the two datasets collected in 2001-07 and 2010-11. The lack of significant decline in any of the parameters analyzed for Maui's dolphins is not surprising given the low power to detect a low to moderate decline over the short interval (<1 generation) between the two sampling periods. Compared to minimum viable effective population sizes proposed to guide management decisions, the Maui's dolphin has declined below the recommended threshold of N[subscript e] = 50, recently increased to N[subscript e] ≥100, thought to be necessary to avoid inbreeding depression in the short term (5 generations, ~65.2 years for Maui's and Hector's dolphins). Additionally, both the Maui's dolphin and Cloudy Bay Hector's dolphin populations are below the recommended threshold of N[subscript e] = 500, recently increased to N[subscript e] ≥1000, thought to be necessary to preserve long-term evolutionary potential. This is less of a concern for the Cloudy Bay Hector's population, which is thought to maintain gene flow with neighboring populations. However, for the small, isolated Maui's dolphin population, inbreeding depression is likely to be an increasing concern. Furthermore, each Maui's dolphin individual holds a disproportionate amount of the total genetic variation of the subspecies and would represent a disproportionately large demographic and genetic loss if it died before realizing its reproductive potential in the population. There is, however, potential for genetic restoration by interbreeding with Hector's dolphins, as genetic monitoring of Maui's dolphins revealed the first contemporary dispersal of four (two living females, one dead female, one dead male) Hector's dolphins into the Maui's dolphin distribution. Two Hector's dolphins (one dead female neonate, one living male) were also sampled along the North Island's southwest coast, outside the presumed range of either subspecies. Together, these records provide evidence of long-distance dispersal by Hector's dolphins (≥400 km) and the possibility of an unsampled Hector's dolphin population along the southwest coast of the North Island or northern South Island. These results highlight the value of genetic monitoring for subspecies lacking distinctive physical appearances, as such discoveries are not detected by other means but have important conservation implications. Although the Maui's dolphin is critically endangered, it is not necessarily doomed to extinction. The subspecies appears to be maintaining an equal sex ratio and connectivity within its remnant range, and the highly diverse locus PPHO104 could potentially offer clues to an inbreeding avoidance mechanism. If Maui's dolphins interbreed with the recently identified Hector's dolphin immigrants, it could provide genetic restoration, enhancing chances of long-term survival of the Maui's dolphin. Continued genetic monitoring and examination of recovered carcasses for phenotypic signs of inbreeding are important for gauging genetic threats to the survival of Maui's dolphins, as well as determining if any Hector's dolphin populations appear to be declining toward the critically endangered state of the Maui's dolphin. The results of this work contributed to the decision by the New Zealand Department of Conservation and Ministry for Primary Industries to conduct an updated risk assessment for Maui's dolphins and accelerate the review of the Maui's Dolphin Threat Management Plan. Consequently, commercial and recreational set net restrictions were extended slightly to reduce entanglement risk to Maui's dolphins utilizing the southern part of their distribution, as well as any Hector's dolphins that disperse north into that area. The results related to the population of Hector's dolphins in Cloudy Bay provide information that will contribute to the upcoming review of the Hector's dolphin component of the Threat Management Plan. Close

• 1059. [Article] Lithofacies, stratiography, and geology of the middle eocene type cowlitz formation and associated volcanic and sedimentary units, Eastern Willapa Hills, southwest Washington

  Stratigraphic measurement of the 1,238-rn thick Cowlitz Formation in the southwest Washington type section along Olequa and Stillwater creeks reveals complex facies succession of wave- to tide-dominated ...

  Citation × Citation Citation Abstract Copy Title: Lithofacies, stratiography, and geology of the middle eocene type cowlitz formation and associated volcanic and sedimentary units, Eastern Willapa Hills, southwest Washington Author: Payne, Charles William Stratigraphic measurement of the 1,238-rn thick Cowlitz Formation in the southwest Washington type section along Olequa and Stillwater creeks reveals complex facies succession of wave- to tide-dominated deltaic sequences. The underlying, 625-rn thick upper member of the McIntosh Formation (as mapped by Wells, 1981) is composed of two units: a basal 130-m thick prograding offshore to marginal marine coal-bearing, lithic-arkosic sandstone facies succession (upper McIntosh sandstone) and a thicker, 500- m thick bathyal foraminilera-rich siltstone facies that is, in part, in fault contact with the overlying Cowlitz Formation. The lower member of the McIntosh Formation is 375 rn thick in Stillwater Creek, with the base not exposed in the study area. The Cowlitz Formation is subdivided into five informal units. The basal 558-m thick unit consists of (1) multiple prograding, wave-dominated shoreface hummocky stratified lithic arkosic sandstone successions (unit 1A) that comprise several thickeningand coarsening-upwards parasequences and (2) coal-bearing delta plain facies associations (unit 1B). The 205-m thick second unit is composed of five coarsening-up stormdominated, hummocky-bedded shelf to delta-front arkosic sandstone parasequences. Fining-upwards subtidal, intertidal, and supratidal facies associations constitute the 170-m thick third member. Tidal-estuarine facies in unit 3 include: (1) nested subtidal micaceous lithic-arkosic sandstone channels, (2) cross-bedded subtidal sandstone ridges with brackish water mollusc hash, (3) sandy and muddy accretionary-bank, and (4) coalbearing marsh-swamp deposits. Thin basaltic volcaniclastic interbeds occur within units one, two, and three. A 155-m thick fourth unit, consists of wave-dominated, arkosic sandstone, shoreface to offshore bioturbated mudstone facies successions; these successions form 10 coarsening-upward parasequences that overall define a retrogradational parasequence set. Thick, transgressive, bioturbated outer shelfal molluscbearing sandy siltstone and glauconitic mudstone in the Big Bend type locality along the Cowlitz River can be correlated to this unit in the type section in Olequa Creek. The uppermost unit consists of 150 m of deeper marine laminated siltstone, subordinate finegrained and thin-bedded turbidites, thick amalgamated submarine-channel sandstone and chaotic mudstone conglomerate, and slump-folded and soft-sediment deformed laminated siltstone intervals. Petrography of lithic-arkosic micaceous sandstones of the McIntosh and Cowlitz formations indicates there was a distant eastern, extrabasinal acid plutonic-metamorphic source for the arkosic component of these sandstones. The predominant quartz, feldspar, and mica constituents of Cowlitz Formation were transported from a distant dissected arc (such as the Idaho Batholith and metamorphic core complexes to the east) through an ancestral Columbia River drainage system. A second, local and active intrabasinal basaltic source (Grays River volcanics) supplied basaltic scoria and lava rock fragments to form volcaniclastic interbeds. Some volcaniclastics were reworked and mixed with the arkosic extrabasinal sediments in the shallow marine and nonmarine environments of units 2 and 3 of the Cowlitz Formation. Explosive calc-alkaline volcanic activity (Northcraft Formation or Goble Volcanics) is also evident in the silicic and pumiceous tuff beds interbedded with coal marsh/swamp strata in units 1 and 3. Paleocurrent directions indicated by crossbedded tidal strata of unit 3 are to the north-northwest and south-southeast as a resultof shore parallel transport and deflection around a proposed growing volcanic edifice of Grays River volcanics to the south and southwest. A very high sedimentation rate of 1.6 m/1,000 years was calculated for the upper part of the Cowlitz Formation (units 3 to 5) using thickness measurement and 39Ar/40Ar age dates from the Cowlitz Formation (i. e., from tuff in unit 3) and the easternmost locality in the unconformably overlying Grays River volcanics at Bebe Mountain. The large influx of sediment deposited over a relatively short time period was accommodated by this rapidly subsiding forearc basin. In this study area, subaerial flows of the Grays River volcanics locally unconformably overlie the Cowlitz Formation. A 38.9± 0.1 Ma 39Ar/40Ar age date from a tuff bed in unit 3 of the underlying Cowlitz Formation (Irving et al., 1996) and three 39Ar/40Ar age dates of 38.640.40 (south Abernathy Mtn.), 37.44±0.45 (west Bebe Mtn.), and 36.85 ± 0.46 Ma (east Bebe Mtn.) from the overlying Grays River volcanics bracket the timing of this regional unconformity. Additionally, field mapping (this study) and drill hole data supplied by Weyerhaeuser Company (Pauli, written communications) show there is a valley-fill unit at the base of the Grays River volcanics exposed on the surface and in the subsurface, respectively. These data confirm the volcanic- and tectonically-controlled unconformable relationship of the Cowlitz Formation to the overlying the Grays River volcanics. The Cowlitz Formation is in disconformable contact (a tectonically forced sequence boundary) with an overlying second, younger lowstand valley-fill unit (Toutle Formation unit A) recognized in this study along Olequa Creek. The 265-m thick, newly discovered, Toutle Formation in this area is subdivided into three informal units: (1) a basal incised, non-marine valley-fill sequence (unit A), (2) a marginal marine (estuarine or nearshore) sequence (unit B), and (3) an upper fluvial sequence (unit C). A 31.9 ± 0.4Ma 39Ar/40Ar date from a homblende-bearing pumiceous lapilli tuff in unit A indicates that the Toutle Formation is a time equivalent of the upper fluvial member of the Oligocene type Toutle Formation and the middle part of the Lincoln Creek Formation far from the center of the forearc basin to the west. Unit C of the Toutle Formation grades upward into the overlying deeper marine tuffaceous siltstone of the Lincoln Creek Formation. Deformation in this area resulted from two plate tectonic events: (1) latest middle Eocene highly oblique subduction that resulted in short-lived, normal faulting and intrusion of Grays River basalt dikes along small faults and (2) rapid post mid-Miocene oblique subduction that formed northeast-trending dextral and northwest-trending sinistral conjugate faults and broad regional compressional folding throughout southwest Washington. The broad open Arkansas anticline that trends northwest-southeast between Bebe and Abernathy mountains is an eastward extension of the Willapa Hills basement uplift to the west and is extensively cut by northeast and northwest trending faults (Plate I). This compressional event deformed both the Cowlitz Formation and the overlying Grays River volcanics. A similar structural pattern recognized in regional field mapping by Wells (1981) indicates this folding event also deformed mid-Miocene volcanic and sedimentary unit (i.e., Astoria Formation and Columbia River basalts). Reservoir quality of the Cowlitz and upper McIntosh formations micaceous lithicarkosic sandstones is good. These sandstones are clean, highly friable and porous except where carbonate and smectite clay rim cements formed in the lithic arkose. Unit 5 siltstone could act as a cap rock in the subsurface and the 1- to 10-rn thick coals could be a source for natural gas. The McIntosh marine siltstone is another possible source for gas and the micaceous arkosic sandstone in the upper McIntosh is a potential reservoir. Stratigraphic pinchouts and normal and wrench fault traps are similar to the Mist gas field of northwest Oregon. Title: Lithofacies, stratiography, and geology of the middle eocene type cowlitz formation and associated volcanic and sedimentary units, Eastern Willapa Hills, southwest Washington Author: Payne, Charles William Stratigraphic measurement of the 1,238-rn thick Cowlitz Formation in the southwest Washington type section along Olequa and Stillwater creeks reveals complex facies succession of wave- to tide-dominated deltaic sequences. The underlying, 625-rn thick upper member of the McIntosh Formation (as mapped by Wells, 1981) is composed of two units: a basal 130-m thick prograding offshore to marginal marine coal-bearing, lithic-arkosic sandstone facies succession (upper McIntosh sandstone) and a thicker, 500- m thick bathyal foraminilera-rich siltstone facies that is, in part, in fault contact with the overlying Cowlitz Formation. The lower member of the McIntosh Formation is 375 rn thick in Stillwater Creek, with the base not exposed in the study area. The Cowlitz Formation is subdivided into five informal units. The basal 558-m thick unit consists of (1) multiple prograding, wave-dominated shoreface hummocky stratified lithic arkosic sandstone successions (unit 1A) that comprise several thickeningand coarsening-upwards parasequences and (2) coal-bearing delta plain facies associations (unit 1B). The 205-m thick second unit is composed of five coarsening-up stormdominated, hummocky-bedded shelf to delta-front arkosic sandstone parasequences. Fining-upwards subtidal, intertidal, and supratidal facies associations constitute the 170-m thick third member. Tidal-estuarine facies in unit 3 include: (1) nested subtidal micaceous lithic-arkosic sandstone channels, (2) cross-bedded subtidal sandstone ridges with brackish water mollusc hash, (3) sandy and muddy accretionary-bank, and (4) coalbearing marsh-swamp deposits. Thin basaltic volcaniclastic interbeds occur within units one, two, and three. A 155-m thick fourth unit, consists of wave-dominated, arkosic sandstone, shoreface to offshore bioturbated mudstone facies successions; these successions form 10 coarsening-upward parasequences that overall define a retrogradational parasequence set. Thick, transgressive, bioturbated outer shelfal molluscbearing sandy siltstone and glauconitic mudstone in the Big Bend type locality along the Cowlitz River can be correlated to this unit in the type section in Olequa Creek. The uppermost unit consists of 150 m of deeper marine laminated siltstone, subordinate finegrained and thin-bedded turbidites, thick amalgamated submarine-channel sandstone and chaotic mudstone conglomerate, and slump-folded and soft-sediment deformed laminated siltstone intervals. Petrography of lithic-arkosic micaceous sandstones of the McIntosh and Cowlitz formations indicates there was a distant eastern, extrabasinal acid plutonic-metamorphic source for the arkosic component of these sandstones. The predominant quartz, feldspar, and mica constituents of Cowlitz Formation were transported from a distant dissected arc (such as the Idaho Batholith and metamorphic core complexes to the east) through an ancestral Columbia River drainage system. A second, local and active intrabasinal basaltic source (Grays River volcanics) supplied basaltic scoria and lava rock fragments to form volcaniclastic interbeds. Some volcaniclastics were reworked and mixed with the arkosic extrabasinal sediments in the shallow marine and nonmarine environments of units 2 and 3 of the Cowlitz Formation. Explosive calc-alkaline volcanic activity (Northcraft Formation or Goble Volcanics) is also evident in the silicic and pumiceous tuff beds interbedded with coal marsh/swamp strata in units 1 and 3. Paleocurrent directions indicated by crossbedded tidal strata of unit 3 are to the north-northwest and south-southeast as a resultof shore parallel transport and deflection around a proposed growing volcanic edifice of Grays River volcanics to the south and southwest. A very high sedimentation rate of 1.6 m/1,000 years was calculated for the upper part of the Cowlitz Formation (units 3 to 5) using thickness measurement and 39Ar/40Ar age dates from the Cowlitz Formation (i. e., from tuff in unit 3) and the easternmost locality in the unconformably overlying Grays River volcanics at Bebe Mountain. The large influx of sediment deposited over a relatively short time period was accommodated by this rapidly subsiding forearc basin. In this study area, subaerial flows of the Grays River volcanics locally unconformably overlie the Cowlitz Formation. A 38.9± 0.1 Ma 39Ar/40Ar age date from a tuff bed in unit 3 of the underlying Cowlitz Formation (Irving et al., 1996) and three 39Ar/40Ar age dates of 38.640.40 (south Abernathy Mtn.), 37.44±0.45 (west Bebe Mtn.), and 36.85 ± 0.46 Ma (east Bebe Mtn.) from the overlying Grays River volcanics bracket the timing of this regional unconformity. Additionally, field mapping (this study) and drill hole data supplied by Weyerhaeuser Company (Pauli, written communications) show there is a valley-fill unit at the base of the Grays River volcanics exposed on the surface and in the subsurface, respectively. These data confirm the volcanic- and tectonically-controlled unconformable relationship of the Cowlitz Formation to the overlying the Grays River volcanics. The Cowlitz Formation is in disconformable contact (a tectonically forced sequence boundary) with an overlying second, younger lowstand valley-fill unit (Toutle Formation unit A) recognized in this study along Olequa Creek. The 265-m thick, newly discovered, Toutle Formation in this area is subdivided into three informal units: (1) a basal incised, non-marine valley-fill sequence (unit A), (2) a marginal marine (estuarine or nearshore) sequence (unit B), and (3) an upper fluvial sequence (unit C). A 31.9 ± 0.4Ma 39Ar/40Ar date from a homblende-bearing pumiceous lapilli tuff in unit A indicates that the Toutle Formation is a time equivalent of the upper fluvial member of the Oligocene type Toutle Formation and the middle part of the Lincoln Creek Formation far from the center of the forearc basin to the west. Unit C of the Toutle Formation grades upward into the overlying deeper marine tuffaceous siltstone of the Lincoln Creek Formation. Deformation in this area resulted from two plate tectonic events: (1) latest middle Eocene highly oblique subduction that resulted in short-lived, normal faulting and intrusion of Grays River basalt dikes along small faults and (2) rapid post mid-Miocene oblique subduction that formed northeast-trending dextral and northwest-trending sinistral conjugate faults and broad regional compressional folding throughout southwest Washington. The broad open Arkansas anticline that trends northwest-southeast between Bebe and Abernathy mountains is an eastward extension of the Willapa Hills basement uplift to the west and is extensively cut by northeast and northwest trending faults (Plate I). This compressional event deformed both the Cowlitz Formation and the overlying Grays River volcanics. A similar structural pattern recognized in regional field mapping by Wells (1981) indicates this folding event also deformed mid-Miocene volcanic and sedimentary unit (i.e., Astoria Formation and Columbia River basalts). Reservoir quality of the Cowlitz and upper McIntosh formations micaceous lithicarkosic sandstones is good. These sandstones are clean, highly friable and porous except where carbonate and smectite clay rim cements formed in the lithic arkose. Unit 5 siltstone could act as a cap rock in the subsurface and the 1- to 10-rn thick coals could be a source for natural gas. The McIntosh marine siltstone is another possible source for gas and the micaceous arkosic sandstone in the upper McIntosh is a potential reservoir. Stratigraphic pinchouts and normal and wrench fault traps are similar to the Mist gas field of northwest Oregon. Close

• 1060. [Article] Distribution and movements of Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin

  Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin and other large river systems in western Alaska have declined dramatically since the late 1990s. This continuing trend has ...

  Citation × Citation Citation Abstract Copy Title: Distribution and movements of Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin Author: Eiler, John H. Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin and other large river systems in western Alaska have declined dramatically since the late 1990s. This continuing trend has raised concerns over the future status of the returns, and severely impacted commercial and subsistence fisheries within the drainage. Management is further complicated by the mixed-stock composition of the run, the presence of other temporally similar salmon species, and the need to equitably allocate harvests between the numerous fisheries and user groups scattered throughout the basin. Detailed information is needed on Chinook salmon run characteristics to better understand and manage the returns, and facilitate conservation efforts. However, this goal is exacerbated by the massive size and remote nature of the basin, the large number of highly mobile fish, and the compressed timing of the run. To address these challenges, radio telemetry was used to determine the stock composition and spawning distribution of the returns, and the migratory characteristics of the fish. The migratory patterns exhibited by returning salmon provide a number of insights into the status of the run. Since the Yukon River is essentially free-flowing (i.e., not regulated), this study also presented an opportunity to document the distribution and upriver movements of large returns of wild Chinook salmon under natural conditions. During 2002-2004, returning adult Chinook salmon were captured in the lower Yukon River (approximately 300 km upriver from the river mouth), tagged with radio transmitters, and tracked upriver using remote tracking stations located on important migratory routes and major spawning tributaries. Aerial tracking surveys were used to locate fish in spawning areas and between stations. The fish responded well to the capture and handling procedures, with most (2,790, 98%) resuming upriver movements. Although the fish initially displayed a negative tagging response, with slower migration rates observed immediately after release, the duration of this response was relatively short (several days) and less severe as the fish moved upriver. Independent measures indicated that the swimming speeds and timing of the fish upriver from the tagging area were comparable to untagged fish, suggesting that the tagging methods used were relatively benign. Fish returned to spawning areas throughout the basin, ranging from several hundred to over 3,000 km from the tagging area. Distribution patterns were similar across years, suggesting that the principal components of the run were identified. Most spawning fish were clustered in a number of key tributaries, with smaller numbers of fish located in other spatially isolated areas. The fish typically returned to clear water tributaries that were relatively entrenched, had moderate gradients, and were associated with upland areas. Fish were largely absent in lowland reaches characterized by meandering, low gradient, highly alluvial channels often associated with main river floodplains. There was suggestive evidence of mainstem spawning in reaches of the Upper Yukon. The status of fish remaining in other mainstem areas was less certain, and may represent local spawning activity or fish that died while in-transit to upriver areas. Although Chinook salmon spawned throughout the basin, the run was dominated by two regional components (Tanana and Upper Yukon), which annually comprised over 70% of the return. Substantially fewer fish returned to other areas ranging from 2-9% of the return, although the collective contribution of these stocks was appreciable. Most regional returns consisted of several principal stocks and a number of small, spatially isolated populations. Regional and stock composition estimates were similar across years even though differences in run abundance were reported, suggesting that these abundance differences were not related to regional or stock-specific differences. Run timing was relatively compressed compared to rivers in the southern portion of the range, with most stocks passing through the lower river over a 6-week period, ranging from 16 to 38 d. Run timing was generally earlier for stocks traveling farther upriver, although exceptions were noted. Lower basin stocks were primarily later run fish. Pronounced differences were observed in the migration rates (km/d) exhibited by regional stocks. Substantially slower swimming speeds were observed for fish returning to terminal tributaries in the lower basin ranging from 28-40 km/d compared to 52-62 km/d for upper basin stocks. The migratory patterns (migration rates in sequential reaches) of the fish also showed distinct regional differences. Average migration rates through the lower river were remarkably similar for the different stocks, ranging from 57-62 km/d, with most stocks exhibiting a general decline as the fish moved farther upriver. Tanana River stocks displayed a pronounced reduction in swimming speed after leaving the Yukon River main stem, with migration rates declining to 24 km/d on average as the fish approached their terminal tributaries. Conversely, upper basin stocks exhibited a relatively gradual (but variable) overall decline in migration rate even though these fish were traveling substantially greater distances upriver. Average migration rates for upper basin stocks ranged from 43-61 km/d as the fish approached their terminal tributaries. There was substantial variation in the migratory patterns exhibited by individual fish, although these patterns tended to be similar to the patterns exhibited by the regional stocks, particularly as the fish moved farther upriver from the tagging area. The dominant source of variation among fish reflected the average migration rate, with individual fish traveling slower in the lower basin exhibiting consistently slower migration rates as they moved upriver compared to their faster moving counterparts. This migratory pattern was consistent across stocks, and on average explained 74% of the within-stock variation in migration rate represented by the multivariate data. The second source of variation in migration rate reflected a shift in the relative swimming speeds of the individual fish as they progressed upriver. Although movement rates declined for nearly all of the fish during the migration, differences were observed in the pattern of the decline. Fish with faster migration rates in the lower river exhibited a pronounced decline in swimming speed as they moved upriver, whereas fish moving slower in the lower river displayed a more gradual decline in migration rate. On average, this migratory pattern explained 22% of the within-stock variation in migration rate represented by the multivariate data. Most fish (98%) exhibited continuous upriver movements and strong fidelity to the rivers they entered. However a small number of fish (n = 66) deviated from this pattern. Some of these individuals initially passed their final destination and continued upriver for varying distances before reversing direction, swimming back downstream, and entering their terminal tributary. Although most of these excursions were relatively short (< 30 km), there were several instances where fish traveled hundreds of kilometers out of their way. Thirty-four fish tracked to terminal tributaries subsequently left these rivers, and traveled to other terminal tributaries within the basin (n = 31) or were harvested in upriver fisheries (n = 3). Although most of these incidents involved nearby tributaries, major diversions were also observed, with several fish traveling over 300 km to natal rivers after leaving the initial tributary. Chinook salmon returns to the Yukon River typically consisted of a series of distinct and sizable increases in the number fish entering the river over the course of the run, commonly referred to as pulses. A large number of fish (n = 251) were radio tagged over a 4-day period during a pulse in 2003 to provide information on the progression of the pulse as it moved upriver. The time taken by the pulse to move past subsequent upriver locations increased as the fish moved farther upriver from the tagging area, with the fish passing sites located 580 and 800 km upriver over a span of 14 and 21 d, respectively. Although not surprising considering the extensive variation in migration rates observed among individual fish, this finding does suggest that these pulses do not represent cohesive aggregates of fish moving upriver. Unlike the well established methods used to estimate other life history characteristics, the development of quantitative methods for analyzing and modeling fish movements has lagged noticeably behind, due in part to the complexity associated with movement data and (prior to the advent of telemetry) the difficulty of collecting this type of information on free-ranging individuals. Two fundamentally different analytical approaches, hierarchical linear regression models and multivariate ordination, were used during this study to evaluate factors thought to influence the upriver movements of the fish. In spite of the inherent differences, both methods provided strikingly similar results, indicating that the study findings were not dependent on the approach used, and suggesting that the results were plausible based on the information available and the weight of evidence. Both analytical methods had advantages, and provided complementary information. With hierarchical linear models, it was possible to simultaneously evaluate a wide range of explanatory variables (in our case, both biological and environmental), which provided standardized comparisons and simplified the interpretation of the results. Since both fixed and random effects were incorporated in the models, it was possible to account for sources of variation when insufficient information was available to identify the underlining factors – an important consideration since few field studies provide comprehensive data. With multivariate ordination, separate analyzes were needed to examine the relationships between the migration rates and the biotic and physical variables. In addition to being cumbersome, this limitation made it more difficult to compare the relative influence of the different factors and interactions between factors. However, ordination was very useful as an exploratory tool. Although compartmentalized by stock, across fish comparisons were simple and relatively straightforward. Because the explanatory variables were evaluated separately in relation to the ordination score assigned to the fish, it was possible to examine and compare highly correlated variables. Ordination was also able to identify overall patterns within the data and assess the relative importance. While this can be accomplished within the framework of linear regression using mixture models to determine whether multiple distributions exist within the data, the process is much simpler with ordination. The migratory patterns of the fish were influenced by a wide range of factors, with evidentiary support for complex, multi-faceted relationships. Physical features of the basin demonstrated stronger explanatory power, accounting for over 70% of the observed variation in migration rate compared to 18% for the biological characteristics of the fish. Parameter estimates associated with the steepness of the migratory route and remaining distance the fish had to travel to reach their natal rivers were most strongly correlated with migration rate, with consistent relationships observed across stocks. Migration rates were also noticeably slower in extensively braided reaches of the basin. The weaker relationships between migration rate and biotic factors may reflect stabilizing selection on long-distance migrants. Smaller fish exhibited minimally faster swimming speeds on average than larger individuals. This relationship was stronger in highly braided reaches. Run timing was positively related to migration rate for most stocks. Surprisingly, upper basin stocks traveling farther upriver displayed progressively negative relationships, suggesting that late-run fish were moving slower. Ancillary information suggests that this decline may relate to deteriorating fish condition later in the season. Title: Distribution and movements of Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin Author: Eiler, John H. Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin and other large river systems in western Alaska have declined dramatically since the late 1990s. This continuing trend has raised concerns over the future status of the returns, and severely impacted commercial and subsistence fisheries within the drainage. Management is further complicated by the mixed-stock composition of the run, the presence of other temporally similar salmon species, and the need to equitably allocate harvests between the numerous fisheries and user groups scattered throughout the basin. Detailed information is needed on Chinook salmon run characteristics to better understand and manage the returns, and facilitate conservation efforts. However, this goal is exacerbated by the massive size and remote nature of the basin, the large number of highly mobile fish, and the compressed timing of the run. To address these challenges, radio telemetry was used to determine the stock composition and spawning distribution of the returns, and the migratory characteristics of the fish. The migratory patterns exhibited by returning salmon provide a number of insights into the status of the run. Since the Yukon River is essentially free-flowing (i.e., not regulated), this study also presented an opportunity to document the distribution and upriver movements of large returns of wild Chinook salmon under natural conditions. During 2002-2004, returning adult Chinook salmon were captured in the lower Yukon River (approximately 300 km upriver from the river mouth), tagged with radio transmitters, and tracked upriver using remote tracking stations located on important migratory routes and major spawning tributaries. Aerial tracking surveys were used to locate fish in spawning areas and between stations. The fish responded well to the capture and handling procedures, with most (2,790, 98%) resuming upriver movements. Although the fish initially displayed a negative tagging response, with slower migration rates observed immediately after release, the duration of this response was relatively short (several days) and less severe as the fish moved upriver. Independent measures indicated that the swimming speeds and timing of the fish upriver from the tagging area were comparable to untagged fish, suggesting that the tagging methods used were relatively benign. Fish returned to spawning areas throughout the basin, ranging from several hundred to over 3,000 km from the tagging area. Distribution patterns were similar across years, suggesting that the principal components of the run were identified. Most spawning fish were clustered in a number of key tributaries, with smaller numbers of fish located in other spatially isolated areas. The fish typically returned to clear water tributaries that were relatively entrenched, had moderate gradients, and were associated with upland areas. Fish were largely absent in lowland reaches characterized by meandering, low gradient, highly alluvial channels often associated with main river floodplains. There was suggestive evidence of mainstem spawning in reaches of the Upper Yukon. The status of fish remaining in other mainstem areas was less certain, and may represent local spawning activity or fish that died while in-transit to upriver areas. Although Chinook salmon spawned throughout the basin, the run was dominated by two regional components (Tanana and Upper Yukon), which annually comprised over 70% of the return. Substantially fewer fish returned to other areas ranging from 2-9% of the return, although the collective contribution of these stocks was appreciable. Most regional returns consisted of several principal stocks and a number of small, spatially isolated populations. Regional and stock composition estimates were similar across years even though differences in run abundance were reported, suggesting that these abundance differences were not related to regional or stock-specific differences. Run timing was relatively compressed compared to rivers in the southern portion of the range, with most stocks passing through the lower river over a 6-week period, ranging from 16 to 38 d. Run timing was generally earlier for stocks traveling farther upriver, although exceptions were noted. Lower basin stocks were primarily later run fish. Pronounced differences were observed in the migration rates (km/d) exhibited by regional stocks. Substantially slower swimming speeds were observed for fish returning to terminal tributaries in the lower basin ranging from 28-40 km/d compared to 52-62 km/d for upper basin stocks. The migratory patterns (migration rates in sequential reaches) of the fish also showed distinct regional differences. Average migration rates through the lower river were remarkably similar for the different stocks, ranging from 57-62 km/d, with most stocks exhibiting a general decline as the fish moved farther upriver. Tanana River stocks displayed a pronounced reduction in swimming speed after leaving the Yukon River main stem, with migration rates declining to 24 km/d on average as the fish approached their terminal tributaries. Conversely, upper basin stocks exhibited a relatively gradual (but variable) overall decline in migration rate even though these fish were traveling substantially greater distances upriver. Average migration rates for upper basin stocks ranged from 43-61 km/d as the fish approached their terminal tributaries. There was substantial variation in the migratory patterns exhibited by individual fish, although these patterns tended to be similar to the patterns exhibited by the regional stocks, particularly as the fish moved farther upriver from the tagging area. The dominant source of variation among fish reflected the average migration rate, with individual fish traveling slower in the lower basin exhibiting consistently slower migration rates as they moved upriver compared to their faster moving counterparts. This migratory pattern was consistent across stocks, and on average explained 74% of the within-stock variation in migration rate represented by the multivariate data. The second source of variation in migration rate reflected a shift in the relative swimming speeds of the individual fish as they progressed upriver. Although movement rates declined for nearly all of the fish during the migration, differences were observed in the pattern of the decline. Fish with faster migration rates in the lower river exhibited a pronounced decline in swimming speed as they moved upriver, whereas fish moving slower in the lower river displayed a more gradual decline in migration rate. On average, this migratory pattern explained 22% of the within-stock variation in migration rate represented by the multivariate data. Most fish (98%) exhibited continuous upriver movements and strong fidelity to the rivers they entered. However a small number of fish (n = 66) deviated from this pattern. Some of these individuals initially passed their final destination and continued upriver for varying distances before reversing direction, swimming back downstream, and entering their terminal tributary. Although most of these excursions were relatively short (< 30 km), there were several instances where fish traveled hundreds of kilometers out of their way. Thirty-four fish tracked to terminal tributaries subsequently left these rivers, and traveled to other terminal tributaries within the basin (n = 31) or were harvested in upriver fisheries (n = 3). Although most of these incidents involved nearby tributaries, major diversions were also observed, with several fish traveling over 300 km to natal rivers after leaving the initial tributary. Chinook salmon returns to the Yukon River typically consisted of a series of distinct and sizable increases in the number fish entering the river over the course of the run, commonly referred to as pulses. A large number of fish (n = 251) were radio tagged over a 4-day period during a pulse in 2003 to provide information on the progression of the pulse as it moved upriver. The time taken by the pulse to move past subsequent upriver locations increased as the fish moved farther upriver from the tagging area, with the fish passing sites located 580 and 800 km upriver over a span of 14 and 21 d, respectively. Although not surprising considering the extensive variation in migration rates observed among individual fish, this finding does suggest that these pulses do not represent cohesive aggregates of fish moving upriver. Unlike the well established methods used to estimate other life history characteristics, the development of quantitative methods for analyzing and modeling fish movements has lagged noticeably behind, due in part to the complexity associated with movement data and (prior to the advent of telemetry) the difficulty of collecting this type of information on free-ranging individuals. Two fundamentally different analytical approaches, hierarchical linear regression models and multivariate ordination, were used during this study to evaluate factors thought to influence the upriver movements of the fish. In spite of the inherent differences, both methods provided strikingly similar results, indicating that the study findings were not dependent on the approach used, and suggesting that the results were plausible based on the information available and the weight of evidence. Both analytical methods had advantages, and provided complementary information. With hierarchical linear models, it was possible to simultaneously evaluate a wide range of explanatory variables (in our case, both biological and environmental), which provided standardized comparisons and simplified the interpretation of the results. Since both fixed and random effects were incorporated in the models, it was possible to account for sources of variation when insufficient information was available to identify the underlining factors – an important consideration since few field studies provide comprehensive data. With multivariate ordination, separate analyzes were needed to examine the relationships between the migration rates and the biotic and physical variables. In addition to being cumbersome, this limitation made it more difficult to compare the relative influence of the different factors and interactions between factors. However, ordination was very useful as an exploratory tool. Although compartmentalized by stock, across fish comparisons were simple and relatively straightforward. Because the explanatory variables were evaluated separately in relation to the ordination score assigned to the fish, it was possible to examine and compare highly correlated variables. Ordination was also able to identify overall patterns within the data and assess the relative importance. While this can be accomplished within the framework of linear regression using mixture models to determine whether multiple distributions exist within the data, the process is much simpler with ordination. The migratory patterns of the fish were influenced by a wide range of factors, with evidentiary support for complex, multi-faceted relationships. Physical features of the basin demonstrated stronger explanatory power, accounting for over 70% of the observed variation in migration rate compared to 18% for the biological characteristics of the fish. Parameter estimates associated with the steepness of the migratory route and remaining distance the fish had to travel to reach their natal rivers were most strongly correlated with migration rate, with consistent relationships observed across stocks. Migration rates were also noticeably slower in extensively braided reaches of the basin. The weaker relationships between migration rate and biotic factors may reflect stabilizing selection on long-distance migrants. Smaller fish exhibited minimally faster swimming speeds on average than larger individuals. This relationship was stronger in highly braided reaches. Run timing was positively related to migration rate for most stocks. Surprisingly, upper basin stocks traveling farther upriver displayed progressively negative relationships, suggesting that late-run fish were moving slower. Ancillary information suggests that this decline may relate to deteriorating fish condition later in the season. Close