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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] The Oligocene Fossil Caudates of Oregon: Classification, Analysis, and Insights on the Paleoecology and Conservation Biology of Pacific Newts

  Newts, abundant worldwide, have unclear pre-Pliocene evolution and phylogenetic relationships. North America has a sporadic pre-Pliocene newt record. Several undescribed fossils can address this lack ...

  Citation × Citation Citation Abstract Copy Title: The Oligocene Fossil Caudates of Oregon: Classification, Analysis, and Insights on the Paleoecology and Conservation Biology of Pacific Newts Author: Jacisin, John Year: 2014 Newts, abundant worldwide, have unclear pre-Pliocene evolution and phylogenetic relationships. North America has a sporadic pre-Pliocene newt record. Several undescribed fossils can address this lack of information. I built a character matrix of >70 morphological characters for extant newts and two fossil species, Taricha oligocenica and Taricha lindoei. Phylogenetic analyses were used to investigate the relationships of the fossil taxa within newts. The morphology of the fossil taxa was compared with extant North American newts to redescribe the fossil specimens. The past ecology and biogeography of North American fossil newts was compared with their current ecologies and distribution to better understand their evolution and dispersal and to predict possible changes for newts in the face of environmental change. Results indicate that T. oligocenica and T. lindoei are closely-related species nested within Taricha, but their relationships with extant species are unresolved; the genus itself is rooted at least 32 Ma. Title: The Oligocene Fossil Caudates of Oregon: Classification, Analysis, and Insights on the Paleoecology and Conservation Biology of Pacific Newts Author: Jacisin, John Year: 2014 Newts, abundant worldwide, have unclear pre-Pliocene evolution and phylogenetic relationships. North America has a sporadic pre-Pliocene newt record. Several undescribed fossils can address this lack of information. I built a character matrix of >70 morphological characters for extant newts and two fossil species, Taricha oligocenica and Taricha lindoei. Phylogenetic analyses were used to investigate the relationships of the fossil taxa within newts. The morphology of the fossil taxa was compared with extant North American newts to redescribe the fossil specimens. The past ecology and biogeography of North American fossil newts was compared with their current ecologies and distribution to better understand their evolution and dispersal and to predict possible changes for newts in the face of environmental change. Results indicate that T. oligocenica and T. lindoei are closely-related species nested within Taricha, but their relationships with extant species are unresolved; the genus itself is rooted at least 32 Ma. Close

• 10. [Article] Stratigraphy and sedimentation of the Spencer Formation in Yamhill and Washington counties, Oregon

  The Spencer Formation in Yamhill and Washington Counties, Oregon, is exposed in a narrow belt 27 km long, from 1/4 to 3 km wide and with a maximum thickness of about 400 m. The formation is composed entirely ...

  Citation × Citation Citation Abstract Copy Title: Stratigraphy and sedimentation of the Spencer Formation in Yamhill and Washington counties, Oregon Author: Al-Azzaby, Fathi Ayoub Year: 1980 The Spencer Formation in Yamhill and Washington Counties, Oregon, is exposed in a narrow belt 27 km long, from 1/4 to 3 km wide and with a maximum thickness of about 400 m. The formation is composed entirely of sandstone with interbedded thin layers of mudstone in the uppermost member. The sedimentary structure and paleoecology indicate a shallow marine depositional environment. The upper member of the Spencer Formation contains more quartz, plagioclase, and hornblende than does the lower member, but K-feldspar is less than that of the lower member. Shallower water conditions for the deposition of the upper member are indicated by sedimentary structures and the abundance of pebbly lenses and coaly material. Eighteen species of megafossils collected from the formation indicate that the Spencer Formation is of the Tejon stage (late Eocene of the West Coast). Title: Stratigraphy and sedimentation of the Spencer Formation in Yamhill and Washington counties, Oregon Author: Al-Azzaby, Fathi Ayoub Year: 1980 The Spencer Formation in Yamhill and Washington Counties, Oregon, is exposed in a narrow belt 27 km long, from 1/4 to 3 km wide and with a maximum thickness of about 400 m. The formation is composed entirely of sandstone with interbedded thin layers of mudstone in the uppermost member. The sedimentary structure and paleoecology indicate a shallow marine depositional environment. The upper member of the Spencer Formation contains more quartz, plagioclase, and hornblende than does the lower member, but K-feldspar is less than that of the lower member. Shallower water conditions for the deposition of the upper member are indicated by sedimentary structures and the abundance of pebbly lenses and coaly material. Eighteen species of megafossils collected from the formation indicate that the Spencer Formation is of the Tejon stage (late Eocene of the West Coast). Close

• 11. [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

• 12. [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

• 13. [Article] Comparative hazard assessment for protected species in a fire-prone landscape

  This is the author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/forest-ecology-...

  Citation × Citation Citation Abstract Copy Title: Comparative hazard assessment for protected species in a fire-prone landscape Author: Mealey, Stephen P., Roloff, Gary J., Bailey, John D. This is the author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/forest-ecology-and-management/. Title: Comparative hazard assessment for protected species in a fire-prone landscape Author: Mealey, Stephen P., Roloff, Gary J., Bailey, John D. This is the author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/forest-ecology-and-management/. Close

• 14. [Article] Utilizing hunter harvest effort to survey for wildlife disease: A case study of West Nile virus in greater sage‐grouse

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

  Citation × Citation Citation Abstract Copy Title: Utilizing hunter harvest effort to survey for wildlife disease: A case study of West Nile virus in greater sage‐grouse Author: Hofmeister, Erik K., Dusek, Robert J., Franson, J. Christian, Hagen, Christian A., Budeau, David A. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by Wildlife Society and published by John Wiley & Sons, Ltd. It can be found at: http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291938-5463a Title: Utilizing hunter harvest effort to survey for wildlife disease: A case study of West Nile virus in greater sage‐grouse Author: Hofmeister, Erik K., Dusek, Robert J., Franson, J. Christian, Hagen, Christian A., Budeau, David A. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by Wildlife Society and published by John Wiley & Sons, Ltd. It can be found at: http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291938-5463a Close

• 15. [Article] Annual reversible plasticity of feeding structures: cyclical changes of jaw allometry in a sea urchin

  This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the Royal Society and can be found at: http://rspb.royalsocietypublishing.org/....

  Citation × Citation Citation Abstract Copy Title: Annual reversible plasticity of feeding structures: cyclical changes of jaw allometry in a sea urchin Author: Hernández, José Carlos, Clemente, Sabrina, Ebert, Thomas A. This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the Royal Society and can be found at: http://rspb.royalsocietypublishing.org/. Title: Annual reversible plasticity of feeding structures: cyclical changes of jaw allometry in a sea urchin Author: Hernández, José Carlos, Clemente, Sabrina, Ebert, Thomas A. This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the Royal Society and can be found at: http://rspb.royalsocietypublishing.org/. Close

• 16. [Article] Carbon isotopes show snowpack acts as a valuable moisture subsidy to mountain forests in the Oregon Cascades

  This study examines climatological influences, particularly that of snowpack, on tree growth and stable carbon isotope discrimination (Δ¹³C) from ~1980 to 2013 at two sites located in the upper reaches ...

  Citation × Citation Citation Abstract Copy Title: Carbon isotopes show snowpack acts as a valuable moisture subsidy to mountain forests in the Oregon Cascades Author: Ratcliff, Christopher J. This study examines climatological influences, particularly that of snowpack, on tree growth and stable carbon isotope discrimination (Δ¹³C) from ~1980 to 2013 at two sites located in the upper reaches of the McKenzie River watershed of the Oregon Cascade Mountains. We tested the use of Δ¹³C values from latewood, corroborated by tree-ring width chronologies as precipitation proxies to develop correlations between moisture stress and climate variables. Tree species at each site included Douglas-fir and mountain hemlock. Interpolated meteorological and snowpack data included snow water equivalent (SWE), precipitation, atmospheric temperature, vapor pressure deficit (VPD), relative humidity (RH), and a metric estimating growing season length. Significant correlations between latewood Δ¹³C and winter SWE at each site indicated the importance of winter snowpack to our selected tree species (r = 0.35, r = 0.43). Late summer precipitation and relative humidity (RH) were also significantly correlated with Δ¹³C (r = 0.49, r = 0.46; r = 0.43, r = 0.44). High correlations at both sites reinforced that late summer VPD was the primary driver of Δ¹³C (r = - 0.67, r = -0.61), which is often associated with moisture stress. This was further supported by correlations between air temperature and Δ¹³C (r = -0.46, r = -0.47), which drives much of the variation in VPD. Growing season length also showed significance in mountain hemlocks at the site with longer average snowpack (r = -0.22, r = -0.44). Moisture supplied by spring snow melt is a seasonably limited resource, nonetheless both sites clearly showed that snowpack acts as a valuable moisture subsidy to coniferous mountain forests in the Oregon Cascades. This study acts as a useful case study for future investigations into the relationship between snowpack and forest health in the Pacific North West. Title: Carbon isotopes show snowpack acts as a valuable moisture subsidy to mountain forests in the Oregon Cascades Author: Ratcliff, Christopher J. This study examines climatological influences, particularly that of snowpack, on tree growth and stable carbon isotope discrimination (Δ¹³C) from ~1980 to 2013 at two sites located in the upper reaches of the McKenzie River watershed of the Oregon Cascade Mountains. We tested the use of Δ¹³C values from latewood, corroborated by tree-ring width chronologies as precipitation proxies to develop correlations between moisture stress and climate variables. Tree species at each site included Douglas-fir and mountain hemlock. Interpolated meteorological and snowpack data included snow water equivalent (SWE), precipitation, atmospheric temperature, vapor pressure deficit (VPD), relative humidity (RH), and a metric estimating growing season length. Significant correlations between latewood Δ¹³C and winter SWE at each site indicated the importance of winter snowpack to our selected tree species (r = 0.35, r = 0.43). Late summer precipitation and relative humidity (RH) were also significantly correlated with Δ¹³C (r = 0.49, r = 0.46; r = 0.43, r = 0.44). High correlations at both sites reinforced that late summer VPD was the primary driver of Δ¹³C (r = - 0.67, r = -0.61), which is often associated with moisture stress. This was further supported by correlations between air temperature and Δ¹³C (r = -0.46, r = -0.47), which drives much of the variation in VPD. Growing season length also showed significance in mountain hemlocks at the site with longer average snowpack (r = -0.22, r = -0.44). Moisture supplied by spring snow melt is a seasonably limited resource, nonetheless both sites clearly showed that snowpack acts as a valuable moisture subsidy to coniferous mountain forests in the Oregon Cascades. This study acts as a useful case study for future investigations into the relationship between snowpack and forest health in the Pacific North West. Close

• 17. [Article] Vegetation and Small Mammal Responses to Western Juniper (Juniperus occidentalis) Control in Eastern Oregon

  Shrub-steppe ecosystems of western North America provide habitat for many wildlife species, are important components of public and private rangelands, and offer recreational opportunities for millions ...

  Citation × Citation Citation Abstract Copy Title: Vegetation and Small Mammal Responses to Western Juniper (Juniperus occidentalis) Control in Eastern Oregon Author: Morozumi, Corinne N. Shrub-steppe ecosystems of western North America provide habitat for many wildlife species, are important components of public and private rangelands, and offer recreational opportunities for millions of people. They are some of the most vulnerable ecosystems in the United States and have been altered by human activities such as livestock grazing, active fire suppression, conversion to agriculture, and urbanization of the west. Since the late 1800s woody encroachment of piñon-juniper species has also contributed to the loss of shrub-steppe habitat. Presently, land managers remove woody tree species in order to recover shrub-steppe although it is unclear how responses to these management activities differ due to site-specific conditions and existing woodland development. I studied post juniper-thinning responses in eastern Oregon at a wildlife area important as winter range for mule deer (Odocoileus hemionus). I investigated vegetative responses to western juniper (Juniperus occidentalis) thinning across a woodland development gradient and tested for interactive effects of juniper cutting and cattle exclusion. In addition, I explored plant and small mammal successional dynamics after juniper thinning and examined plant community responses within microhabitats created by the felled trees. I compared vegetative responses to juniper thinning as well as cattle exclusion among sites where juniper were subordinate (Phase I), co-dominant (Phase II), and dominant to shrubs and grasses (Phase III, sensu Miller et al. 2005). At the Phase I site, thinning did not increase herbaceous biomass while thinned plots at the Phase II site had 2.71 times more median herbaceous biomass (99.17% CI: 1.37 to 5.37 times more biomass) than unthinned plots. Conversely, herbaceous biomass at the Phase III juniper woodland site was 0.36 times lower in thinned plots when compared to unthinned plots (99.17% CI: 0.17 to 0.78 times less biomass). Unfortunately, many of the responses were driven by exotic species release. Where juniper were subordinate (Phase I), mean percent cover by exotic grass increased by 24.58 percentage points in thinned plots as compared to unthinned plots (98.30% CI: 0.27 to 48.90 percentage points higher). Thinning at the Phase II site increased mean exotic grass cover by an estimated 28.47 percentage points as compared to mean exotic cover in the same plots before treatment (98.30% CI: 4.15 to 52.79 percentage points higher cover). Median native bunchgrass cover at this site was 5.06 times greater after juniper treatment (99.7% CI: 1.78 to 14.35 times higher percent cover). I found few main or interactive effects of cattle exclosure after one year of treatment. Responses to grazing exclosure may take longer to develop. These results indicate that sites within the wildlife area respond differently to juniper management and that exotic grass control will be key to successful shrub-steppe recovery. In addition, I used a time-since-juniper thinning chronoseries consisting of plots cut in 2008, 2009, 2010, 2012, and an adjacent uncut control to explore how shrub-steppe flora and fauna are responding to juniper treatment through time. Shrub cover and seedling density were low in each plot. I recorded the highest seedling abundance (mean of 0.25 seedlings) in the uncut control plot. Median grass cover in the uncut control was 9.50% while in the most recently treated plot (2012) it was 26.75%. Small mammal relative abundance and diversity was low across all time-since-treatment plots though highest in the plot with the greatest time-since-treatment. Deer mouse (Peromyscus maniculatus) was the most abundant species in all plots and accounted for 70-95% of all unique captures. Least chipmunk (Tamias minimus) were present in the plot with greatest time-since-treatment indicating the potential recovery of key native shrubs since these small mammals perform an important seed dispersal role. I also investigated how potential microhabitats created by the felled juniper might support different plant communities. I assessed plant responses within zones created by 1) the felled tree (canopy zone), 2) the original duff zone, and 3) the between - tree interspace zone. The three zones had different plant community compositions as analyzed multivariately with non-metric multidimensional scaling (NMS). Canopy and duff zones were forb - dominated and had less exotic grass invasion while interspace zones were heavily invested with medusahead (Taeniatherum caput-medusae) and ventenata (Ventenata dubia). Exotic herbaceous productivity was lowest under the standing trees of the control plot and high in the interspace of all plots with juniper thinning. In the 2012 cut plot, grass cover was 27.90 percentage points less in the canopy zone compared to the interspace zone (98.75% CI: 17.64 to 38.16 percentage points less grass cover). In the uncut control, median native biomass was 2.08 times greater under the standing trees compared to the interspace (96.25% CI: 1.09 to 3.97 times more biomass). Results from the time-since-treatment chronoseries indicated that exotic grass dominance might be limiting shrub-steppe recovery. Active restoration of shrubs and native grasses may be necessary to address the dominance of exotic grass after juniper thinning. Positive signs of habitat recovery included small mammal responses though I was unable to calculate population estimates due to plot size. Title: Vegetation and Small Mammal Responses to Western Juniper (Juniperus occidentalis) Control in Eastern Oregon Author: Morozumi, Corinne N. Shrub-steppe ecosystems of western North America provide habitat for many wildlife species, are important components of public and private rangelands, and offer recreational opportunities for millions of people. They are some of the most vulnerable ecosystems in the United States and have been altered by human activities such as livestock grazing, active fire suppression, conversion to agriculture, and urbanization of the west. Since the late 1800s woody encroachment of piñon-juniper species has also contributed to the loss of shrub-steppe habitat. Presently, land managers remove woody tree species in order to recover shrub-steppe although it is unclear how responses to these management activities differ due to site-specific conditions and existing woodland development. I studied post juniper-thinning responses in eastern Oregon at a wildlife area important as winter range for mule deer (Odocoileus hemionus). I investigated vegetative responses to western juniper (Juniperus occidentalis) thinning across a woodland development gradient and tested for interactive effects of juniper cutting and cattle exclusion. In addition, I explored plant and small mammal successional dynamics after juniper thinning and examined plant community responses within microhabitats created by the felled trees. I compared vegetative responses to juniper thinning as well as cattle exclusion among sites where juniper were subordinate (Phase I), co-dominant (Phase II), and dominant to shrubs and grasses (Phase III, sensu Miller et al. 2005). At the Phase I site, thinning did not increase herbaceous biomass while thinned plots at the Phase II site had 2.71 times more median herbaceous biomass (99.17% CI: 1.37 to 5.37 times more biomass) than unthinned plots. Conversely, herbaceous biomass at the Phase III juniper woodland site was 0.36 times lower in thinned plots when compared to unthinned plots (99.17% CI: 0.17 to 0.78 times less biomass). Unfortunately, many of the responses were driven by exotic species release. Where juniper were subordinate (Phase I), mean percent cover by exotic grass increased by 24.58 percentage points in thinned plots as compared to unthinned plots (98.30% CI: 0.27 to 48.90 percentage points higher). Thinning at the Phase II site increased mean exotic grass cover by an estimated 28.47 percentage points as compared to mean exotic cover in the same plots before treatment (98.30% CI: 4.15 to 52.79 percentage points higher cover). Median native bunchgrass cover at this site was 5.06 times greater after juniper treatment (99.7% CI: 1.78 to 14.35 times higher percent cover). I found few main or interactive effects of cattle exclosure after one year of treatment. Responses to grazing exclosure may take longer to develop. These results indicate that sites within the wildlife area respond differently to juniper management and that exotic grass control will be key to successful shrub-steppe recovery. In addition, I used a time-since-juniper thinning chronoseries consisting of plots cut in 2008, 2009, 2010, 2012, and an adjacent uncut control to explore how shrub-steppe flora and fauna are responding to juniper treatment through time. Shrub cover and seedling density were low in each plot. I recorded the highest seedling abundance (mean of 0.25 seedlings) in the uncut control plot. Median grass cover in the uncut control was 9.50% while in the most recently treated plot (2012) it was 26.75%. Small mammal relative abundance and diversity was low across all time-since-treatment plots though highest in the plot with the greatest time-since-treatment. Deer mouse (Peromyscus maniculatus) was the most abundant species in all plots and accounted for 70-95% of all unique captures. Least chipmunk (Tamias minimus) were present in the plot with greatest time-since-treatment indicating the potential recovery of key native shrubs since these small mammals perform an important seed dispersal role. I also investigated how potential microhabitats created by the felled juniper might support different plant communities. I assessed plant responses within zones created by 1) the felled tree (canopy zone), 2) the original duff zone, and 3) the between - tree interspace zone. The three zones had different plant community compositions as analyzed multivariately with non-metric multidimensional scaling (NMS). Canopy and duff zones were forb - dominated and had less exotic grass invasion while interspace zones were heavily invested with medusahead (Taeniatherum caput-medusae) and ventenata (Ventenata dubia). Exotic herbaceous productivity was lowest under the standing trees of the control plot and high in the interspace of all plots with juniper thinning. In the 2012 cut plot, grass cover was 27.90 percentage points less in the canopy zone compared to the interspace zone (98.75% CI: 17.64 to 38.16 percentage points less grass cover). In the uncut control, median native biomass was 2.08 times greater under the standing trees compared to the interspace (96.25% CI: 1.09 to 3.97 times more biomass). Results from the time-since-treatment chronoseries indicated that exotic grass dominance might be limiting shrub-steppe recovery. Active restoration of shrubs and native grasses may be necessary to address the dominance of exotic grass after juniper thinning. Positive signs of habitat recovery included small mammal responses though I was unable to calculate population estimates due to plot size. Close

• 18. [Article] A new model to simulate climate-change impacts on forest succession for local land management

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

  Citation × Citation Citation Abstract Copy Title: A new model to simulate climate-change impacts on forest succession for local land management Author: Bolte, John P., Bridgham, Scott D., Neilson, Ronald P., et al., Yospin, Gabriel I. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the Ecological Society of America and can be found at: http://www.esajournals.org/loi/ecap. Title: A new model to simulate climate-change impacts on forest succession for local land management Author: Bolte, John P., Bridgham, Scott D., Neilson, Ronald P., et al., Yospin, Gabriel I. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the Ecological Society of America and can be found at: http://www.esajournals.org/loi/ecap. Close

• 19. [Article] Examining ectomycorrhizal communities of ponderosa pine and lodgepole pine in the south-central Oregon pumice zone

  Background information is presented that provides historical perspectives on the field of mycology in the Pacific Northwest and its role in forest management. The series of events and decisions that have ...

  Citation × Citation Citation Abstract Copy Title: Examining ectomycorrhizal communities of ponderosa pine and lodgepole pine in the south-central Oregon pumice zone Author: Garcia, Maria Osuna Background information is presented that provides historical perspectives on the field of mycology in the Pacific Northwest and its role in forest management. The series of events and decisions that have led to previous studies (or lack of studies) in the field also dictate the directions of current research. Culture, philosophy, and history all play a role in the questions that may be asked today. Examining the past gives light to the questions that are asked in the present and future. Forest ecosystems of the Pacific Northwest are changing as a result of climate change. Rise of global temperatures, decline of winter precipitation, earlier loss of snowpack, and increased summer drought are altering the range of Pinus contorta. As environmental conditions change, Pinus ponderosa may establish within the historic Pinus contorta range. Successful pine species migration will be constrained by the distribution or co-migration of ectomycorrhizal fungi (EMF). Knowledge of the linkages among soil fungal diversity, community structure, and environmental factors is critical to understanding the organization and stability of pine ecosystems. The objectives of this study are to establish an informational foundation of the EMF communities of P. ponderosa and P. contorta in the Deschutes National Forest and to examine soil characteristics associated with community composition. We examined EMF root tips of P. ponderosa and P. contorta in soil cores and conducted soil chemistry analysis for P. ponderosa. Results indicate that Cenococcum geophilum, Rhizopogon salebrosus, and Inocybe flocculosa are dominant in both P. contorta and P. ponderosa soil cores. Rhizopogon spp. were ubiquitous in P. ponderosa. There was no significant difference between EMF communities of P. ponderosa and P. contorta at the species level. Ordination analysis suggests that pH, Bray-phosphorus, total phosphorus (P), carbon (C), mineralizable nitrogen (N), ammonium (NH₄) and nitrate (NO₃) are driving EMF community composition in P. ponderosa. We found a significant linear relationship between EMF species richness and mineralizable N. Title: Examining ectomycorrhizal communities of ponderosa pine and lodgepole pine in the south-central Oregon pumice zone Author: Garcia, Maria Osuna Background information is presented that provides historical perspectives on the field of mycology in the Pacific Northwest and its role in forest management. The series of events and decisions that have led to previous studies (or lack of studies) in the field also dictate the directions of current research. Culture, philosophy, and history all play a role in the questions that may be asked today. Examining the past gives light to the questions that are asked in the present and future. Forest ecosystems of the Pacific Northwest are changing as a result of climate change. Rise of global temperatures, decline of winter precipitation, earlier loss of snowpack, and increased summer drought are altering the range of Pinus contorta. As environmental conditions change, Pinus ponderosa may establish within the historic Pinus contorta range. Successful pine species migration will be constrained by the distribution or co-migration of ectomycorrhizal fungi (EMF). Knowledge of the linkages among soil fungal diversity, community structure, and environmental factors is critical to understanding the organization and stability of pine ecosystems. The objectives of this study are to establish an informational foundation of the EMF communities of P. ponderosa and P. contorta in the Deschutes National Forest and to examine soil characteristics associated with community composition. We examined EMF root tips of P. ponderosa and P. contorta in soil cores and conducted soil chemistry analysis for P. ponderosa. Results indicate that Cenococcum geophilum, Rhizopogon salebrosus, and Inocybe flocculosa are dominant in both P. contorta and P. ponderosa soil cores. Rhizopogon spp. were ubiquitous in P. ponderosa. There was no significant difference between EMF communities of P. ponderosa and P. contorta at the species level. Ordination analysis suggests that pH, Bray-phosphorus, total phosphorus (P), carbon (C), mineralizable nitrogen (N), ammonium (NH₄) and nitrate (NO₃) are driving EMF community composition in P. ponderosa. We found a significant linear relationship between EMF species richness and mineralizable N. Close

• 20. [Article] Variability in mesoscale circulation and its effects on zooplankton distribution in the Northern California Current

  In eastern boundary current upwelling ecosystems, mesoscale circulation features such as eddies and upwelling filaments play a prominent role in the transfer of water and the associated plankton from the ...

  Citation × Citation Citation Abstract Copy Title: Variability in mesoscale circulation and its effects on zooplankton distribution in the Northern California Current Author: Keister, Julie Eileen In eastern boundary current upwelling ecosystems, mesoscale circulation features such as eddies and upwelling filaments play a prominent role in the transfer of water and the associated plankton from the productive nearshore to the oligotrophic deep sea. The relationship between mesoscale circulation, zooplankton distributions, and the across-shelf transport of coastal taxa and biomass in the California Current System was studied using data collected as part of the U.S. Global Ocean Ecosystems Dynamics (GLOBEC) Northeast Pacific Program. Sea surface height from >13 years of satellite altimeter data was used to characterize the spatial and temporal variability in mesoscale circulation in the northern California Current (35°N-49°N) and explore mechanisms of variability. High spatial and temporal variation in mesoscale energy occurred. Energy was not strongly linked to upwelling winds, but did correspond to climate indices, indicating that basin-scale processes play a role in controlling the circulation. CTD casts, zooplankton net tows, and Acoustic Doppler Current Profiler (ADCP) velocities collected during a research cruise conducted in summer 2000 off Oregon and northern California were used to describe the effects of mesoscale circulation on distributions of zooplankton. During the cruise, a filament of the coastal upwelling jet extended seaward of Cape Blanco (42.8°N) resulting in the displacement of coastal zooplankton to >100 km off the continental shelf. Velocities and standing stocks of zooplankton were used to estimate seaward transport of 0.5 Sv in the upper 100 m of the filament, in which zooplankton biomass averaged ~20 mg carbon/m³. That offshore transport equated to >900 metric tons of carbon each day, and 4-5x10⁴ tons over the 6-8 week lifetime of the circulation feature. Although the flux represented a small portion (<2%) of the shelf zooplankton biomass, the transport resulted in an offshore "hot-spot" in which biomass was 3-4X higher than in the surrounding ocean. Distributions of early life history stages of euphausiids indicated that retention of coastal populations may be strongly affected by the offshore advection. Finally, satellite sea surface temperature (SST) and sampling conducted during five summers were used to explore variability in the relationship between mesoscale circulation features and distributions of zooplankton. Circulation patterns differed among cruises and were reflected in zooplankton distributions. Circulation features resulted in the occurrence of cold surface water and coastal taxa offshore, but species abundances and presence/absence of taxa at specific locations were not predictable from satellite SSTs. These results are relevant to studies of ecosystem dynamics and the global carbon cycle because mesoscale circulation plays an important role in the seaward transport of carbon, retention and loss of taxa from the continental shelf, and creation of offshore structure which may be exploited by upper trophic level organisms. Title: Variability in mesoscale circulation and its effects on zooplankton distribution in the Northern California Current Author: Keister, Julie Eileen In eastern boundary current upwelling ecosystems, mesoscale circulation features such as eddies and upwelling filaments play a prominent role in the transfer of water and the associated plankton from the productive nearshore to the oligotrophic deep sea. The relationship between mesoscale circulation, zooplankton distributions, and the across-shelf transport of coastal taxa and biomass in the California Current System was studied using data collected as part of the U.S. Global Ocean Ecosystems Dynamics (GLOBEC) Northeast Pacific Program. Sea surface height from >13 years of satellite altimeter data was used to characterize the spatial and temporal variability in mesoscale circulation in the northern California Current (35°N-49°N) and explore mechanisms of variability. High spatial and temporal variation in mesoscale energy occurred. Energy was not strongly linked to upwelling winds, but did correspond to climate indices, indicating that basin-scale processes play a role in controlling the circulation. CTD casts, zooplankton net tows, and Acoustic Doppler Current Profiler (ADCP) velocities collected during a research cruise conducted in summer 2000 off Oregon and northern California were used to describe the effects of mesoscale circulation on distributions of zooplankton. During the cruise, a filament of the coastal upwelling jet extended seaward of Cape Blanco (42.8°N) resulting in the displacement of coastal zooplankton to >100 km off the continental shelf. Velocities and standing stocks of zooplankton were used to estimate seaward transport of 0.5 Sv in the upper 100 m of the filament, in which zooplankton biomass averaged ~20 mg carbon/m³. That offshore transport equated to >900 metric tons of carbon each day, and 4-5x10⁴ tons over the 6-8 week lifetime of the circulation feature. Although the flux represented a small portion (<2%) of the shelf zooplankton biomass, the transport resulted in an offshore "hot-spot" in which biomass was 3-4X higher than in the surrounding ocean. Distributions of early life history stages of euphausiids indicated that retention of coastal populations may be strongly affected by the offshore advection. Finally, satellite sea surface temperature (SST) and sampling conducted during five summers were used to explore variability in the relationship between mesoscale circulation features and distributions of zooplankton. Circulation patterns differed among cruises and were reflected in zooplankton distributions. Circulation features resulted in the occurrence of cold surface water and coastal taxa offshore, but species abundances and presence/absence of taxa at specific locations were not predictable from satellite SSTs. These results are relevant to studies of ecosystem dynamics and the global carbon cycle because mesoscale circulation plays an important role in the seaward transport of carbon, retention and loss of taxa from the continental shelf, and creation of offshore structure which may be exploited by upper trophic level organisms. Close