Fine sediments in excess of natural background conditions are one of most globally common causes ... more Fine sediments in excess of natural background conditions are one of most globally common causes of stream degradation, with well documented impacts on aquatic communities. The lack of agreement on methods for monitoring fine sediments makes it difficult to share data, limiting assessments of stream conditions across jurisdictions. We present a model that circumvents these limitations by inferring fine sediments in Oregon streams through sampling of macroinvertebrates. Tolerances to fine sediments (<0.06 mm diameter) were calculated for 240 macroinvertebrate taxa, from a calibration dataset of 446 sites across Oregon, as well as an independent validation dataset of 50 samples. Weighted averaging methods were used to infer fine sediment levels in streams by weighting the tolerances of modeled taxa observed in a sample by their abundances. The final model, the Biological Sediment Tolerance Index (BSTI), showed a strong relationship to measured fine sediments (calibration r 2 = 0.49, validation r 2 = 0.58). Rootmean-squared-error was small in the calibration dataset (2% fines), but larger in the validation dataset (14% fines). Repeatability was assessed by examining variability in BSTI at 14 sites across Oregon. Because field methods for sampling macroinvertebrates are standardized across resource agencies in Oregon and the responses of macroinvertebrates represent the actual effects of fine sediments on stream ecosystems, the BSTI may offer water resource managers' a cost-effective method for assessing fine sediment conditions in their ongoing efforts to improve water quality across the state.
Recent acoustic tagging of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the southern por... more Recent acoustic tagging of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the southern portion of California's Sacramento-San Joaquin Delta has revealed extremely low survival rates (<1%), possibly due to predation by piscivorous fishes. We evaluated predation as a cause of low survival by designing and testing freely floating GPSenabled predation-event recorders (PERs) baited with juvenile Chinook salmon. We estimated predation rates and identified predation locations within a 1-kilometer reach of the Lower San Joaquin River. We modeled the relationship between time to predation and environmental variables with a Cox proportional hazards analysis that accounts for censored data. Our results indicated that an increase of 1 m/s in water velocity elevated the minute-by-minute hazard of predation by a factor of 9.6. Similarly, each increase in median depth decreased the predation hazard by a factor of 0.5. The mean relative predation rate in the study area was 15.3% over 9 sampling events between March and May 2014. Waterproof video cameras attached to a subset (48 of 216) of PERs successfully identified predator species 25% of the time. Our GPS-enabled PERs proved to be an inexpensive and reliable tool, which quantified predation, identified predation locations, and provided complementary information for acoustic telemetry and predator diet studies.
Invasive mammals on islands pose severe, ongoing threats to global biodiversity. However, the sev... more Invasive mammals on islands pose severe, ongoing threats to global biodiversity. However, the severity of threats from different mammals, and the role of interacting biotic and abiotic factors in driving extinctions, remain poorly understood at a global scale. Here we model global extirpation patterns for island populations of threatened and extinct vertebrates. Extirpations are driven by interacting factors including invasive rats, cats, pigs, mustelids and mongooses, native species taxonomic class and volancy, island size, precipitation and human presence. We show that controlling or eradicating the relevant invasive mammals could prevent 41–75% of predicted future extirpations. The magnitude of benefits varies across species and environments; for example, managing invasive mammals on small, dry islands could halve the extirpation risk for highly threatened birds and mammals, while doing so on large, wet islands may have little benefit. Our results provide quantitative estimates of conservation benefits and, when combined with costs in a return-on-investment framework, can guide efficient conservation strategies.
Integrated Environmental Assessment and Management, 2010
Data from 7 coastwide and regional benthic surveys were combined and used to assess the number an... more Data from 7 coastwide and regional benthic surveys were combined and used to assess the number and distribution of estuarine benthic macrofaunal assemblages of the western United States. Q-mode cluster analysis was applied to 714 samples and site groupings were tested for differences in 4 habitat factors (latitude, salinity, sediment grain size, and depth). Eight macrofaunal assemblages, structured primarily by latitude, salinity, and sediment grain size, were identified: (A) Puget Sound fine sediment, (B) Puget Sound coarse sediment, (C) southern California marine bays, (D) polyhaline central San Francisco Bay, (E) shallow estuaries and wetlands, (F) saline very coarse sediment, (G) mesohaline San Francisco Bay, and (H) limnetic and oligohaline. The Puget Sound, southern California, and San Francisco Bay assemblages were geographically distinct, while Assemblages E, F and H were distributed widely along the entire coast. A second Q-mode cluster analysis was conducted after adding replicate samples that were available from some of the sites and temporal replicates that were available for sites that were sampled in successive years. Variabilities due to small spatial scale habitat heterogeneity and temporal change were both low in Puget Sound, but temporal variability was high in the San Francisco estuary where large fluctuations in freshwater inputs and salinity among years leads to spatial relocation of the assemblages. Integr Environ Assess Manag 2012;8:638-648. ß 2010 SETAC Keywords: Habitat-related benthic assemblages US west coast bays estuaries Integrated Environmental Assessment and Management -Volume 8, Number 4-pp. 638-648 638 ß 2010 SETAC
Many types of indices have been developed to assess benthic invertebrate community condition, but... more Many types of indices have been developed to assess benthic invertebrate community condition, but there have been few studies evaluating the relative performance of different index approaches. Here we calibrate and compare the performance of five indices: the Benthic Response Index (BRI), Benthic Quality Index (BQI), Relative Benthic Index (RBI), River Invertebrate Prediction and Classification System (RIVPACS), and the Index of Biotic Integrity (IBI). We also examine whether index performance improves when the different indices, which rely on measurement of different properties, are used in combination. The five indices were calibrated for two geographies using 238 samples from southern California marine bays and 125 samples from polyhaline San Francisco Bay. Index performance was evaluated by comparing index assessments of 35 sites to the best professional judgment of nine benthic experts. None of the individual indices performed as well as the average expert in ranking sample condition or evaluating whether benthic assemblages exhibited evidence of disturbance. However, several index combinations outperformed the average expert. When results from both habitats were combined, two four-index combinations and a three-index combination performed best. However, performance differences among several combinations were small enough that factors such as logistics can also become a consideration in index selection.
Integrated Environmental Assessment and Management, 2011
Data from 7 coastwide and regional benthic surveys were combined and used to assess the number an... more Data from 7 coastwide and regional benthic surveys were combined and used to assess the number and distribution of estuarine benthic macrofaunal assemblages of the western United States. Q-mode cluster analysis was applied to 714 samples and site groupings were tested for differences in 4 habitat factors (latitude, salinity, sediment grain size, and depth). Eight macrofaunal assemblages, structured primarily by latitude, salinity, and sediment grain size, were identified: (A) Puget Sound fine sediment, (B) Puget Sound coarse sediment, (C) southern California marine bays, (D) polyhaline central San Francisco Bay, (E) shallow estuaries and wetlands, (F) saline very coarse sediment, (G) mesohaline San Francisco Bay, and (H) limnetic and oligohaline. The Puget Sound, southern California, and San Francisco Bay assemblages were geographically distinct, while Assemblages E, F and H were distributed widely along the entire coast. A second Q-mode cluster analysis was conducted after adding replicate samples that were available from some of the sites and temporal replicates that were available for sites that were sampled in successive years. Variabilities due to small spatial scale habitat heterogeneity and temporal change were both low in Puget Sound, but temporal variability was high in the San Francisco estuary where large fluctuations in freshwater inputs and salinity among years leads to spatial relocation of the assemblages. Integr Environ Assess Manag 2012;8:638-648. ß 2010 SETAC Keywords: Habitat-related benthic assemblages US west coast bays estuaries Integrated Environmental Assessment and Management -Volume 8, Number 4-pp. 638-648 638 ß 2010 SETAC
Fine sediments in excess of natural background conditions are one of most globally common causes ... more Fine sediments in excess of natural background conditions are one of most globally common causes of stream degradation, with well documented impacts on aquatic communities. The lack of agreement on methods for monitoring fine sediments makes it difficult to share data, limiting assessments of stream conditions across jurisdictions. We present a model that circumvents these limitations by inferring fine sediments in Oregon streams through sampling of macroinvertebrates. Tolerances to fine sediments (<0.06 mm diameter) were calculated for 240 macroinvertebrate taxa, from a calibration dataset of 446 sites across Oregon, as well as an independent validation dataset of 50 samples. Weighted averaging methods were used to infer fine sediment levels in streams by weighting the tolerances of modeled taxa observed in a sample by their abundances. The final model, the Biological Sediment Tolerance Index (BSTI), showed a strong relationship to measured fine sediments (calibration r 2 = 0.49, validation r 2 = 0.58). Rootmean-squared-error was small in the calibration dataset (2% fines), but larger in the validation dataset (14% fines). Repeatability was assessed by examining variability in BSTI at 14 sites across Oregon. Because field methods for sampling macroinvertebrates are standardized across resource agencies in Oregon and the responses of macroinvertebrates represent the actual effects of fine sediments on stream ecosystems, the BSTI may offer water resource managers' a cost-effective method for assessing fine sediment conditions in their ongoing efforts to improve water quality across the state.
A fully coupled ecosystem model is used to identify the effects of environmental conditions and u... more A fully coupled ecosystem model is used to identify the effects of environmental conditions and upwelling variability on growth of juvenile Chinook salmon in central California coastal waters. The ecosystem model framework consists of an ocean circulation submodel, a biogeochemical submodel, and an individual-based submodel for salmon. Simulation results indicate that years favorable for juvenile salmon growth off central California are characterized by particularly intense early season upwelling (i.e., March through May), leading to enhanced krill concentrations during summer near the location of ocean entry (i.e., Gulf of the Farallones). Seasonally averaged growth rates in the model are generally consistent with observed values and suggest that juvenile salmon emigrating later in the season (i.e., late May and June) achieve higher weight gains during their first 90 days of ocean residency.
Recent acoustic tagging of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the southern por... more Recent acoustic tagging of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the southern portion of California's Sacramento-San Joaquin Delta has revealed extremely low survival rates (<1%), possibly due to predation by piscivorous fishes. We evaluated predation as a cause of low survival by designing and testing freely floating GPSenabled predation-event recorders (PERs) baited with juvenile Chinook salmon. We estimated predation rates and identified predation locations within a 1-kilometer reach of the Lower San Joaquin River. We modeled the relationship between time to predation and environmental variables with a Cox proportional hazards analysis that accounts for censored data. Our results indicated that an increase of 1 m/s in water velocity elevated the minute-by-minute hazard of predation by a factor of 9.6. Similarly, each increase in median depth decreased the predation hazard by a factor of 0.5. The mean relative predation rate in the study area was 15.3% over 9 sampling events between March and May 2014. Waterproof video cameras attached to a subset (48 of 216) of PERs successfully identified predator species 25% of the time. Our GPS-enabled PERs proved to be an inexpensive and reliable tool, which quantified predation, identified predation locations, and provided complementary information for acoustic telemetry and predator diet studies.
Extreme variability in abundance of California salmon populations is often ascribed to ocean cond... more Extreme variability in abundance of California salmon populations is often ascribed to ocean conditions, yet relatively little is known about their marine life history. To investigate which ocean conditions influence their distribution and abundance, we surveyed juvenile Chinook salmon (Oncorhynchus tshawytscha) within the California Current (central California [37°30 0 N) to Newport, Oregon (44°00 0 N]) for a 2-week period over three summers (2010–2012). At each station, we measured chlorophyll-a as an indicator of primary productivity , acoustic-based metrics of zooplankton density as an indicator of potential prey availability and physical characteristics such as bottom depth, temperature and salinity. We also measured fork lengths and collected genetic samples from each salmon that was caught. Genetic stock identification revealed that the majority of juvenile salmon were from the Central Valley and the Klamath Basin (91–98%). We constructed generalized logistic-linear negative binomial hurdle models and chose the best model(s) using Akaike's Information Criterion (AIC) to determine which covariates influenced the salmon presence and, at locations where salmon were present, determined the variables that influenced their abundance. The probability of salmon presence was highest in shallower waters with a high chlorophyll-a concentration and close to an individual's natal river. Catch abundance was primarily influenced by year, mean fork length and proximity to natal rivers. At the scale of sampling stations, presence and abundance were not related to acoustic indices of zooplankton density. In the weeks to months after ocean entry, California's juvenile Chinook salmon population appears to be primarily constrained to coastal waters near natal river outlets.
We review the suite of biophysical factors in the Northeast Pacific Ocean basin and California Cu... more We review the suite of biophysical factors in the Northeast Pacific Ocean basin and California Current shelf ecosystem that directly or indirectly relate to central California Chinook salmon Oncorhynchus tshawytscha growth and survival upon ocean entry, a critical life-history period for this population. Our synthesis provides a framework for integrating ecosystem process studies with empirical hypothesis testing to benefit fisheries management. Our hypothesis includes seasonality (phenology) as a key element of early salmon growth and survival. The strength and location of the North Pacific High (NPH) pressure system in winter influences salmon growth and survival via 'bottom-up' productivity and retention of key prey (euphausiid crustaceans and juvenile rockfishes Sebastes spp.) in nearshore habitats prior to and during salmon emigration to sea in spring. Prey retention, which is associated with increased consumption of krill and juvenile rockfishes, and is positively correlated with juvenile salmon body condition and ocean survival, appears to set cohort strength and return rates. We examined these mechanistic relationships by reviewing the results of a biophysical model coupled to an individual-based model for salmon. Our review results in a final hypothesis stating that early salmon growth and survival are positively related to intensity of early season upwelling, and associated (forage) nekton production and retention on the shelf during spring and summer.
Reintroductions are commonly employed to preserve intraspecific biodiversity in fragmented landsc... more Reintroductions are commonly employed to preserve intraspecific biodiversity in fragmented landscapes. However, reintroduced populations are frequently smaller and more geographically isolated than native populations. Mixing genetically, divergent sources are often proposed to attenuate potentially low genetic diversity in reintroduced populations that may result from small effective population sizes. However, a possible negative tradeoff for mixing sources is outbreeding depression in hybrid offspring. We examined the consequences of mixed-source reintroductions on several fitness surrogates at nine slimy sculpin (Cottus cognatus) reintroduction sites in south-east Minnesota. We inferred the relative fitness of each crosstype in the reintroduced populations by comparing their growth rate, length, weight, body condition and persistence in reintroduced populations. Pure strain descendents from a single source population persisted in a greater proportion than expected in the reintroduced populations, whereas all other crosstypes occurred in a lesser proportion. Length, weight and growth rate were lower for second-generation intra-population hybrid descendents than for pure strain and first-generation hybrids. In the predominant pure strain, young-of the-year size was significantly greater than any other crosstype. Our results suggested that differences in fitness surrogates among crosstypes were consistent with disrupted co-adapted gene complexes associated with beneficial adaptations in these reintroduced populations. Future reintroductions may be improved by evaluating the potential for local adaptation in source populations or by avoiding the use of mixed sources by default when information on local adaptations or other genetic characteristics is lacking.
An understanding of population-level adaptations to local conditions may be critical for the effe... more An understanding of population-level adaptations to local conditions may be critical for the effective conservation and management of struggling species. However, local adaptations may be difficult to detect without conducting experiments because there are few predictable patterns in their occurrence and because phenotypic plasticity may confound determination of a genetic basis for a trait. Mixed-source reintroductions provide an opportunity to study local adaptations because potentially divergent strains are grown under identical conditions. We identified local adaptations in two strains of reintroduced fish by simulating a reciprocal transplant experiment. We developed strain-specific regression models from multiple common-garden configurations that were represented by the reintroductions sites. Fitness response predictions from these regressions, based on source habitats, indicated divergent local adaptations in each strain through differential responses to habitat features amon...
A fully coupled ecosystem model is used to identify the effects of environmental conditions and u... more A fully coupled ecosystem model is used to identify the effects of environmental conditions and upwelling variability on growth of juvenile Chinook salmon in central California coastal waters. The ecosystem model framework consists of an ocean circulation submodel, a biogeochemical submodel, and an individual-based submodel for salmon. Simulation results indicate that years favorable for juvenile salmon growth off central California are characterized by particularly intense early season upwelling (i.e., March through May), leading to enhanced krill concentrations during summer near the location of ocean entry (i.e., Gulf of the Farallones). Seasonally averaged growth rates in the model are generally consistent with observed values and suggest that juvenile salmon emigrating later in the season (i.e., late May and June) achieve higher weight gains during their first 90 days of ocean residency.
Transactions of the American Fisheries Society, 2004
The roles of temperature and ultraviolet radiation (UVR) in determining the spawning success of y... more The roles of temperature and ultraviolet radiation (UVR) in determining the spawning success of yellow perch Perca flavescens were investigated in two Pennsylvania lakes with different dissolved organic carbon (DOC) concentrations. In situ incubation experiments were used to manipulate temperature and UVR and to examine hatching time and hatching success. Extensive scuba surveys were used to document actual spawning depths. Differences in the temperature and UVR profiles of the two lakes led to contrasting responses of incubated yellow perch eggs. Higher temperatures in the surface waters of the higher-DOC lake led to hatching times that were 10-26 d shorter than those in the surface waters of the low-DOC lake or in the deeper waters of the higher-DOC lake. The high levels of UVR in the surface waters of the low-DOC lake killed 100% of the eggs before hatching. Ultraviolet radiation had little effect on survival in the higher-DOC lake or in deeper waters of the low-DOC lake. Scuba surveys revealed that spawning in the low-DOC lake occurred at greater depths than previously recognized. Ninety-two percent of the eggs spawned in the low-DOC lake were located at depths greater than 3 m, while 76% of eggs in the higher-DOC lake were spawned in water less than 1 m deep. Temperature and UVR are both important in determining among-lake differences in spawning depths of yellow perch. Yellow perch are able to spawn at shallow depths in higher-DOC lakes, where warmer temperatures accelerate developmental rates and DOC blocks potentially damaging UVR. In low-DOC lakes, yellow perch must spawn at greater depths to avoid UVR damage. Spawning at greater depths may be costly due to the substantially slower developmental rates at lower temperatures. Our data suggest that the conflicting selective pressures of UVR and temperature create an optimal spawningdepth range for yellow perch that differs among lakes as a function of DOC concentration.
The green sturgeon (Acipenser medirostris), which is found in the eastern Pacific Ocean from Baja... more The green sturgeon (Acipenser medirostris), which is found in the eastern Pacific Ocean from Baja California to the Bering Sea, tends to be highly migratory, moving long distances among estuaries, spawning rivers, and distant coastal regions. Factors that determine the oceanic distribution of green sturgeon are unclear, but broad-scale physical conditions interacting with migration behavior may play an important role. We estimated the distribution of green sturgeon by modeling species-environment relationships using oceanographic and migration behavior covariates with maximum entropy modeling (MaxEnt) of species geographic distributions. The primary concentration of green sturgeon was estimated from approximately 41-51.5u N latitude in the coastal waters of Washington, Oregon, and Vancouver Island and in the vicinity of San Francisco and Monterey Bays from 36-37u N latitude. Unsuitably cold water temperatures in the far north and energetic efficiencies associated with prevailing water currents may provide the best explanation for the rangewide marine distribution of green sturgeon. Independent trawl records, fisheries observer records, and tagging studies corroborated our findings. However, our model also delineated patchily distributed habitat south of Monterey Bay, though there are few records of green sturgeon from this region. Green sturgeon are likely influenced by countervailing pressures governing their dispersal. They are behaviorally directed to revisit natal freshwater spawning rivers and persistent overwintering grounds in coastal marine habitats, yet they are likely physiologically bounded by abiotic and biotic environmental features. Impacts of human activities on green sturgeon or their habitat in coastal waters, such as bottomdisturbing trawl fisheries, may be minimized through marine spatial planning that makes use of high-quality species distribution information.
The green sturgeon (Acipenser medirostris) is a highly migratory, oceanic, anadromous species wit... more The green sturgeon (Acipenser medirostris) is a highly migratory, oceanic, anadromous species with a complex life history that makes it vulnerable to species-wide threats in both freshwater and at sea. Green sturgeon population declines have preceded legal protection and curtailment of activities in marine environments deemed to increase its extinction risk. Yet, its marine habitat is poorly understood. We built a statistical model to characterize green sturgeon marine habitat using data from a coastal tracking array located along the Siletz Reef near Newport, Oregon, USA that recorded the passage of 37 acoustically tagged green sturgeon. We classified seafloor physical habitat features with high-resolution bathymetric and backscatter data. We then described the distribution of habitat components and their relationship to green sturgeon presence using ordination and subsequently used generalized linear model selection to identify important habitat components. Finally, we summarized depth and temperature recordings from seven green sturgeon present off the Oregon coast that were fitted with pop-off archival geolocation tags. Our analyses indicated that green sturgeon, on average, spent a longer duration in areas with high seafloor complexity, especially where a greater proportion of the substrate consists of boulders. Green sturgeon in marine habitats are primarily found at depths of 20-60 meters and from 9.5-16.0uC. Many sturgeon in this study were likely migrating in a northward direction, moving deeper, and may have been using complex seafloor habitat because it coincides with the distribution of benthic prey taxa or provides refuge from predators. Identifying important green sturgeon marine habitat is an essential step towards accurately defining the conditions that are necessary for its survival and will eventually yield range-wide, spatially explicit predictions of green sturgeon distribution.
Fine sediments in excess of natural background conditions are one of most globally common causes ... more Fine sediments in excess of natural background conditions are one of most globally common causes of stream degradation, with well documented impacts on aquatic communities. The lack of agreement on methods for monitoring fine sediments makes it difficult to share data, limiting assessments of stream conditions across jurisdictions. We present a model that circumvents these limitations by inferring fine sediments in Oregon streams through sampling of macroinvertebrates. Tolerances to fine sediments (<0.06 mm diameter) were calculated for 240 macroinvertebrate taxa, from a calibration dataset of 446 sites across Oregon, as well as an independent validation dataset of 50 samples. Weighted averaging methods were used to infer fine sediment levels in streams by weighting the tolerances of modeled taxa observed in a sample by their abundances. The final model, the Biological Sediment Tolerance Index (BSTI), showed a strong relationship to measured fine sediments (calibration r 2 = 0.49, validation r 2 = 0.58). Rootmean-squared-error was small in the calibration dataset (2% fines), but larger in the validation dataset (14% fines). Repeatability was assessed by examining variability in BSTI at 14 sites across Oregon. Because field methods for sampling macroinvertebrates are standardized across resource agencies in Oregon and the responses of macroinvertebrates represent the actual effects of fine sediments on stream ecosystems, the BSTI may offer water resource managers' a cost-effective method for assessing fine sediment conditions in their ongoing efforts to improve water quality across the state.
Recent acoustic tagging of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the southern por... more Recent acoustic tagging of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the southern portion of California's Sacramento-San Joaquin Delta has revealed extremely low survival rates (<1%), possibly due to predation by piscivorous fishes. We evaluated predation as a cause of low survival by designing and testing freely floating GPSenabled predation-event recorders (PERs) baited with juvenile Chinook salmon. We estimated predation rates and identified predation locations within a 1-kilometer reach of the Lower San Joaquin River. We modeled the relationship between time to predation and environmental variables with a Cox proportional hazards analysis that accounts for censored data. Our results indicated that an increase of 1 m/s in water velocity elevated the minute-by-minute hazard of predation by a factor of 9.6. Similarly, each increase in median depth decreased the predation hazard by a factor of 0.5. The mean relative predation rate in the study area was 15.3% over 9 sampling events between March and May 2014. Waterproof video cameras attached to a subset (48 of 216) of PERs successfully identified predator species 25% of the time. Our GPS-enabled PERs proved to be an inexpensive and reliable tool, which quantified predation, identified predation locations, and provided complementary information for acoustic telemetry and predator diet studies.
Invasive mammals on islands pose severe, ongoing threats to global biodiversity. However, the sev... more Invasive mammals on islands pose severe, ongoing threats to global biodiversity. However, the severity of threats from different mammals, and the role of interacting biotic and abiotic factors in driving extinctions, remain poorly understood at a global scale. Here we model global extirpation patterns for island populations of threatened and extinct vertebrates. Extirpations are driven by interacting factors including invasive rats, cats, pigs, mustelids and mongooses, native species taxonomic class and volancy, island size, precipitation and human presence. We show that controlling or eradicating the relevant invasive mammals could prevent 41–75% of predicted future extirpations. The magnitude of benefits varies across species and environments; for example, managing invasive mammals on small, dry islands could halve the extirpation risk for highly threatened birds and mammals, while doing so on large, wet islands may have little benefit. Our results provide quantitative estimates of conservation benefits and, when combined with costs in a return-on-investment framework, can guide efficient conservation strategies.
Integrated Environmental Assessment and Management, 2010
Data from 7 coastwide and regional benthic surveys were combined and used to assess the number an... more Data from 7 coastwide and regional benthic surveys were combined and used to assess the number and distribution of estuarine benthic macrofaunal assemblages of the western United States. Q-mode cluster analysis was applied to 714 samples and site groupings were tested for differences in 4 habitat factors (latitude, salinity, sediment grain size, and depth). Eight macrofaunal assemblages, structured primarily by latitude, salinity, and sediment grain size, were identified: (A) Puget Sound fine sediment, (B) Puget Sound coarse sediment, (C) southern California marine bays, (D) polyhaline central San Francisco Bay, (E) shallow estuaries and wetlands, (F) saline very coarse sediment, (G) mesohaline San Francisco Bay, and (H) limnetic and oligohaline. The Puget Sound, southern California, and San Francisco Bay assemblages were geographically distinct, while Assemblages E, F and H were distributed widely along the entire coast. A second Q-mode cluster analysis was conducted after adding replicate samples that were available from some of the sites and temporal replicates that were available for sites that were sampled in successive years. Variabilities due to small spatial scale habitat heterogeneity and temporal change were both low in Puget Sound, but temporal variability was high in the San Francisco estuary where large fluctuations in freshwater inputs and salinity among years leads to spatial relocation of the assemblages. Integr Environ Assess Manag 2012;8:638-648. ß 2010 SETAC Keywords: Habitat-related benthic assemblages US west coast bays estuaries Integrated Environmental Assessment and Management -Volume 8, Number 4-pp. 638-648 638 ß 2010 SETAC
Many types of indices have been developed to assess benthic invertebrate community condition, but... more Many types of indices have been developed to assess benthic invertebrate community condition, but there have been few studies evaluating the relative performance of different index approaches. Here we calibrate and compare the performance of five indices: the Benthic Response Index (BRI), Benthic Quality Index (BQI), Relative Benthic Index (RBI), River Invertebrate Prediction and Classification System (RIVPACS), and the Index of Biotic Integrity (IBI). We also examine whether index performance improves when the different indices, which rely on measurement of different properties, are used in combination. The five indices were calibrated for two geographies using 238 samples from southern California marine bays and 125 samples from polyhaline San Francisco Bay. Index performance was evaluated by comparing index assessments of 35 sites to the best professional judgment of nine benthic experts. None of the individual indices performed as well as the average expert in ranking sample condition or evaluating whether benthic assemblages exhibited evidence of disturbance. However, several index combinations outperformed the average expert. When results from both habitats were combined, two four-index combinations and a three-index combination performed best. However, performance differences among several combinations were small enough that factors such as logistics can also become a consideration in index selection.
Integrated Environmental Assessment and Management, 2011
Data from 7 coastwide and regional benthic surveys were combined and used to assess the number an... more Data from 7 coastwide and regional benthic surveys were combined and used to assess the number and distribution of estuarine benthic macrofaunal assemblages of the western United States. Q-mode cluster analysis was applied to 714 samples and site groupings were tested for differences in 4 habitat factors (latitude, salinity, sediment grain size, and depth). Eight macrofaunal assemblages, structured primarily by latitude, salinity, and sediment grain size, were identified: (A) Puget Sound fine sediment, (B) Puget Sound coarse sediment, (C) southern California marine bays, (D) polyhaline central San Francisco Bay, (E) shallow estuaries and wetlands, (F) saline very coarse sediment, (G) mesohaline San Francisco Bay, and (H) limnetic and oligohaline. The Puget Sound, southern California, and San Francisco Bay assemblages were geographically distinct, while Assemblages E, F and H were distributed widely along the entire coast. A second Q-mode cluster analysis was conducted after adding replicate samples that were available from some of the sites and temporal replicates that were available for sites that were sampled in successive years. Variabilities due to small spatial scale habitat heterogeneity and temporal change were both low in Puget Sound, but temporal variability was high in the San Francisco estuary where large fluctuations in freshwater inputs and salinity among years leads to spatial relocation of the assemblages. Integr Environ Assess Manag 2012;8:638-648. ß 2010 SETAC Keywords: Habitat-related benthic assemblages US west coast bays estuaries Integrated Environmental Assessment and Management -Volume 8, Number 4-pp. 638-648 638 ß 2010 SETAC
Fine sediments in excess of natural background conditions are one of most globally common causes ... more Fine sediments in excess of natural background conditions are one of most globally common causes of stream degradation, with well documented impacts on aquatic communities. The lack of agreement on methods for monitoring fine sediments makes it difficult to share data, limiting assessments of stream conditions across jurisdictions. We present a model that circumvents these limitations by inferring fine sediments in Oregon streams through sampling of macroinvertebrates. Tolerances to fine sediments (<0.06 mm diameter) were calculated for 240 macroinvertebrate taxa, from a calibration dataset of 446 sites across Oregon, as well as an independent validation dataset of 50 samples. Weighted averaging methods were used to infer fine sediment levels in streams by weighting the tolerances of modeled taxa observed in a sample by their abundances. The final model, the Biological Sediment Tolerance Index (BSTI), showed a strong relationship to measured fine sediments (calibration r 2 = 0.49, validation r 2 = 0.58). Rootmean-squared-error was small in the calibration dataset (2% fines), but larger in the validation dataset (14% fines). Repeatability was assessed by examining variability in BSTI at 14 sites across Oregon. Because field methods for sampling macroinvertebrates are standardized across resource agencies in Oregon and the responses of macroinvertebrates represent the actual effects of fine sediments on stream ecosystems, the BSTI may offer water resource managers' a cost-effective method for assessing fine sediment conditions in their ongoing efforts to improve water quality across the state.
A fully coupled ecosystem model is used to identify the effects of environmental conditions and u... more A fully coupled ecosystem model is used to identify the effects of environmental conditions and upwelling variability on growth of juvenile Chinook salmon in central California coastal waters. The ecosystem model framework consists of an ocean circulation submodel, a biogeochemical submodel, and an individual-based submodel for salmon. Simulation results indicate that years favorable for juvenile salmon growth off central California are characterized by particularly intense early season upwelling (i.e., March through May), leading to enhanced krill concentrations during summer near the location of ocean entry (i.e., Gulf of the Farallones). Seasonally averaged growth rates in the model are generally consistent with observed values and suggest that juvenile salmon emigrating later in the season (i.e., late May and June) achieve higher weight gains during their first 90 days of ocean residency.
Recent acoustic tagging of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the southern por... more Recent acoustic tagging of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the southern portion of California's Sacramento-San Joaquin Delta has revealed extremely low survival rates (<1%), possibly due to predation by piscivorous fishes. We evaluated predation as a cause of low survival by designing and testing freely floating GPSenabled predation-event recorders (PERs) baited with juvenile Chinook salmon. We estimated predation rates and identified predation locations within a 1-kilometer reach of the Lower San Joaquin River. We modeled the relationship between time to predation and environmental variables with a Cox proportional hazards analysis that accounts for censored data. Our results indicated that an increase of 1 m/s in water velocity elevated the minute-by-minute hazard of predation by a factor of 9.6. Similarly, each increase in median depth decreased the predation hazard by a factor of 0.5. The mean relative predation rate in the study area was 15.3% over 9 sampling events between March and May 2014. Waterproof video cameras attached to a subset (48 of 216) of PERs successfully identified predator species 25% of the time. Our GPS-enabled PERs proved to be an inexpensive and reliable tool, which quantified predation, identified predation locations, and provided complementary information for acoustic telemetry and predator diet studies.
Extreme variability in abundance of California salmon populations is often ascribed to ocean cond... more Extreme variability in abundance of California salmon populations is often ascribed to ocean conditions, yet relatively little is known about their marine life history. To investigate which ocean conditions influence their distribution and abundance, we surveyed juvenile Chinook salmon (Oncorhynchus tshawytscha) within the California Current (central California [37°30 0 N) to Newport, Oregon (44°00 0 N]) for a 2-week period over three summers (2010–2012). At each station, we measured chlorophyll-a as an indicator of primary productivity , acoustic-based metrics of zooplankton density as an indicator of potential prey availability and physical characteristics such as bottom depth, temperature and salinity. We also measured fork lengths and collected genetic samples from each salmon that was caught. Genetic stock identification revealed that the majority of juvenile salmon were from the Central Valley and the Klamath Basin (91–98%). We constructed generalized logistic-linear negative binomial hurdle models and chose the best model(s) using Akaike's Information Criterion (AIC) to determine which covariates influenced the salmon presence and, at locations where salmon were present, determined the variables that influenced their abundance. The probability of salmon presence was highest in shallower waters with a high chlorophyll-a concentration and close to an individual's natal river. Catch abundance was primarily influenced by year, mean fork length and proximity to natal rivers. At the scale of sampling stations, presence and abundance were not related to acoustic indices of zooplankton density. In the weeks to months after ocean entry, California's juvenile Chinook salmon population appears to be primarily constrained to coastal waters near natal river outlets.
We review the suite of biophysical factors in the Northeast Pacific Ocean basin and California Cu... more We review the suite of biophysical factors in the Northeast Pacific Ocean basin and California Current shelf ecosystem that directly or indirectly relate to central California Chinook salmon Oncorhynchus tshawytscha growth and survival upon ocean entry, a critical life-history period for this population. Our synthesis provides a framework for integrating ecosystem process studies with empirical hypothesis testing to benefit fisheries management. Our hypothesis includes seasonality (phenology) as a key element of early salmon growth and survival. The strength and location of the North Pacific High (NPH) pressure system in winter influences salmon growth and survival via 'bottom-up' productivity and retention of key prey (euphausiid crustaceans and juvenile rockfishes Sebastes spp.) in nearshore habitats prior to and during salmon emigration to sea in spring. Prey retention, which is associated with increased consumption of krill and juvenile rockfishes, and is positively correlated with juvenile salmon body condition and ocean survival, appears to set cohort strength and return rates. We examined these mechanistic relationships by reviewing the results of a biophysical model coupled to an individual-based model for salmon. Our review results in a final hypothesis stating that early salmon growth and survival are positively related to intensity of early season upwelling, and associated (forage) nekton production and retention on the shelf during spring and summer.
Reintroductions are commonly employed to preserve intraspecific biodiversity in fragmented landsc... more Reintroductions are commonly employed to preserve intraspecific biodiversity in fragmented landscapes. However, reintroduced populations are frequently smaller and more geographically isolated than native populations. Mixing genetically, divergent sources are often proposed to attenuate potentially low genetic diversity in reintroduced populations that may result from small effective population sizes. However, a possible negative tradeoff for mixing sources is outbreeding depression in hybrid offspring. We examined the consequences of mixed-source reintroductions on several fitness surrogates at nine slimy sculpin (Cottus cognatus) reintroduction sites in south-east Minnesota. We inferred the relative fitness of each crosstype in the reintroduced populations by comparing their growth rate, length, weight, body condition and persistence in reintroduced populations. Pure strain descendents from a single source population persisted in a greater proportion than expected in the reintroduced populations, whereas all other crosstypes occurred in a lesser proportion. Length, weight and growth rate were lower for second-generation intra-population hybrid descendents than for pure strain and first-generation hybrids. In the predominant pure strain, young-of the-year size was significantly greater than any other crosstype. Our results suggested that differences in fitness surrogates among crosstypes were consistent with disrupted co-adapted gene complexes associated with beneficial adaptations in these reintroduced populations. Future reintroductions may be improved by evaluating the potential for local adaptation in source populations or by avoiding the use of mixed sources by default when information on local adaptations or other genetic characteristics is lacking.
An understanding of population-level adaptations to local conditions may be critical for the effe... more An understanding of population-level adaptations to local conditions may be critical for the effective conservation and management of struggling species. However, local adaptations may be difficult to detect without conducting experiments because there are few predictable patterns in their occurrence and because phenotypic plasticity may confound determination of a genetic basis for a trait. Mixed-source reintroductions provide an opportunity to study local adaptations because potentially divergent strains are grown under identical conditions. We identified local adaptations in two strains of reintroduced fish by simulating a reciprocal transplant experiment. We developed strain-specific regression models from multiple common-garden configurations that were represented by the reintroductions sites. Fitness response predictions from these regressions, based on source habitats, indicated divergent local adaptations in each strain through differential responses to habitat features amon...
A fully coupled ecosystem model is used to identify the effects of environmental conditions and u... more A fully coupled ecosystem model is used to identify the effects of environmental conditions and upwelling variability on growth of juvenile Chinook salmon in central California coastal waters. The ecosystem model framework consists of an ocean circulation submodel, a biogeochemical submodel, and an individual-based submodel for salmon. Simulation results indicate that years favorable for juvenile salmon growth off central California are characterized by particularly intense early season upwelling (i.e., March through May), leading to enhanced krill concentrations during summer near the location of ocean entry (i.e., Gulf of the Farallones). Seasonally averaged growth rates in the model are generally consistent with observed values and suggest that juvenile salmon emigrating later in the season (i.e., late May and June) achieve higher weight gains during their first 90 days of ocean residency.
Transactions of the American Fisheries Society, 2004
The roles of temperature and ultraviolet radiation (UVR) in determining the spawning success of y... more The roles of temperature and ultraviolet radiation (UVR) in determining the spawning success of yellow perch Perca flavescens were investigated in two Pennsylvania lakes with different dissolved organic carbon (DOC) concentrations. In situ incubation experiments were used to manipulate temperature and UVR and to examine hatching time and hatching success. Extensive scuba surveys were used to document actual spawning depths. Differences in the temperature and UVR profiles of the two lakes led to contrasting responses of incubated yellow perch eggs. Higher temperatures in the surface waters of the higher-DOC lake led to hatching times that were 10-26 d shorter than those in the surface waters of the low-DOC lake or in the deeper waters of the higher-DOC lake. The high levels of UVR in the surface waters of the low-DOC lake killed 100% of the eggs before hatching. Ultraviolet radiation had little effect on survival in the higher-DOC lake or in deeper waters of the low-DOC lake. Scuba surveys revealed that spawning in the low-DOC lake occurred at greater depths than previously recognized. Ninety-two percent of the eggs spawned in the low-DOC lake were located at depths greater than 3 m, while 76% of eggs in the higher-DOC lake were spawned in water less than 1 m deep. Temperature and UVR are both important in determining among-lake differences in spawning depths of yellow perch. Yellow perch are able to spawn at shallow depths in higher-DOC lakes, where warmer temperatures accelerate developmental rates and DOC blocks potentially damaging UVR. In low-DOC lakes, yellow perch must spawn at greater depths to avoid UVR damage. Spawning at greater depths may be costly due to the substantially slower developmental rates at lower temperatures. Our data suggest that the conflicting selective pressures of UVR and temperature create an optimal spawningdepth range for yellow perch that differs among lakes as a function of DOC concentration.
The green sturgeon (Acipenser medirostris), which is found in the eastern Pacific Ocean from Baja... more The green sturgeon (Acipenser medirostris), which is found in the eastern Pacific Ocean from Baja California to the Bering Sea, tends to be highly migratory, moving long distances among estuaries, spawning rivers, and distant coastal regions. Factors that determine the oceanic distribution of green sturgeon are unclear, but broad-scale physical conditions interacting with migration behavior may play an important role. We estimated the distribution of green sturgeon by modeling species-environment relationships using oceanographic and migration behavior covariates with maximum entropy modeling (MaxEnt) of species geographic distributions. The primary concentration of green sturgeon was estimated from approximately 41-51.5u N latitude in the coastal waters of Washington, Oregon, and Vancouver Island and in the vicinity of San Francisco and Monterey Bays from 36-37u N latitude. Unsuitably cold water temperatures in the far north and energetic efficiencies associated with prevailing water currents may provide the best explanation for the rangewide marine distribution of green sturgeon. Independent trawl records, fisheries observer records, and tagging studies corroborated our findings. However, our model also delineated patchily distributed habitat south of Monterey Bay, though there are few records of green sturgeon from this region. Green sturgeon are likely influenced by countervailing pressures governing their dispersal. They are behaviorally directed to revisit natal freshwater spawning rivers and persistent overwintering grounds in coastal marine habitats, yet they are likely physiologically bounded by abiotic and biotic environmental features. Impacts of human activities on green sturgeon or their habitat in coastal waters, such as bottomdisturbing trawl fisheries, may be minimized through marine spatial planning that makes use of high-quality species distribution information.
The green sturgeon (Acipenser medirostris) is a highly migratory, oceanic, anadromous species wit... more The green sturgeon (Acipenser medirostris) is a highly migratory, oceanic, anadromous species with a complex life history that makes it vulnerable to species-wide threats in both freshwater and at sea. Green sturgeon population declines have preceded legal protection and curtailment of activities in marine environments deemed to increase its extinction risk. Yet, its marine habitat is poorly understood. We built a statistical model to characterize green sturgeon marine habitat using data from a coastal tracking array located along the Siletz Reef near Newport, Oregon, USA that recorded the passage of 37 acoustically tagged green sturgeon. We classified seafloor physical habitat features with high-resolution bathymetric and backscatter data. We then described the distribution of habitat components and their relationship to green sturgeon presence using ordination and subsequently used generalized linear model selection to identify important habitat components. Finally, we summarized depth and temperature recordings from seven green sturgeon present off the Oregon coast that were fitted with pop-off archival geolocation tags. Our analyses indicated that green sturgeon, on average, spent a longer duration in areas with high seafloor complexity, especially where a greater proportion of the substrate consists of boulders. Green sturgeon in marine habitats are primarily found at depths of 20-60 meters and from 9.5-16.0uC. Many sturgeon in this study were likely migrating in a northward direction, moving deeper, and may have been using complex seafloor habitat because it coincides with the distribution of benthic prey taxa or provides refuge from predators. Identifying important green sturgeon marine habitat is an essential step towards accurately defining the conditions that are necessary for its survival and will eventually yield range-wide, spatially explicit predictions of green sturgeon distribution.
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