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• 1. [Article] Onshore-offshore variations in copepod community structure off the Oregon coast during the summer upwelling season

  The published version of this article is copyrighted by Inter-Research and can be found here: http://www.int-res.com/journals/meps/meps-home/

  Citation × Citation Citation Abstract Copy Title: Onshore-offshore variations in copepod community structure off the Oregon coast during the summer upwelling season Author: Emmett, Robert L., Morgan, Cheryl A., Peterson, William T. The published version of this article is copyrighted by Inter-Research and can be found here: http://www.int-res.com/journals/meps/meps-home/ Title: Onshore-offshore variations in copepod community structure off the Oregon coast during the summer upwelling season Author: Emmett, Robert L., Morgan, Cheryl A., Peterson, William T. The published version of this article is copyrighted by Inter-Research and can be found here: http://www.int-res.com/journals/meps/meps-home/ Close

• 2. [Article] Spatiotemporal Drivers of Seabird Distribution at the Pacific Marine Energy Center off Newport, Oregon

  The central Oregon coast was selected as an ideal site for wave energy development and establishment of the Pacific Marine Energy Center (PMEC). PMEC will consist of two nearshore sites, one north (NETS) ...

  Citation × Citation Citation Abstract Copy Title: Spatiotemporal Drivers of Seabird Distribution at the Pacific Marine Energy Center off Newport, Oregon Author: Porquez, Jessica M. The central Oregon coast was selected as an ideal site for wave energy development and establishment of the Pacific Marine Energy Center (PMEC). PMEC will consist of two nearshore sites, one north (NETS) and one south (SETS) of the Yaquina River, Oregon. Our study aims to assess how the development of wave energy sites might impact marine birds. We used vessel-based strip transect surveys to detect spatial and temporal patterns of seabirds during 28 surveys of NETS and SETS from 2013-2015. We also conducted 29 surveys along the Newport Hydrographic Line (NHL) (2006-2009, 2013-2015), a cross-shelf oceanographic sampling line that extends 40 km west of NETS. We collected in situ measurements of surface conductivity, temperature and fluorescence to test correlations between spatial variables and seabird abundance. Common murres (Uria aalge) were the most abundant resident species (70%) while sooty shearwaters (Puffinus griseus) were the most abundant migratory species (78%). We identified 7 focal species (common murres, sooty shearwaters, Brandt's and pelagic cormorants (Phalacrocorax penicillatus and pelagicus), western gull (Larus occidentalis), Cassin's auklet (Ptychoramphus aleuticus), and red-necked phalaropes (Phalaropus lobatus), 5 foraging niches and 3 species of interest for analysis. We used non-metric multidimensional scaling ordinations to assess seasonal shifts in the seabird community at a focal species and foraging group level. Both ordinations depicted strong seasonal gradients with distinct seasonal communities. Focal species were also driven by a distance to shore gradient, while foraging niches were more influenced by foraging type (diving versus surface feeding). The shoreward shift or outward dispersal of species appears driven by a combination of factors, including the diffusion of nearshore concentration of murres and cormorants on Yaquina Head post chick fledging, and the inshore movement of migratory species with the onset of upwelling and greater prey abundance. We employed generalized additive mixed models for the focal species, and tested for correlations with in situ data (salinity, temperature and fluorescence), depth, substrate, season, and a random 'site' effect. We identified correlations between several species and measured oceanographic variables, which indicated species' selection of specific water masses. With Inverse Distance Weighted maps we detected high use zones by sooty shearwaters and common murres outside of both site boundaries, except during the spring and summer, when murres occur densely within the NETS. None of our observed species of concern (brown pelicans (Pelicanus occidentalis), black footed albatrosses (Phoebastria nigiripes) and marbled murrelets, (Brachyramphus marmoratus)) were detected within either site boundary. Rather, pelicans and murrelets were observed inshore of the SETS and south of the NETS, and albatrosses were all detected west of the sites. We observed overall low abundance of focal species within the sites, relative to adjacent areas, although the whole study area appears to be productive foraging habitat used by many species. As a baseline characterization of the seabird community off Newport, this work can help inform citing and permitting processes of similar wave energy test facilities and provide a platform for continued monitoring of seabirds in the area. Title: Spatiotemporal Drivers of Seabird Distribution at the Pacific Marine Energy Center off Newport, Oregon Author: Porquez, Jessica M. The central Oregon coast was selected as an ideal site for wave energy development and establishment of the Pacific Marine Energy Center (PMEC). PMEC will consist of two nearshore sites, one north (NETS) and one south (SETS) of the Yaquina River, Oregon. Our study aims to assess how the development of wave energy sites might impact marine birds. We used vessel-based strip transect surveys to detect spatial and temporal patterns of seabirds during 28 surveys of NETS and SETS from 2013-2015. We also conducted 29 surveys along the Newport Hydrographic Line (NHL) (2006-2009, 2013-2015), a cross-shelf oceanographic sampling line that extends 40 km west of NETS. We collected in situ measurements of surface conductivity, temperature and fluorescence to test correlations between spatial variables and seabird abundance. Common murres (Uria aalge) were the most abundant resident species (70%) while sooty shearwaters (Puffinus griseus) were the most abundant migratory species (78%). We identified 7 focal species (common murres, sooty shearwaters, Brandt's and pelagic cormorants (Phalacrocorax penicillatus and pelagicus), western gull (Larus occidentalis), Cassin's auklet (Ptychoramphus aleuticus), and red-necked phalaropes (Phalaropus lobatus), 5 foraging niches and 3 species of interest for analysis. We used non-metric multidimensional scaling ordinations to assess seasonal shifts in the seabird community at a focal species and foraging group level. Both ordinations depicted strong seasonal gradients with distinct seasonal communities. Focal species were also driven by a distance to shore gradient, while foraging niches were more influenced by foraging type (diving versus surface feeding). The shoreward shift or outward dispersal of species appears driven by a combination of factors, including the diffusion of nearshore concentration of murres and cormorants on Yaquina Head post chick fledging, and the inshore movement of migratory species with the onset of upwelling and greater prey abundance. We employed generalized additive mixed models for the focal species, and tested for correlations with in situ data (salinity, temperature and fluorescence), depth, substrate, season, and a random 'site' effect. We identified correlations between several species and measured oceanographic variables, which indicated species' selection of specific water masses. With Inverse Distance Weighted maps we detected high use zones by sooty shearwaters and common murres outside of both site boundaries, except during the spring and summer, when murres occur densely within the NETS. None of our observed species of concern (brown pelicans (Pelicanus occidentalis), black footed albatrosses (Phoebastria nigiripes) and marbled murrelets, (Brachyramphus marmoratus)) were detected within either site boundary. Rather, pelicans and murrelets were observed inshore of the SETS and south of the NETS, and albatrosses were all detected west of the sites. We observed overall low abundance of focal species within the sites, relative to adjacent areas, although the whole study area appears to be productive foraging habitat used by many species. As a baseline characterization of the seabird community off Newport, this work can help inform citing and permitting processes of similar wave energy test facilities and provide a platform for continued monitoring of seabirds in the area. Close

• 3. [Article] Biological indicators of the timing and direction of warm-water advection during the 1997/1998 El Niño off the central Oregon coast, USA

  The published version of this article is copyrighted by Inter-Research and can be found here: http://www.int-res.com/journals/meps/meps-home/

  Citation × Citation Citation Abstract Copy Title: Biological indicators of the timing and direction of warm-water advection during the 1997/1998 El Niño off the central Oregon coast, USA Author: Johnson, Travis B., Morgan, Cheryl A., Keister, Julie E., Peterson, William T. The published version of this article is copyrighted by Inter-Research and can be found here: http://www.int-res.com/journals/meps/meps-home/ Title: Biological indicators of the timing and direction of warm-water advection during the 1997/1998 El Niño off the central Oregon coast, USA Author: Johnson, Travis B., Morgan, Cheryl A., Keister, Julie E., Peterson, William T. The published version of this article is copyrighted by Inter-Research and can be found here: http://www.int-res.com/journals/meps/meps-home/ Close

• 4. [Article] Fire effects on wetland prairie species: final report

  Project No. 14-48-0001-96749

  Citation × Citation Citation Abstract Copy Title: Fire effects on wetland prairie species: final report Author: Wilson, Mark V., Clark, Deborah Louise, 1950- Project No. 14-48-0001-96749 Title: Fire effects on wetland prairie species: final report Author: Wilson, Mark V., Clark, Deborah Louise, 1950- Project No. 14-48-0001-96749 Close

• 5. [Article] Seed viability studies for recovery of Plagiobothrys hirtus (Boraginaceae), the rough popcornflower

  The original submitted file is the .ppt file. The .pdf file was made for preservation purposes.

  Citation × Citation Citation Abstract Copy Title: Seed viability studies for recovery of Plagiobothrys hirtus (Boraginaceae), the rough popcornflower Author: Amsberry, Kelly, Wilson, Courtney, Meinke, Robert J. The original submitted file is the .ppt file. The .pdf file was made for preservation purposes. Title: Seed viability studies for recovery of Plagiobothrys hirtus (Boraginaceae), the rough popcornflower Author: Amsberry, Kelly, Wilson, Courtney, Meinke, Robert J. The original submitted file is the .ppt file. The .pdf file was made for preservation purposes. Close

• 6. [Article] Reviving Whychus Creek: Averting Collisions between the Endangered Species Act and Agricultural Water Use through Proactive Streamflow Restoration

  In the wake of policies catalyzing settlement through agrarian-based land ‘improvement’, private property rights absorbed water resources through Western water law. Consequently, these dominant user regimes ...

  Citation × Citation Citation Abstract Copy Title: Reviving Whychus Creek: Averting Collisions between the Endangered Species Act and Agricultural Water Use through Proactive Streamflow Restoration Author: Dengel, Jeff In the wake of policies catalyzing settlement through agrarian-based land ‘improvement’, private property rights absorbed water resources through Western water law. Consequently, these dominant user regimes and the doctrine of prior appropriation allocated nearly 80 percent of freshwater resources to agricultural use. Following enactment of the Endangered Species Act (ESA) in 1973 agricultural water users and the federal government were set on a collision course, as private property was now subject to regulatory imposition. Within Western states water bodies contiguous to private agrarian lands host the majority of aquatic species listed under the ESA. Of all the effects associated with agricultural water use, streamflow depletion constitutes the primary source of species imperilment. Customary irrigation practices often dewater streams completely or render aquatic habitat inhospitable. Consequently, curtailment of water use is increasingly sought during enforcement of ESA regulations. Encounters between ESA regulation and impositions upon agricultural water use are largely reactionary, litigious, and costly; this begs the question of remedy. Responses attending to the matter indicate collaborative and precautionary measures as prospective solutions. Within the context of streamflow-based habitat modification the answer consistently indicates transactional mechanisms reallocating water to instream use. Due to priority-based allocation developed through the doctrine of prior appropriation acquisition of senior water rights is imperative for streamflow restoration. Within Oregon's Whychus Creek agricultural water users employed a series of water right transactions serving to bolster instream flow to avert ESA regulation. Many of these transactions have been implemented through Oregon's Conserved Water Program; a unique statute providing benefits for the environment and agricultural water users alike. Through these transactions senior water rights have been reallocated to instream use and are being met, resulting in a robust presence of instream flow. Title: Reviving Whychus Creek: Averting Collisions between the Endangered Species Act and Agricultural Water Use through Proactive Streamflow Restoration Author: Dengel, Jeff In the wake of policies catalyzing settlement through agrarian-based land ‘improvement’, private property rights absorbed water resources through Western water law. Consequently, these dominant user regimes and the doctrine of prior appropriation allocated nearly 80 percent of freshwater resources to agricultural use. Following enactment of the Endangered Species Act (ESA) in 1973 agricultural water users and the federal government were set on a collision course, as private property was now subject to regulatory imposition. Within Western states water bodies contiguous to private agrarian lands host the majority of aquatic species listed under the ESA. Of all the effects associated with agricultural water use, streamflow depletion constitutes the primary source of species imperilment. Customary irrigation practices often dewater streams completely or render aquatic habitat inhospitable. Consequently, curtailment of water use is increasingly sought during enforcement of ESA regulations. Encounters between ESA regulation and impositions upon agricultural water use are largely reactionary, litigious, and costly; this begs the question of remedy. Responses attending to the matter indicate collaborative and precautionary measures as prospective solutions. Within the context of streamflow-based habitat modification the answer consistently indicates transactional mechanisms reallocating water to instream use. Due to priority-based allocation developed through the doctrine of prior appropriation acquisition of senior water rights is imperative for streamflow restoration. Within Oregon's Whychus Creek agricultural water users employed a series of water right transactions serving to bolster instream flow to avert ESA regulation. Many of these transactions have been implemented through Oregon's Conserved Water Program; a unique statute providing benefits for the environment and agricultural water users alike. Through these transactions senior water rights have been reallocated to instream use and are being met, resulting in a robust presence of instream flow. Close

• 7. [Article] Surfgrasses (Phyllospadix spp.) as dynamic foundation species for macroinvertebrates along the Oregon coast

  Foundation species are important components of ecosystems because they provide habitat and ameliorate stressful conditions for residents. This thesis considers the role of surfgrasses (Phyllospadix spp.) ...

  Citation × Citation Citation Abstract Copy Title: Surfgrasses (Phyllospadix spp.) as dynamic foundation species for macroinvertebrates along the Oregon coast Author: Moulton, Orissa M. Foundation species are important components of ecosystems because they provide habitat and ameliorate stressful conditions for residents. This thesis considers the role of surfgrasses (Phyllospadix spp.) as dynamic foundation species on the coast of Oregon in two studies. Chapter 2, which presents an observational survey of two Phyllospadix congeners, investigates the ways in which surfgrass morphology and observed oceanographic conditions influence associated macroinvertebrate communities throughout a calendar year. Chapter 3, which presents an experimental manipulation of the system, considers the ways in which macroinvertebrates and surfgrass interact. Surfgrasses (Phyllospadix spp.) are ubiquitous foundation species on the coast of Oregon, USA, protecting resident invertebrates from waves and providing them access to sandy substrate in an otherwise rocky habitat. We investigated whether native congeneric species function similarly by comparing the two species' resident macroinvertebrates, plant morphology, and sediment accretion at three capes that vary in oceanographic conditions. The results showed that while the macroinvertebrate abundance was the same between surfgrass species, species richness, composition, and functional groups varied considerably. P. serrulatus also had fewer tillers, rhizomes, and lower biomass per given area but greater sediment accretion than its congener P. scouleri. There was a large difference in macroinvertebrate abundance among capes, with Cape Perpetua having 2.5-3 times more animals per given area than Cape Foulweather or Cape Blanco. Overall, we found that while the two co-occurring surfgrass congeners provided functionally different habitat for resident macroinvertebrate species, regional oceanographic processes (upwelling, productivity) were more influential in determining the overall abundance and productivity of these highly diverse animal communities. The interaction between surfgrass (P. scouleri) and resident macroinvertebrates may be an example of mutual facilitation if surfgrass provides shelter and macroinvertebrate residents reciprocate with nutrient input. We hypothesized that this positive interaction could vary depending on oceanographic conditions. Sites with intermittent upwelling, low retention of upwelled waters, and high nutrient delivery to the intertidal are often dominated by macroalgae and seagrasses, while sessile invertebrates dominate intermittent upwelling sites with high water higher retention and relatively low nutrient delivery to the intertidal. We expected the positive influence of macroinvertebrates upon surfgrass to be strongest at a site with possible nutrient limitation stress. We used manipulative field experiments to examine the interaction between Phyllospadix and macroinvertebrate residents at sites known to differ in coastal oceanography. Treatments were applied in situ to vary presence/absence of residents and nutrient conditions. Results indicate that the community of macroinvertebrates varies greatly in both abundance and composition between the two sites (ca. three fold higher abundance at Strawberry Hill than at Fogarty Creek), but the amount Phyllospadix habitat available to macroinvertebrates does not vary between the two sites. This variation is therefore driven by something external to local habitat, and is likely related to regional oceanography. Furthermore, there is some evidence that macroinvertebrates do have some positive nutrient effect upon surfgrass productivity. Together, these studies provide critical descriptive information about community structure associated with the Phyllospadix system on the Oregon coast. This work contributes to the ever-increasing body of literature suggesting importance of regional oceanography in structuring coastal communities. Title: Surfgrasses (Phyllospadix spp.) as dynamic foundation species for macroinvertebrates along the Oregon coast Author: Moulton, Orissa M. Foundation species are important components of ecosystems because they provide habitat and ameliorate stressful conditions for residents. This thesis considers the role of surfgrasses (Phyllospadix spp.) as dynamic foundation species on the coast of Oregon in two studies. Chapter 2, which presents an observational survey of two Phyllospadix congeners, investigates the ways in which surfgrass morphology and observed oceanographic conditions influence associated macroinvertebrate communities throughout a calendar year. Chapter 3, which presents an experimental manipulation of the system, considers the ways in which macroinvertebrates and surfgrass interact. Surfgrasses (Phyllospadix spp.) are ubiquitous foundation species on the coast of Oregon, USA, protecting resident invertebrates from waves and providing them access to sandy substrate in an otherwise rocky habitat. We investigated whether native congeneric species function similarly by comparing the two species' resident macroinvertebrates, plant morphology, and sediment accretion at three capes that vary in oceanographic conditions. The results showed that while the macroinvertebrate abundance was the same between surfgrass species, species richness, composition, and functional groups varied considerably. P. serrulatus also had fewer tillers, rhizomes, and lower biomass per given area but greater sediment accretion than its congener P. scouleri. There was a large difference in macroinvertebrate abundance among capes, with Cape Perpetua having 2.5-3 times more animals per given area than Cape Foulweather or Cape Blanco. Overall, we found that while the two co-occurring surfgrass congeners provided functionally different habitat for resident macroinvertebrate species, regional oceanographic processes (upwelling, productivity) were more influential in determining the overall abundance and productivity of these highly diverse animal communities. The interaction between surfgrass (P. scouleri) and resident macroinvertebrates may be an example of mutual facilitation if surfgrass provides shelter and macroinvertebrate residents reciprocate with nutrient input. We hypothesized that this positive interaction could vary depending on oceanographic conditions. Sites with intermittent upwelling, low retention of upwelled waters, and high nutrient delivery to the intertidal are often dominated by macroalgae and seagrasses, while sessile invertebrates dominate intermittent upwelling sites with high water higher retention and relatively low nutrient delivery to the intertidal. We expected the positive influence of macroinvertebrates upon surfgrass to be strongest at a site with possible nutrient limitation stress. We used manipulative field experiments to examine the interaction between Phyllospadix and macroinvertebrate residents at sites known to differ in coastal oceanography. Treatments were applied in situ to vary presence/absence of residents and nutrient conditions. Results indicate that the community of macroinvertebrates varies greatly in both abundance and composition between the two sites (ca. three fold higher abundance at Strawberry Hill than at Fogarty Creek), but the amount Phyllospadix habitat available to macroinvertebrates does not vary between the two sites. This variation is therefore driven by something external to local habitat, and is likely related to regional oceanography. Furthermore, there is some evidence that macroinvertebrates do have some positive nutrient effect upon surfgrass productivity. Together, these studies provide critical descriptive information about community structure associated with the Phyllospadix system on the Oregon coast. This work contributes to the ever-increasing body of literature suggesting importance of regional oceanography in structuring coastal communities. Close

• 8. [Article] The influence of biophysical feedbacks and species interactions on grass invasions and coastal dune morphology in the Pacific Northwest, USA

  Biological invasions provide a unique opportunity to study the mechanisms that regulate community composition and ecosystem function. Invasive species that are also ecosystem engineers can substantially ...

  Citation × Citation Citation Abstract Copy Title: The influence of biophysical feedbacks and species interactions on grass invasions and coastal dune morphology in the Pacific Northwest, USA Author: Zarnetske, Phoebe Lehmann, 1979- Biological invasions provide a unique opportunity to study the mechanisms that regulate community composition and ecosystem function. Invasive species that are also ecosystem engineers can substantially alter physical features in an environment, and this can lead to cascading effects on the biological community. Aquatic-terrestrial interface ecosystems are excellent systems to study the interactions among invasive ecosystem engineers, physical features, and biological communities, because interactions among vegetation, sediment, and fluids within biophysical feedbacks create and modify distinct physical features. Further, these systems provide important ecosystem services including coastal protection afforded by their natural features. In this dissertation, I investigate the interactions and feedbacks among sand-binding beach grass species (a native, Elymus mollis (Trin.), and two non-natives, Ammophila arenaria (L.) Link and A. breviligulata Fernald), sediment supply, and dune shape along the U.S. Pacific Northwest coast. Dunes dominated by A. arenaria tend to be taller and narrower compared to the shorter, wider dunes dominated by A. breviligulata. These patterns suggest an ecological control on dune shape, and thus, coastal vulnerability to overtopping waves. I investigate the causes and consequences of these patterns with experiments, field observations, and modeling. Specifically, I investigate the relative roles of vegetation and sediment supply in shaping coastal dunes over inter-annual and multi-decadal time scales (Chapter 2), characterize a biophysical feedback between beach grass species growth habit and sediment supply (Chapter 3), uncover the mechanisms leading to beach grass coexistence and whether A. breviligulata can invade and dominate new sections of coastline (Chapter 4), and examine the non-target effects resulting from management actions that remove Ammophila for the recovery of the threatened Western Snowy plover (Charadrius alexandrinus nivosus) (Chapter 5). I found that vegetation and sediment supply play important roles in dune shape changes across inter-annual and multi-decadal time scales (Chapter 2). I determined that a biophysical feedback between the beach grass growth habits and sediment supply results in species-specific differences in sand capture ability, and thus, is a likely explanation for differences in dune shape (Chapter 3). I found that all three beach grass species can coexist across different sediment deposition rates, and that this coexistence is largely mediated by positive direct and indirect species interactions. I further determined that A. breviligulata is capable of invading and dominating the beach grass community in regions where it is currently absent (Chapter 4). Combined, these findings indicate that A. breviligulata is an inferior dune building species as compared to A. arenaria, and suggest that in combination with sediment supply gradients, these species differences ultimately lead to differences in dune shape. Potential further invasions of A. breviligulata into southern regions of the Pacific Northwest may diminish the coastal protection ability of dunes currently dominated by A. arenaria, but this effect could be moderated by the predicted near co-dominance of A. arenaria in these lower sediment supply conditions. Finally, I found that the techniques used to remove Ammophila for plover recovery have unintended consequences for the native and endemic dune plant communities, and disrupt the natural disturbance regime of shifting sand. A whole-ecosystem restoration focus would be an improvement over the target-species approach, as it would promote the return of the natural disturbance regime, which in turn, would help recover the native biological community. The findings from this dissertation research provide a robust knowledge base that can guide further investigations of biological and physical changes to the coastal dunes, can help improve the management of dune ecosystem services and the restoration of native communities, and can help anticipate the impacts of future beach grass invasions and climate change induced changes to the coast. Title: The influence of biophysical feedbacks and species interactions on grass invasions and coastal dune morphology in the Pacific Northwest, USA Author: Zarnetske, Phoebe Lehmann, 1979- Biological invasions provide a unique opportunity to study the mechanisms that regulate community composition and ecosystem function. Invasive species that are also ecosystem engineers can substantially alter physical features in an environment, and this can lead to cascading effects on the biological community. Aquatic-terrestrial interface ecosystems are excellent systems to study the interactions among invasive ecosystem engineers, physical features, and biological communities, because interactions among vegetation, sediment, and fluids within biophysical feedbacks create and modify distinct physical features. Further, these systems provide important ecosystem services including coastal protection afforded by their natural features. In this dissertation, I investigate the interactions and feedbacks among sand-binding beach grass species (a native, Elymus mollis (Trin.), and two non-natives, Ammophila arenaria (L.) Link and A. breviligulata Fernald), sediment supply, and dune shape along the U.S. Pacific Northwest coast. Dunes dominated by A. arenaria tend to be taller and narrower compared to the shorter, wider dunes dominated by A. breviligulata. These patterns suggest an ecological control on dune shape, and thus, coastal vulnerability to overtopping waves. I investigate the causes and consequences of these patterns with experiments, field observations, and modeling. Specifically, I investigate the relative roles of vegetation and sediment supply in shaping coastal dunes over inter-annual and multi-decadal time scales (Chapter 2), characterize a biophysical feedback between beach grass species growth habit and sediment supply (Chapter 3), uncover the mechanisms leading to beach grass coexistence and whether A. breviligulata can invade and dominate new sections of coastline (Chapter 4), and examine the non-target effects resulting from management actions that remove Ammophila for the recovery of the threatened Western Snowy plover (Charadrius alexandrinus nivosus) (Chapter 5). I found that vegetation and sediment supply play important roles in dune shape changes across inter-annual and multi-decadal time scales (Chapter 2). I determined that a biophysical feedback between the beach grass growth habits and sediment supply results in species-specific differences in sand capture ability, and thus, is a likely explanation for differences in dune shape (Chapter 3). I found that all three beach grass species can coexist across different sediment deposition rates, and that this coexistence is largely mediated by positive direct and indirect species interactions. I further determined that A. breviligulata is capable of invading and dominating the beach grass community in regions where it is currently absent (Chapter 4). Combined, these findings indicate that A. breviligulata is an inferior dune building species as compared to A. arenaria, and suggest that in combination with sediment supply gradients, these species differences ultimately lead to differences in dune shape. Potential further invasions of A. breviligulata into southern regions of the Pacific Northwest may diminish the coastal protection ability of dunes currently dominated by A. arenaria, but this effect could be moderated by the predicted near co-dominance of A. arenaria in these lower sediment supply conditions. Finally, I found that the techniques used to remove Ammophila for plover recovery have unintended consequences for the native and endemic dune plant communities, and disrupt the natural disturbance regime of shifting sand. A whole-ecosystem restoration focus would be an improvement over the target-species approach, as it would promote the return of the natural disturbance regime, which in turn, would help recover the native biological community. The findings from this dissertation research provide a robust knowledge base that can guide further investigations of biological and physical changes to the coastal dunes, can help improve the management of dune ecosystem services and the restoration of native communities, and can help anticipate the impacts of future beach grass invasions and climate change induced changes to the coast. Close

• 9. [Article] Young-of-the-year rockfish (Sebastes spp.) settlement dynamics in Oregon estuaries

  In the Pacific Northwest, several species of rockfishes (Sebastes spp.) are under extreme conservation measures due to low population levels. Although currently at healthy population levels, one species ...

  Citation × Citation Citation Abstract Copy Title: Young-of-the-year rockfish (Sebastes spp.) settlement dynamics in Oregon estuaries Author: Dauble, Alison D. In the Pacific Northwest, several species of rockfishes (Sebastes spp.) are under extreme conservation measures due to low population levels. Although currently at healthy population levels, one species of interest is the black rockfish (S. melanops), which has been shown to utilize estuarine habitat during its early life history stages. Black rockfish constitute a large portion of the recreational harvest in the Pacific Northwest, and are also a commercially fished species along the majority of the west coast. Annual recruitment in rockfishes has been shown to be extremely variable, and a better understanding of the factors behind successful recruitment and the subsequent settlement process would assist in prioritizing management and conservation efforts for this and other species. The overall goal of my study was to investigate the role that natural and anthropogenic influences play in the estuarine settlement dynamics of northeast Pacific rockfishes, using black rockfish as the primary study species. Genetic identifications confirmed that the majority of the young-of-the-year (YOY) rockfish captured during this study were S. melanops, with small numbers of S. caurinus and S. emphaeus present as well. Results from trapping surveys indicated that YOY black rockfish utilize multiple estuaries on the Oregon coast from spring through late fall, and may be present in highly developed estuaries through their first winter before moving to deeper habitats, as shown by late season increases in catch-per-unit-effort (CPUEs) and the capture of multiple age-1 juveniles in the estuary. Catches were higher in the more developed estuaries on the coast, suggesting that the presence of structure is an extremely important component to the settlement process in this species and that the continued development of Oregon estuaries may not adversely affect YOY rockfish settlement. Two years of dive surveys on a standardized set of artificial reef structures in Yaquina Bay showed that a settlement index of YOY rockfish within the estuary could reflect larger trends in the YOY population and suggest that habitat saturation is not a factor that affects the settlement process of YOY rockfish in estuaries. This study provides strong evidence of widespread use of estuarine habitat on the Oregon coast by black rockfish during their first year of life, and provides additional support that structure is an important component to the settlement process, and has set the groundwork for investigating inter-annual variation in the estuarine settlement of rockfish. Title: Young-of-the-year rockfish (Sebastes spp.) settlement dynamics in Oregon estuaries Author: Dauble, Alison D. In the Pacific Northwest, several species of rockfishes (Sebastes spp.) are under extreme conservation measures due to low population levels. Although currently at healthy population levels, one species of interest is the black rockfish (S. melanops), which has been shown to utilize estuarine habitat during its early life history stages. Black rockfish constitute a large portion of the recreational harvest in the Pacific Northwest, and are also a commercially fished species along the majority of the west coast. Annual recruitment in rockfishes has been shown to be extremely variable, and a better understanding of the factors behind successful recruitment and the subsequent settlement process would assist in prioritizing management and conservation efforts for this and other species. The overall goal of my study was to investigate the role that natural and anthropogenic influences play in the estuarine settlement dynamics of northeast Pacific rockfishes, using black rockfish as the primary study species. Genetic identifications confirmed that the majority of the young-of-the-year (YOY) rockfish captured during this study were S. melanops, with small numbers of S. caurinus and S. emphaeus present as well. Results from trapping surveys indicated that YOY black rockfish utilize multiple estuaries on the Oregon coast from spring through late fall, and may be present in highly developed estuaries through their first winter before moving to deeper habitats, as shown by late season increases in catch-per-unit-effort (CPUEs) and the capture of multiple age-1 juveniles in the estuary. Catches were higher in the more developed estuaries on the coast, suggesting that the presence of structure is an extremely important component to the settlement process in this species and that the continued development of Oregon estuaries may not adversely affect YOY rockfish settlement. Two years of dive surveys on a standardized set of artificial reef structures in Yaquina Bay showed that a settlement index of YOY rockfish within the estuary could reflect larger trends in the YOY population and suggest that habitat saturation is not a factor that affects the settlement process of YOY rockfish in estuaries. This study provides strong evidence of widespread use of estuarine habitat on the Oregon coast by black rockfish during their first year of life, and provides additional support that structure is an important component to the settlement process, and has set the groundwork for investigating inter-annual variation in the estuarine settlement of rockfish. Close

• 10. [Article] Twenty-year changes in riparian bird communities of east-central Oregon

  Over the last 50 years, riparian zones in the semi-arid West have gained recognition as disproportionately important habitats for both breeding bird communities and agricultural operations. Despite growing ...

  Citation × Citation Citation Abstract Copy Title: Twenty-year changes in riparian bird communities of east-central Oregon Author: Ellis, Michael S. Over the last 50 years, riparian zones in the semi-arid West have gained recognition as disproportionately important habitats for both breeding bird communities and agricultural operations. Despite growing interest in exploring avian-habitat relationships in these systems to better inform land management, few studies have attempted to describe temporal changes in the region's riparian bird communities. To provide a frame of reference for these changes, we compared indices of avian abundance and diversity from three streamside vegetation associations in east-central Oregon during the 2014 breeding season with baseline data collected by TA Sanders and WD Edge in 1993 and 1994 (Sanders and Edge 1998). Our objectives were to identify patterns of change in the avian community with a focus on riparian shrub-dependent species, to re-examine previously reported relationships between avian abundance and vegetation volume, and to identify possible causes of declines in abundance and diversity with the goal of providing land managers in the semi-arid region information to be used in the guidance and adaptation of management practices. We combined field protocols used by Sanders and Edge to survey birds along point count transects and to measure riparian vegetation with modern analytical techniques. We found few major differences in overall diversity between study periods, but documented precipitous declines in detections for two of three riparian shrub-dependent focal species - Yellow Warbler (Setophaga petechia) and Willow Flycatcher (Empidonax trailii). Song Sparrow (Melospiza melodia) detections declined by a smaller margin. Changes in number of detections for these species did not reflect trends in mesic shrub volume, which had been identified as a likely driver of obligate species abundance by Sanders and Edge but remained relatively unchanged between study periods. Declines of all three focal species reflected regional Breeding Bird Survey trends, corroborating our finding that their declines may not be a result of changes in local site conditions. Compositional similarity between avian communities was significantly higher in 2014 than in 1993-1994, exhibiting a shift toward greater homogenization between structurally distinct riparian habitats. Our results suggest managing working lands for riparian shrub cover or volume, an important metric of grazing intensity and riparian system health, may not be enough to conserve diversity and abundance of riparian-shrub dependent birds, and more work should be done to identify and alleviate factors contributing to these species' declines. Title: Twenty-year changes in riparian bird communities of east-central Oregon Author: Ellis, Michael S. Over the last 50 years, riparian zones in the semi-arid West have gained recognition as disproportionately important habitats for both breeding bird communities and agricultural operations. Despite growing interest in exploring avian-habitat relationships in these systems to better inform land management, few studies have attempted to describe temporal changes in the region's riparian bird communities. To provide a frame of reference for these changes, we compared indices of avian abundance and diversity from three streamside vegetation associations in east-central Oregon during the 2014 breeding season with baseline data collected by TA Sanders and WD Edge in 1993 and 1994 (Sanders and Edge 1998). Our objectives were to identify patterns of change in the avian community with a focus on riparian shrub-dependent species, to re-examine previously reported relationships between avian abundance and vegetation volume, and to identify possible causes of declines in abundance and diversity with the goal of providing land managers in the semi-arid region information to be used in the guidance and adaptation of management practices. We combined field protocols used by Sanders and Edge to survey birds along point count transects and to measure riparian vegetation with modern analytical techniques. We found few major differences in overall diversity between study periods, but documented precipitous declines in detections for two of three riparian shrub-dependent focal species - Yellow Warbler (Setophaga petechia) and Willow Flycatcher (Empidonax trailii). Song Sparrow (Melospiza melodia) detections declined by a smaller margin. Changes in number of detections for these species did not reflect trends in mesic shrub volume, which had been identified as a likely driver of obligate species abundance by Sanders and Edge but remained relatively unchanged between study periods. Declines of all three focal species reflected regional Breeding Bird Survey trends, corroborating our finding that their declines may not be a result of changes in local site conditions. Compositional similarity between avian communities was significantly higher in 2014 than in 1993-1994, exhibiting a shift toward greater homogenization between structurally distinct riparian habitats. Our results suggest managing working lands for riparian shrub cover or volume, an important metric of grazing intensity and riparian system health, may not be enough to conserve diversity and abundance of riparian-shrub dependent birds, and more work should be done to identify and alleviate factors contributing to these species' declines. Close