Geology topics

Jeffrey A. Falke

Publications and source records attributed to Jeffrey A. Falke.

51 records · Page 3Linked to original sources

USGS2017

A rapid assessment method to estimate the distribution of juvenile Chinook Salmon in tributary habitats using eDNA and occupancy estimation

Identification and protection of water bodies used by anadromous species are critical in light of increasing threats to fish populations, yet often challenging given budgetary and logistical limitations. Noninvasive, rapid‐assessment, sampling techniques may reduce costs and effort while increasing species detection efficiencies. We used an intrinsic potential (IP) habitat model to identify high‐quality rearing habitats for Chinook Salmon Oncorhynchus tshawytscha and select sites to sample throughout the Chena River basin, Alaska, for juvenile occupancy using an environmental DNA (eDNA) approach. Water samples were collected from 75 tributary sites in 2014 and 2015. The presence of Chinook Salmon DNA in water samples was assessed using a species‐specific quantitative PCR (qPCR) assay. The IP model predicted over 900 stream kilometers in the basin to support high‐quality (IP ≥ 0.75) rearing habitat. Occupancy estimation based on eDNA samples indicated that 80% and 56% of previously unsampled sites classified as high or low IP (IP < 0.75), respectively, were occupied. The probability of detection ( p ) of Chinook Salmon DNA from three replicate water samples was high ( p = 0.76) but varied with drainage area (km 2 ). A power analysis indicated high power to detect proportional changes in occupancy based on parameter values estimated from eDNA occupancy models, although power curves were not symmetrical around zero, indicating greater power to detect positive than negative proportional changes in occupancy. Overall, the combination of IP habitat modeling and occupancy estimation provided a useful, rapid‐assessment method to predict and subsequently quantify the distribution of juvenile salmon in previously unsampled tributary habitats. Additionally, these methods are flexible and can be modified for application to other species and in other locations, which may contribute towards improved population monitoring and management.

Alaska↗

USGS2017

Thermal adaptation and phenotypic plasticity in a warming world: Insights from common garden experiments on Alaskan sockeye salmon

An important unresolved question is how populations of coldwater-dependent fishes will respond to rapidly warming water temperatures. For example, the culturally and economically important group, Pacific salmon ( Oncorhynchus spp.), experience site-specific thermal regimes during early development that could be disrupted by warming. To test for thermal local adaptation and heritable phenotypic plasticity in Pacific salmon embryos, we measured the developmental rate, survival, and body size at hatching in two populations of sockeye salmon ( Oncorhynchus nerka ) that overlap in timing of spawning but incubate in contrasting natural thermal regimes. Using a split half-sibling design, we exposed embryos of 10 families from each of two populations to variable and constant thermal regimes. These represented both experienced temperatures by each population, and predicted temperatures under plausible future conditions based on a warming scenario from the downscaled global climate model (MIROC A1B scenario). We did not find evidence of thermal local adaptation during the embryonic stage for developmental rate or survival. Within treatments, populations hatched within 1 day of each other, on average, and among treatments, did not differ in survival in response to temperature. We did detect plasticity to temperature; embryos developed 2.5 times longer (189 days) in the coolest regime compared to the warmest regime (74 days). We also detected variation in developmental rates among families within and among temperature regimes, indicating heritable plasticity. Families exhibited a strong positive relationship between thermal variability and phenotypic variability in developmental rate but body length and mass at hatching were largely insensitive to temperature. Overall, our results indicated a lack of thermal local adaptation, but a presence of plasticity in populations experiencing contrasting conditions, as well as family-specific heritable plasticity that could facilitate adaptive change.

Global Change Biology↗

USGS2017

Groundwater declines are linked to changes in Great Plains stream fish assemblages

Groundwater pumping for agriculture is a major driver causing declines of global freshwater ecosystems, yet the ecological consequences for stream fish assemblages are rarely quantified. We combined retrospective (1950–2010) and prospective (2011–2060) modeling approaches within a multiscale framework to predict change in Great Plains stream fish assemblages associated with groundwater pumping from the United States High Plains Aquifer. We modeled the relationship between the length of stream receiving water from the High Plains Aquifer and the occurrence of fishes characteristic of small and large streams in the western Great Plains at a regional scale and for six subwatersheds nested within the region. Water development at the regional scale was associated with construction of 154 barriers that fragment stream habitats, increased depth to groundwater and loss of 558 km of stream, and transformation of fish assemblage structure from dominance by large-stream to small-stream fishes. Scaling down to subwatersheds revealed consistent transformations in fish assemblage structure among western subwatersheds with increasing depths to groundwater. Although transformations occurred in the absence of barriers, barriers along mainstem rivers isolate depauperate western fish assemblages from relatively intact eastern fish assemblages. Projections to 2060 indicate loss of an additional 286 km of stream across the region, as well as continued replacement of large-stream fishes by small-stream fishes where groundwater pumping has increased depth to groundwater. Our work illustrates the shrinking of streams and homogenization of Great Plains stream fish assemblages related to groundwater pumping, and we predict similar transformations worldwide where local and regional aquifer depletions occur.

Colorado, Kansas, Nebraska↗

USGS2017

The role of density-dependent and –independent processes in spawning habitat selection by salmon in an Arctic riverscape

Density-dependent (DD) and density-independent (DI) habitat selection is strongly linked to a species’ evolutionary history. Determining the relative importance of each is necessary because declining populations are not always the result of altered DI mechanisms but can often be the result of DD via a reduced carrying capacity. We developed spatially and temporally explicit models throughout the Chena River, Alaska to predict important DI mechanisms that influence Chinook salmon spawning success. We used resource-selection functions to predict suitable spawning habitat based on geomorphic characteristics, a semi-distributed water-and-energy balance hydrologic model to generate stream flow metrics, and modeled stream temperature as a function of climatic variables. Spawner counts were predicted throughout the core and periphery spawning sections of the Chena River from escapement estimates (DD) and DI variables. Additionally, we used isodar analysis to identify whether spawners actively defend spawning habitat or follow an ideal free distribution along the riverscape. Aerial counts were best explained by escapement and reference to the core or periphery, while no models with DI variables were supported in the candidate set. Furthermore, isodar plots indicated habitat selection was best explained by ideal free distributions, although there was strong evidence for active defense of core spawning habitat. Our results are surprising, given salmon commonly defend spawning resources, and are likely due to competition occurring at finer spatial scales than addressed in this study.

Alaska↗

USGS2017

Global synthesis of the documented and projected effects of climate change on inland fishes

Although climate change is an important factor affecting inland fishes globally, a comprehensive review of how climate change has impacted and will continue to impact inland fishes worldwide does not currently exist. We conducted an extensive, systematic primary literature review to identify English-language, peer-reviewed journal publications with projected and documented examples of climate change impacts on inland fishes globally. Since the mid-1980s, scientists have projected the effects of climate change on inland fishes, and more recently, documentation of climate change impacts on inland fishes has increased. Of the thousands of title and abstracts reviewed, we selected 624 publications for a full text review: 63 of these publications documented an effect of climate change on inland fishes, while 116 publications projected inland fishes’ response to future climate change. Documented and projected impacts of climate change varied, but several trends emerged including differences between documented and projected impacts of climate change on salmonid abundance ( P = 0.0002). Salmonid abundance decreased in 89.5% of documented effects compared to 35.7% of projected effects, where variable effects were more commonly reported (64.3%). Studies focused on responses of salmonids (61% of total) to climate change in North America and Europe, highlighting major gaps in the literature for taxonomic groups and geographic focus. Elucidating global patterns and identifying knowledge gaps of climate change effects on inland fishes will help managers better anticipate local changes in fish populations and assemblages, resulting in better development of management plans, particularly in systems with little information on climate change effects on fish.

Reviews in Fish Biology and Fisheries↗

USGS2017

Fish assemblages

Methods to sample fishes in stream ecosystems and to analyze the raw data, focusing primarily on assemblage-level (all fish species combined) analyses, are presented in this chapter. We begin with guidance on sample site selection, permitting for fish collection, and information-gathering steps to be completed prior to conducting fieldwork. Basic sampling methods (visual surveying, electrofishing, and seining) are presented with specific instructions for estimating population sizes via visual, capture-recapture, and depletion surveys, in addition to new guidance on environmental DNA (eDNA) methods. Steps to process fish specimens in the field including the use of anesthesia and preservation of whole specimens or tissue samples (for genetic or stable isotope analysis) are also presented. Data analysis methods include characterization of size-structure within populations, estimation of species richness and diversity, and application of fish functional traits. We conclude with three advanced topics in assemblage-level analysis: multidimensional scaling (MDS), ecological networks, and loop analysis.

Book chapter↗

USGS2016

Seasonal movements and habitat use of Potamodromous Rainbow Trout across a complex Alaska riverscape

Potamodromous Rainbow Trout Oncorhynchus mykiss are an important ecological and recreational resource in freshwater ecosystems of Alaska, and increased human development, hydroelectric projects, and reduced escapement of Chinook Salmon Oncorhynchus tshawytscha may threaten their populations. We used aerial and on-the-ground telemetry tracking, a digital landscape model, and resource selection functions to characterize seasonal movements and habitat use of 232 adult (>400 mm FL) Rainbow Trout across the complex, large (31,221 km 2 ) Susitna River basin of south-central Alaska during 2003–2004 and 2013–2014. We found that fish overwintered in main-stem habitats near tributary mouths from November to April. After ice-out in May, fish ascended tributaries up to 51 km to spawn and afterward moved downstream to lower tributary reaches, assumedly to intercept egg and flesh subsidies provided by spawning salmonids in July and August. Fish transitioned back to main-stem overwintering habitats at the onset of autumn when salmonid spawning waned. Fidelity to tributaries where fish were initially tagged varied across seasons but was high (>0.75) in three out of four drainages. Model-averaged resource selection functions suggested that Rainbow Trout habitat use varied seasonally; fish selected low-gradient, sinuous, main-stem stream reaches in the winter, reaches with suitably sized substrate during spawning, larger reaches during the feeding season prior to the arrival of spawning salmonids, and reaches with high Chinook Salmon spawning habitat potential following the arrival of adult fish. We found little difference in movement patterns between males and females among a subset of fish for which sex was determined using genetic analysis. As most Rainbow Trout undertake extensive movements within and among tributaries and make use of a variety of seasonal habitats to complete their life histories, it will be critical to take a basinwide approach to their management (i.e., habitat protection and angling bag limits) in light of anticipated land-use changes.

Alaska↗

USGS2016

Climate change effects on North American inland fish populations and assemblages

Climate is a critical driver of many fish populations, assemblages, and aquatic communities. However, direct observational studies of climate change impacts on North American inland fishes are rare. In this synthesis, we (1) summarize climate trends that may influence North American inland fish populations and assemblages, (2) compile 31 peer-reviewed studies of documented climate change effects on North American inland fish populations and assemblages, and (3) highlight four case studies representing a variety of observed responses ranging from warmwater systems in the southwestern and southeastern United States to coldwater systems along the Pacific Coast and Canadian Shield. We conclude by identifying key data gaps and research needs to inform adaptive, ecosystem-based approaches to managing North American inland fishes and fisheries in a changing climate.

Fisheries↗

USGS2016

A simple prioritization tool to diagnose impairment of stream temperature for coldwater fishes in the Great Basin

We provide a simple framework for diagnosing the impairment of stream water temperature for coldwater fishes across broad spatial extents based on a weight-of-evidence approach that integrates biological criteria, species distribution models, and geostatistical models of stream temperature. As a test case, we applied our approach to identify stream reaches most likely to be thermally impaired for Lahontan Cutthroat Trout Oncorhynchus clarkii henshawi in the upper Reese River, located in the northern Great Basin, Nevada. We first evaluated the capability of stream thermal regime descriptors to explain variation across 170 sites, and we found that the 7-d moving average of daily maximum stream temperatures (7DADM) provided minimal among-descriptor redundancy and, based on an upper threshold of 20°C, was also a good indicator of acute and chronic thermal stress. Next, we quantified the range of Lahontan Cutthroat Trout within our study area using a geographic distribution model. Finally, we used a geostatistical model to assess spatial variation in 7DADM and predict potential thermal impairment at the stream reach scale. We found that whereas 38% of reaches in our study area exceeded a 7DADM of 20°C and 35% were significantly warmer than predicted, only 17% both exceeded the biological criterion and were significantly warmer than predicted. This filtering allowed us to identify locations where physical and biological impairment were most likely within the network and that would represent the highest management priorities. Although our approach lacks the precision of more comprehensive approaches, it provides a broader context for diagnosing impairment and is a useful means of identifying priorities for more detailed evaluations across broad and heterogeneous stream networks.

Nevada↗

USGS2016

Wildfire may increase habitat quality for spring Chinook salmon in the Wenatchee River subbasin, WA, USA

Pacific Northwest salmonids are adapted to natural disturbance regimes that create dynamic habitat patterns over space and through time. However, human land use, particularly long-term fire suppression, has altered the intensity and frequency of wildfire in forested upland and riparian areas. To examine the potential impacts of wildfire on aquatic systems, we developed stream-reach-scale models of freshwater habitat for three life stages (adult, egg/fry, and juvenile) of spring Chinook salmon ( Oncorhynchus tshawytscha ) in the Wenatchee River subbasin, Washington. We used variables representing pre- and post-fire habitat conditions and employed novel techniques to capture changes in in-stream fine sediment, wood, and water temperature. Watershed-scale comparisons of high-quality habitat for each life stage of spring Chinook salmon habitat suggested that there are smaller quantities of high-quality juvenile overwinter habitat as compared to habitat for other life stages. We found that wildfire has the potential to increase quality of adult and overwintering juvenile habitat through increased delivery of wood, while decreasing the quality of egg and fry habitat due to the introduction of fine sediments. Model results showed the largest effect of fire on habitat quality associated with the juvenile life stage, resulting in increases in high-quality habitat in all watersheds. Due to the limited availability of pre-fire high-quality juvenile habitat, and increased habitat quality for this life stage post-fire, occurrence of characteristic wildfires would likely create a positive effect on spring Chinook salmon habitat in the Wenatchee River subbasin. We also compared pre- and post-fire model results of freshwater habitat for each life stage, and for the geometric mean of habitat quality across all life stages, using current compared to the historic distribution of spring Chinook salmon. We found that spring Chinook salmon are currently distributed in stream channels in which in-stream habitat for most life stages has a consistently positive response to fire. This compares to the historic distribution of spring Chinook, in which in-stream habitat exhibited a variable response to fire, including decreases in habitat quality overall or for specific life stages. This suggests that as the distribution of spring Chinook has decreased, they now occupy those areas with the most positive potential response to fire. Our work shows the potentially positive link between wildfire and aquatic habitat that supports forest managers in setting broader goals for fire management, perhaps leading to less fire suppression in some situations.

Washington↗

USGS2015

Seasonal cues of Arctic grayling movement in a small Arctic stream: the importance of surface water connectivity

In Arctic ecosystems, freshwater fish migrate seasonally between productive shallow water habitats that freeze in winter and deep overwinter refuge in rivers and lakes. How these movements relate to seasonal hydrology is not well understood. We used passive integrated transponder tags and stream wide antennae to track 1035 Arctic grayling in Crea Creek, a seasonally flowing beaded stream on the Arctic Coastal Plain, Alaska. Migration of juvenile and adult fish into Crea Creek peaked in June immediately after ice break-up in the stream. Fish that entered the stream during periods of high flow and cold stream temperature traveled farther upstream than those entering during periods of lower flow and warmer temperature. We used generalized linear models to relate migration of adult and juvenile fish out of Crea Creek to hydrology. Most adults migrated in late June – early July, and there was best support (Akaike weight = 0.46; w i ) for a model indicating that the rate of migration increased with decreasing discharge. Juvenile migration occurred in two peaks; the early peak consisted of larger juveniles and coincided with adult migration, while the later peak occurred shortly before freeze-up in September and included smaller juveniles. A model that included discharge, minimum stream temperature, year, season, and mean size of potential migrants was most strongly supported ( w i = 0.86). Juvenile migration rate increased sharply as daily minimum stream temperature decreased, suggesting fish respond to impending freeze-up. We found fish movements to be intimately tied to the strong seasonality of discharge and temperature, and demonstrate the importance of small stream connectivity for migratory Arctic grayling during the entire open-water period. The ongoing and anticipated effects of climate change and petroleum development on Arctic hydrology (e.g. reduced stream connectivity, earlier peak flows, increased evapotranspiration) have important implications for Arctic freshwater ecosystems.

Alaska↗

USGS2015

Climate change and vulnerability of bull trout (Salvelinus confluentus) in a fire-prone landscape.

Linked atmospheric and wildfire changes will complicate future management of native coldwater fishes in fire-prone landscapes, and new approaches to management that incorporate uncertainty are needed to address this challenge. We used a Bayesian network (BN) approach to evaluate population vulnerability of bull trout ( Salvelinus confluentus ) in the Wenatchee River basin, Washington, USA, under current and future climate and fire scenarios. The BN was based on modeled estimates of wildfire, water temperature, and physical habitat prior to, and following, simulated fires throughout the basin. We found that bull trout population vulnerability depended on the extent to which climate effects can be at least partially offset by managing factors such as habitat connectivity and fire size. Moreover, our analysis showed that local management can significantly reduce the vulnerability of bull trout to climate change given appropriate management actions. Tools such as our BN that explicitly integrate the linked nature of climate and wildfire, and incorporate uncertainty in both input data and vulnerability estimates, will be vital in effective future management to conserve native coldwater fishes.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2014

Applications of spatial statistical network models to stream data

Streams and rivers host a significant portion of Earth's biodiversity and provide important ecosystem services for human populations. Accurate information regarding the status and trends of stream resources is vital for their effective conservation and management. Most statistical techniques applied to data measured on stream networks were developed for terrestrial applications and are not optimized for streams. A new class of spatial statistical model, based on valid covariance structures for stream networks, can be used with many common types of stream data (e.g., water quality attributes, habitat conditions, biological surveys) through application of appropriate distributions (e.g., Gaussian, binomial, Poisson). The spatial statistical network models account for spatial autocorrelation (i.e., nonindependence) among measurements, which allows their application to databases with clustered measurement locations. Large amounts of stream data exist in many areas where spatial statistical analyses could be used to develop novel insights, improve predictions at unsampled sites, and aid in the design of efficient monitoring strategies at relatively low cost. We review the topic of spatial autocorrelation and its effects on statistical inference, demonstrate the use of spatial statistics with stream datasets relevant to common research and management questions, and discuss additional applications and development potential for spatial statistics on stream networks. Free software for implementing the spatial statistical network models has been developed that enables custom applications with many stream databases.

WIREs Water↗

USGS2013

Spatial ecological processes and local factors predict the distribution and abundance of spawning by steelhead ( Oncorhynchus mykiss ) across a complex riverscape

Processes that influence habitat selection in landscapes involve the interaction of habitat composition and configuration and are particularly important for species with complex life cycles. We assessed the relative influence of landscape spatial processes and local habitat characteristics on patterns in the distribution and abundance of spawning steelhead (Oncorhynchus mykiss), a threatened salmonid fish, across ~15,000 stream km in the John Day River basin, Oregon, USA. We used hurdle regression and a multi-model information theoretic approach to identify the relative importance of covariates representing key aspects of the steelhead life cycle (e.g., site access, spawning habitat quality, juvenile survival) at two spatial scales: within 2-km long survey reaches (local sites) and ecological neighborhoods (5 km) surrounding the local sites. Based on Akaike’s Information Criterion, models that included covariates describing ecological neighborhoods provided the best description of the distribution and abundance of steelhead spawning given the data. Among these covariates, our representation of offspring survival (growing-season-degree-days, °C) had the strongest effect size (7x) relative to other predictors. Predictive performances of model-averaged composite and neighborhood-only models were better than a site-only model based on both occurrence (percentage of sites correctly classified = 0.80±0.03 SD, 0.78±0.02 vs. 0.62±0.05, respectively) and counts (root mean square error = 3.37, 3.93 vs. 5.57, respectively). The importance of both temperature and stream flow for steelhead spawning suggest this species may be highly sensitive to impacts of land and water uses, and to projected climate impacts in the region and that landscape context, complementation, and connectivity will drive how this species responds to future environments.

Oregon↗

USGS2013

Modelling dendritic ecological networks in space: anintegrated network perspective

Dendritic ecological networks (DENs) are a unique form of ecological networks that exhibit a dendritic network topology (e.g. stream and cave networks or plant architecture). DENs have a dual spatial representation; as points within the network and as points in geographical space. Consequently, some analytical methods used to quantify relationships in other types of ecological networks, or in 2-D space, may be inadequate for studying the influence of structure and connectivity on ecological processes within DENs. We propose a conceptual taxonomy of network analysis methods that account for DEN characteristics to varying degrees and provide a synthesis of the different approaches within the context of stream ecology. Within this context, we summarise the key innovations of a new family of spatial statistical models that describe spatial relationships in DENs. Finally, we discuss how different network analyses may be combined to address more complex and novel research questions. While our main focus is streams, the taxonomy of network analyses is also relevant anywhere spatial patterns in both network and 2-D space can be used to explore the influence of multi-scale processes on biota and their habitat (e.g. plant morphology and pest infestation, or preferential migration along stream or road corridors).

Ecology Letters↗