Geology topics

David D. Huff

Publications and source records attributed to David D. Huff.

10 recordsLinked to original sources

USGS2025

A comparison of deep-sea coral and sponge species distribution models and the impact of ocean currents in the Southern California Bight

Deep-sea corals and sponges (DSCS) are signature taxa of deep-water habitats, but ecological mechanisms that drive their geographic distributions can be difficult to uncover due to the challenges of surveying deep-water ecosystems and limited oceanographic data. A comparison of species distribution models was made for three DSCS ( Antipathes dendochristos, Plumarella longispina, and an unidentified sponge morphotype known as Porifera #2), two of which are associated with young-of-the-year and adult rockfish taxa ( Sebastes spp.). Models were built using generalized additive models (GAMs) that accounted for spatial autocorrelation. These models were compared to Maxent models, a commonly used method. All models utilized bathymetrically derived variables (including depth, slope, and Bathymetric Position Index) and output from a coupled physical-biogeochemical ocean model (including current direction and magnitude, food abundance, and dissolved oxygen). Direction of benthic ocean currents played an important role in predictions, pointing to large-scale ecological processes that may determine presence of DSCS. GAMs outperformed Maxent models and predicted more ecologically interpretable patterns. Additionally we quantified the predicted amount of suitable habitat that is currently located within some protected areas of the Southern California Bight and show that many hot spots occur outside protected areas. Given the importance of DSCS for multiple demersal fish species of commercial or conservation concerns, this research provides valuable information that natural resource managers can use as a tool in the Southern California Bight.

California↗

USGS2024

Variability in coastal habitat available for Longfin Smelt Spirinchus thaleichthys in the northeastern Pacific Ocean

An understanding of oceanographic conditions and processes important to marine animal ecology is fundamental to the development of effective management and conservation actions. Longfin Smelt ( Spirinchus thaleichthys ) is a pelagic forage fish found in coastal and estuarine waters along the Pacific coast of North America from Alaska to central California. Substantial population declines in California’s San Francisco Estuary, where Longfin Smelt are protected under California’s Endangered Species Act, have prompted extensive study of estuarine factors associated with the decline. However, coastal factors that affect up to two-thirds of the Longfin Smelt life cycle are poorly understood and may be important drivers of population dynamics. We compiled coastal observations from numerous sources to estimate the range-wide coastal marine distribution of Longfin Smelt and assess habitat factors affecting distribution in the northeast Pacific Ocean. Based on maximum entropy species distribution models, Longfin Smelt distribution was correlated with depth, distance from the nearest estuary, sea surface temperature, and sea surface chlorophyll. Longfin Smelt were found in shallow, higher productivity coastal waters closer to estuaries, with depth and temperature the most consistent factors influencing distribution. Habitat suitability was highly variable at the southern extent of the range, particularly off the California coast, and was largely driven by habitat contractions associated with warm-water conditions. Study results provide insights into the habitat and range-wide distribution of an at-risk estuarine-reliant forage fish and are the first step toward identifying processes that affect the marine portion of the Longfin Smelt life cycle.

Frontiers in Marine Science↗

USGS2023

Vulnerability to climate change of managed stocks in the California Current large marine ecosystem

Introduction: Understanding how abundance, productivity and distribution of individual species may respond to climate change is a critical first step towards anticipating alterations in marine ecosystem structure and function, as well as developing strategies to adapt to the full range of potential changes. Methods: This study applies the NOAA (National Oceanic and Atmospheric Administration) Fisheries Climate Vulnerability Assessment method to 64 federally-managed species in the California Current Large Marine Ecosystem to assess their vulnerability to climate change, where vulnerability is a function of a species’ exposure to environmental change and its biological sensitivity to a set of environmental conditions, which includes components of its resiliency and adaptive capacity to respond to these new conditions. Results: Overall, two-thirds of the species were judged to have Moderate or greater vulnerability to climate change, and only one species was anticipated to have a positive response. Species classified as Highly or Very Highly vulnerable share one or more characteristics including: 1) having complex life histories that utilize a wide range of freshwater and marine habitats; 2) having habitat specialization, particularly for areas that are likely to experience increased hypoxia; 3) having long lifespans and low population growth rates; and/or 4) being of high commercial value combined with impacts from non-climate stressors such as anthropogenic habitat degradation. Species with Low or Moderate vulnerability are either habitat generalists, occupy deep-water habitats or are highly mobile and likely to shift their ranges. Discussion: As climate-related changes intensify, this work provides key information for both scientists and managers as they address the long-term sustainability of fisheries in the region. This information can inform near-term advice for prioritizing species-level data collection and research on climate impacts, help managers to determine when and where a precautionary approach might be warranted, in harvest or other management decisions, and help identify habitats or life history stages that might be especially effective to protect or restore.

California, Oregon, Washington↗

USGS2020

Fish predation on a landscape scale

Predator–prey dynamics can have landscape-level impacts on ecosystems, and yet, spatial patterns and environmental predictors of predator–prey dynamics are often investigated at discrete locations, limiting our understanding of the broader impacts. At these broader scales, landscapes often contain multiple complex and heterogeneous habitats, requiring a spatially representative sampling design. This challenge is especially pronounced in California’s Sacramento–San Joaquin River Delta, where managers require information on the landscape-scale impacts of non-native fish predators on multiple imperiled native prey fish populations. We quantified relative predation risk in the southern half of the Delta (South Delta) in 2017 using floating baited tethers that record the exact time and location of predation events. We selected 20 study sites using a generalized random tessellation stratified survey design, which allowed us to infer relationships between key environmental covariates and predation across a broader spatial scale than previous studies. Covariates included distance-to-nearest predators, water temperature, turbidity, depth, bottom slope, bottom roughness, water velocity, and distance-to-nearest riverbank and nearest aquatic vegetation bed. Model selection determined the covariates that best predicted relative predation risk: water temperature, time of day, mean predator distance, and river bottom roughness. Using this model, we estimated predation risk for the South Delta landscape at a 1-day and 1-km resolution. This effort identified hot spots of predation risk and allowed us to generate predicted survival for migrating fish transiting the South Delta. This methodology can be applied to other systems to evaluate spatio-temporal dynamics in predation risk, and their biotic and abiotic predictors.

California↗

USGS2020

Good practices for species distribution modeling of deep-sea corals and sponges for resource management: Data collection, analysis, validation, and communication

Resource managers in the United States and worldwide are tasked with identifying and mitigating trade-offs between human activities in the deep sea (e.g., fishing, energy development, and mining) and their impacts on habitat-forming invertebrates, including deep-sea corals and sponges (DSCS). Related management decisions require information about where DSCS occur and in what densities. Species distribution modeling (SDM) provides a cost-effective means of identifying potential DSCS habitat over large areas to inform these management decisions and data collection. Here we describe good practices for DSCS SDM, especially in the context of data collection and management applications. Managers typically need information regarding DSCS encounter probabilities, densities, and sizes, defined at sub-regional to basin-wide scales and validated using subsequent, targeted data collections. To realistically achieve these goals, we suggest analysts: 1) integrate available data sources in SDMs including fine-scale visual sampling and broad-scale resource surveys (e.g., fisheries trawl surveys); and 2) include environmental predictor variables representing multiple spatial scales, model residual spatial autocorrelation, and quantify prediction uncertainty. When possible, models fitted to presence-absence and density data are preferred over models fitted only to presence data, which are difficult to validate and can confound estimated probability of occurrence or density with sampling effort. Ensembles of models can provide robust predictions, while multi-species models leverage information across taxa and facilitate community inference. To facilitate the use of models by managers, predictions should be expressed in units that are widely understood and validated at an appropriate spatial scale using a sampling design that provides strong statistical inference. We present three case studies for the Pacific Ocean that illustrate good practices with respect to data collection, modeling, and validation; these case studies demonstrate it is possible to implement our good practices in real-world settings.

Frontiers in Marine Science↗

USGS2019

Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all Pacific salmon and steelhead (Oncorhynchus spp.) listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units, and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories.

California↗

USGS2019

Estimating spatial–temporal differences in Chinook salmon outmigration survival with habitat- and predation-related covariates

Low survival rates of Chinook salmon ( Oncorhynchus tshawytscha ) smolts in California’s Central Valley have been attributed to multiple biological and physical factors, but it is not clear which factors have the largest impact. We used 5 years of acoustic telemetry data for 1709 late-fall Chinook salmon smolts to evaluate the effect of habitat- and predation-related covariates on outmigration survival through the Sacramento River. Using a Cormack–Jolly–Seber mark–recapture model, we estimated survival rates both as a function of covariates (covariate model) and as a function of river location and release year (spatial–temporal model). Our covariate model was overwhelmingly supported as the preferred model based on model selection criteria, suggesting the covariates adequately replicated spatial and temporal patterns in smolt survival. The covariates in the selected model included individual fish covariates, habitat-specific covariates, and temporally variable physical conditions. The most important covariate affecting salmon survival was flow. We describe the importance of these parameters in the context of juvenile salmon predation risk and suggest that additional research on predator distribution and density could improve model estimates.

California↗

USGS2019

Changes in adult Chinook salmon (Oncorhynchus tshawytscha) survival within the lower Columbia River amid increasing pinniped abundance

Significant effort towards conservation has contributed to the recovery of historically depleted pinniped populations world-wide. However, in several locations where pinnipeds have increased, they have been blamed for preventing the recovery of commercially valuable fish species through predation. Prompted by increasing pinniped abundance within the Columbia River (CR) USA, over a six year period, we used Passive Integrated Transponder tags to measure the survival of adult spring-run Chinook salmon (Oncorhynchus tshawytscha) through the estuary and lower CR to Bonneville Dam (Rkm 234). We estimated 51 751 - 224 705 salmon died annually from sources other than harvest. Mixed-effects logistic regression modelling identified pinniped predation as the most likely source. The odds of survival was estimated to decrease by 32% (95% CI: 6%-51% decrease) for every additional 467 sea lions, and to increase by 32% (95% CI: 8%-61% increase) for every increase of 1.5 in the log of American shad (Alosa sapidissima), a potential prey item for sea lions. A third covariate was the adipose clip status of the fish, indicating whether it was eligible for harvest.

Oregon, Washington↗

USGS2018

Spatial variability in ocean-mediated growth potential is linked to Chinook salmon survival

Early ocean survival of Chinook salmon, Oncorhynchus tshawytscha, varies greatly inter-annually and may be the period during which later spawning abundance and fishery recruitment are set. Therefore, identifying environmental drivers related to early survival may inform better models for management and sustainability of salmon in a variable environment. With this in mind, our main objectives were to (a) identify regions of high temporal variability in growth potential over a 23-year time series, (b) determine whether the spatial distribution of growth potential was correlated with observed oceanographic conditions, and (c) determine whether these spatial patterns in growth potential could be used to estimate juvenile salmon survival. We applied this method to the fall run of the Central Valley Chinook salmon population, focusing on the spring and summer period after emigration into central California coastal waters. For the period from 1988 to 2010, juvenile salmon growth potential on the central California continental shelf was described by three spatial patterns. These three patterns were most correlated with upwelling, detrended sea level anomalies, and the strength of onshore/offshore currents, respectively. Using the annual strength of these three patterns, as well as the overall growth potential throughout central California coastal waters, in a generalized linear model we explained 82% of the variation in juvenile salmon survival estimates. We attributed the relationship between growth potential and survival to variability in environmental conditions experienced by juvenile salmon during their first year at sea, as well as potential shifts in predation pressure following out-migration into coastal waters.

Fisheries Oceanography↗

USGS2011

Implications of community concordance for assessing stream integrity at three nested spatial scales in Minnesota, U.S.A.

1. Fish and invertebrate assemblage data collected from 670 stream sites in Minnesota (U.S.A.) were used to calculate concordance across three nested spatial scales (statewide, ecoregion and catchment). Predictive taxa richness models, calibrated using the same data, were used to evaluate whether concordant communities exhibited similar trends in human‐induced taxa loss across all three scales. Finally, we evaluated the strength of the relationship between selected environmental variables and the composition of both assemblages at all three spatial scales. 2. Significant concordance between fish and invertebrate communities occurred at the statewide scale as well as in six of seven ecoregions and 17 of the 21 major catchments. However, concordance was not consistently indicative of significant relationships between rates of fish and invertebrate taxa loss at those same scales. 3. Fish and invertebrate communities were largely associated with different environmental variables, although the composition of both communities was strongly correlated with stream size across all three scales. 4. Predictive taxa‐loss models for fish assemblages were less sensitive and precise than models for invertebrate assemblages, likely because of the relatively low number of common fish taxa in our data set. Both models, however, distinguished reference from non‐reference sites. 5. The importance of concordance, geographic context and scale are discussed in relation to the design and interpretation of stream integrity indicators. In particular, our findings suggest that community concordance should not be viewed as a substitute for an evaluation of how assemblages respond to environmental stressors.

Minnesota↗