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James T. Peterson

Publications and source records attributed to James T. Peterson.

At least 73 records · Page 4Linked to original sources
USGS2017

Structured decision making for conservation of bull trout (Salvelinus confluentus) in Long Creek, Klamath River Basin, south-central Oregon

With the decline of bull trout ( Salvelinus confluentus ), managers face multiple, and sometimes contradictory, management alternatives for species recovery. Moreover, effective decision-making involves all stakeholders influenced by the decisions (such as Tribal, State, Federal, private, and non-governmental organizations) because they represent diverse objectives, jurisdictions, policy mandates, and opinions of the best management strategy. The process of structured decision making is explicitly designed to address these elements of the decision making process. Here we report on an application of structured decision making to a population of bull trout believed threatened by high densities of nonnative brook trout ( S. fontinalis ) and habitat fragmentation in Long Creek, a tributary to the Sycan River in the Klamath River Basin, south-central Oregon. This involved engaging stakeholders to identify (1) their fundamental objectives for the conservation of bull trout, (2) feasible management alternatives to achieve their objectives, and (3) biological information and assumptions to incorporate in a decision model. Model simulations suggested an overarching theme among the top decision alternatives, which was a need to simultaneously control brook trout and ensure that the migratory tactic of bull trout can be expressed. More specifically, the optimal management decision, based on the estimated adult abundance at year 10, was to combine the eradication of brook trout from Long Creek with improvement of downstream conditions (for example, connectivity or habitat conditions). Other top decisions included these actions independently, as well as electrofishing removal of brook trout. In contrast, translocating bull trout to a different stream or installing a barrier to prevent upstream spread of brook trout had minimal or negative effects on the bull trout population. Moreover, sensitivity analyses suggested that these actions were consistently identified as optimal across a large range of parameter values. Taken together, these results support the conclusion that management actions focused on controlling brook trout and enhancing migrant bull trout are more likely to yield more adult bull trout within the 10-year time frame specified by stakeholders.

Oregon↗
USGS2017

A hidden-process model for estimating prespawn mortality using carcass survey data

After returning to spawning areas, adult Pacific salmon Oncorhynchus spp. often die without spawning successfully, which is commonly referred to as prespawn mortality. Prespawn mortality reduces reproductive success and can thereby hamper conservation, restoration, and reintroduction efforts. The primary source of information used to estimate prespawn mortality is collected through carcass surveys, but estimation can be difficult with these data due to imperfect detection and carcasses with unknown spawning status. To facilitate unbiased estimation of prespawn mortality and associated uncertainty, we developed a hidden-process mark–recovery model to estimate prespawn mortality rates from carcass survey data while accounting for imperfect detection and unknown spawning success. We then used the model to estimate prespawn mortality and identify potential associated factors for 3,352 adult spring Chinook Salmon O. tshawytscha that were transported above Foster Dam on the South Santiam River (Willamette River basin, Oregon) from 2009 to 2013. Estimated prespawn mortality was relatively low (≤13%) in most years (interannual mean = 28%) but was especially high (74%) in 2013. Variation in prespawn mortality estimates among outplanted groups of fish within each year was also very high, and some of this variation was explained by a trend toward lower prespawn mortality among fish that were outplanted later in the year. Numerous efforts are being made to monitor and, when possible, minimize prespawn mortality in salmon populations; this model can be used to provide unbiased estimates of spawning success that account for unknown fate and imperfect detection, which are common to carcass survey data.

Oregon↗
USGS2017

Distribution and abundance of Millicoma Dace in the Coos River Basin, Oregon

The Millicoma Dace Rhinichthys cataractae is a form of Longnose Dace endemic to the Coos River drainage in southwestern Oregon. Sparse species records in the Oregon State University Ichthyology Collection and database and infrequent recent encounters prompted surveys to assess the current status and distribution of the species. In 2014, we surveyed locations that had historically supported Millicoma Dace using backpack electrofishing to describe their current distribution and abundance at these locations. In 2015, we extended these surveys further upstream in the South Coos River basin, outside of the documented historical range. We used an N-mixture model to estimate abundance and capture probability for Millicoma Dace at each sampling location. We evaluated the effects of habitat covariates on both capture probability and abundance at each sample site. We found Millicoma Dace were widespread throughout their historical range and in the South Coos River sites outside of their documented historical range. We only found Millicoma Dace associated with native fishes; we did not collect any nonnative fish during our surveys. We collected Millicoma Dace exclusively from swift-water habitats, which were relatively uncommon in the basin, and found them typically associated with cobble or boulder substrates. Millicoma Dace were most abundant in the South Fork Coos and West Fork Millicoma River subbasins. We estimated capture probabilities for Millicoma Dace ranging from 9% when substrate was dominated by bedrock to 28% when substrate was dominated by cobble or gravel. Abundance estimates ranged from 1 to 560 dace per sampling location with a total estimated abundance (sum of site estimates) of over 3200 dace for the sites we sampled.

Oregon↗
USGS2016

Preparing future fisheries professionals to make good decisions

Future fisheries professionals will face decision-making challenges in an increasingly complex field of fisheries management. Though fisheries students are well trained in the use of the scientific method to understand the natural world, they are rarely exposed to structured decision making (SDM) as part of an undergraduate or graduate education. Specifically, SDM encourages users (e.g., students, managers) to think critically and communicate the problem and then identify specific, measurable objectives as they relate to the problem. Next, users must think critically and creatively about management alternatives that can be used to meet the objectives—there must be more than one alternative or there is no decision to be made. Lastly, the management alternatives are evaluated with regard to how likely they are to succeed in terms of multiple, possibly completing, objectives, such as how stakeholder groups value outcomes of management actions versus monetary cost. We believe that exposure to SDM and its elements is an important part of preparing future fisheries professional to meet the challenges they may face. These challenges include reduced budgets, the growth of potentially competing natural resource interest groups, and stakeholder desire to be involved in management decisions affecting public trust resources, just to name a few.

Fisheries↗
USGS2016

Patch occupancy of stream fauna across a land cover gradient in the southern Appalachians, USA

We modeled patch occupancy to examine factors that best predicted the prevalence of four functionally important focal stream consumers ( Tallaperla spp., Cambarus spp., Pleurocera proxima , and Cottus bairdi ) among 37 reaches within the Little Tennessee River basin of the southern Appalachian Mountains, USA. We compared 34 models of patch occupancy to examine the association of catchment and reach scale factors that varied as a result of converting forest to agricultural or urban land use. Occupancy of our taxa was linked to parameters reflecting both catchment and reach extent characteristics. At the catchment level, forest cover or its conversion to agriculture was a major determinant of occupancy for all four taxa. Patch occupancies of Tallaperla, Cambarus, and C. bairdi were positively, and Pleurocera negatively, correlated with forest cover. Secondarily at the reach level, local availability of large woody debris was important for Cambarus , availability of large cobble substrate was important for C. bairdi , and stream calcium concentration was important for P. proxima . Our results show the abundance of stream organisms was determined by the taxon-dependent interplay between catchment- and reach-level factors.

Georgia, North Carolina↗
USGS2016

Salinity effects on plasma ion levels, cortisol, and osmolality in Chinook salmon following lethal sampling

Studies on hydromineral balance in fishes frequently employ measurements of electrolytes following euthanasia. We tested the effects of fresh- or salt-water euthanasia baths of tricaine mesylate (MS-222) on plasma magnesium (Mg 2+ ) and sodium (Na + ) ions, cortisoland osmolality in fish exposed to saltwater challenges, and the ion and steroid hormone fluctuations over time following euthanasia in juvenile spring Chinook salmon ( Oncorhynchus tshawytscha ). Salinity of the euthanasia bath affected plasma Mg 2+ and Na + concentrations as well as osmolality, with higher concentrations in fish euthanized in saltwater. Time spent in the bath positively affected plasma Mg 2+ and osmolality, negatively affected cortisol, and had no effect on Na + concentrations. The difference of temporal trends in plasma Mg 2+ and Na + suggests that Mg 2+ may be more sensitive to physiological changes and responds more rapidly than Na + . When electrolytes and cortisol are measured as endpoints after euthanasia, care needs to be taken relative to time after death and the salinity of the euthanasia bath.

Comparative Biochemistry and Physiology, Part A: M↗
USGS2016

Innate and adaptive immune responses in migrating spring-run adult chinook salmon, Oncorhynchus tshawytscha

Adult Chinook salmon ( Oncorhynchus tshawytscha ) migrate from salt water to freshwater streams to spawn. Immune responses in migrating adult salmon are thought to diminish in the run up to spawning, though the exact mechanisms for diminished immune responses remain unknown. Here we examine both adaptive and innate immune responses as well as pathogen burdens in migrating adult Chinook salmon in the Upper Willamette River basin. Messenger RNA transcripts encoding antibody heavy chain molecules slightly diminish as a function of time, but are still present even after fish have successfully spawned. In contrast, the innate anti-bacterial effector proteins present in fish plasma rapidly decrease as spawning approaches. Fish also were examined for the presence and severity of eight different pathogens in different organs. While pathogen burden tended to increase during the migration, no specific pathogen signature was associated with diminished immune responses. Transcript levels of the immunosuppressive cytokines IL-10 and TGF beta were measured and did not change during the migration. These results suggest that loss of immune functions in adult migrating salmon are not due to pathogen infection or cytokine-mediated immune suppression, but is rather part of the life history of Chinook salmon likely induced by diminished energy reserves or hormonal changes which accompany spawning.

Oregon↗
USGS2015

Evaluation of three aging techniques and back-calculated growth for introduced Blue Catfish from Lake Oconee, Georgia

Back-calculation of length-at-age from otoliths and spines is a common technique employed in fisheries biology, but few studies have compared the precision of data collected with this method for catfish populations. We compared precision of back-calculated lengths-at-age for an introduced Ictalurus furcatus (Blue Catfish) population among 3 commonly used cross-sectioning techniques. We used gillnets to collect Blue Catfish ( n = 153) from Lake Oconee, GA. We estimated ages from a basal recess, articulating process, and otolith cross-section from each fish. We employed the Frasier-Lee method to back-calculate length-at-age for each fish, and compared the precision of back-calculated lengths among techniques using hierarchical linear models. Precision in age assignments was highest for otoliths (83.5%) and lowest for basal recesses (71.4%). Back-calculated lengths were variable among fish ages 1–3 for the techniques compared; otoliths and basal recesses yielded variable lengths at age 8. We concluded that otoliths and articulating processes are adequate for age estimation of Blue Catfish.

Georgia↗
USGS2015

Tidal management sffects sub-adult fish assemblages in impounded South Carolina Marshes

In coastal South Carolina, most impounded marshes are managed for waterfowl; fewer are managed for fishes. Tidal control is central to each strategy but raises concerns that nursery function could be impaired. This research examined the assemblage composition of fishes during early-life stages. We sampled two impoundments of each management type monthly in 2008 and 2009. We used light traps to collect 61,527 sub-adult fish representing 21 species and 16 families and push nets to collect 12,670 sub-adult fish representing 13 species and 11 families. The effective number of species detected at larval stage in “fish” impoundments (summer mean = 2.52 ± 0.20, winter mean = 2.02 ± 0.66) was greater than in “waterfowl” impoundments (summer mean = 1.27 ± 0.14, winter mean = 1.06 ± 0.09); CI = 90 %. Species richness did not differ between management types, but hierarchical linear models predicted differences in assemblage composition. These findings underscore the importance of frequent water exchange for maintaining diverse assemblages of early-life-stage fishes in marsh impoundments.

South Carolina↗
USGS2015

An evaluation of the efficiency of minnow traps for estimating the abundance of minnows in desert spring systems

Desert springs are sensitive aquatic ecosystems that pose unique challenges to natural resource managers and researchers. Among the most important of these is the need to accurately quantify population parameters for resident fish, particularly when the species are of special conservation concern. We evaluated the efficiency of baited minnow traps for estimating the abundance of two at-risk species, Foskett Speckled Dace Rhinichthys osculus ssp. and Borax Lake Chub Gila boraxobius , in desert spring systems in southeastern Oregon. We evaluated alternative sample designs using simulation and found that capture–recapture designs with four capture occasions would maximize the accuracy of estimates and minimize fish handling. We implemented the design and estimated capture and recapture probabilities using the Huggins closed-capture estimator. Trap capture probabilities averaged 23% and 26% for Foskett Speckled Dace and Borax Lake Chub, respectively, but differed substantially among sample locations, through time, and nonlinearly with fish body size. Recapture probabilities for Foskett Speckled Dace were, on average, 1.6 times greater than (first) capture probabilities, suggesting “trap-happy” behavior. Comparison of population estimates from the Huggins model with the commonly used Lincoln–Petersen estimator indicated that the latter underestimated Foskett Speckled Dace and Borax Lake Chub population size by 48% and by 20%, respectively. These biases were due to variability in capture and recapture probabilities. Simulation of fish monitoring that included the range of capture and recapture probabilities observed indicated that variability in capture and recapture probabilities in time negatively affected the ability to detect annual decreases by up to 20% in fish population size. Failure to account for variability in capture and recapture probabilities can lead to poor quality data and study inferences. Therefore, we recommend that fishery researchers and managers employ sample designs and estimators that can account for this variability.

Oregon↗
USGS2015

Occupancy modeling for improved accuracy and understanding of pathogen prevalence and dynamics

Most pathogen detection tests are imperfect, with a sensitivity < 100%, thereby resulting in the potential for a false negative, where a pathogen is present but not detected. False negatives in a sample inflate the number of non-detections, negatively biasing estimates of pathogen prevalence. Histological examination of tissues as a diagnostic test can be advantageous as multiple pathogens can be examined and providing important information on associated pathological changes to the host. However, it is usually less sensitive than molecular or microbiological tests for specific pathogens. Our study objectives were to 1) develop a hierarchical occupancy model to examine pathogen prevalence in spring Chinook salmon Oncorhynchus tshawytscha and their distribution among host tissues 2) use the model to estimate pathogen-specific test sensitivities and infection rates, and 3) illustrate the effect of using replicate within host sampling on sample sizes required to detect a pathogen. We examined histological sections of replicate tissue samples from spring Chinook salmon O. tshawytscha collected after spawning for common pathogens seen in this population: Apophallus/ echinostome metacercariae, Parvicapsula minibicornis, Nanophyetus salmincola/ metacercariae, and Renibacterium salmoninarum . A hierarchical occupancy model was developed to estimate pathogen and tissue-specific test sensitivities and unbiased estimation of host- and organ-level infection rates. Model estimated sensitivities and host- and organ-level infections rates varied among pathogens and model estimated infection rate was higher than prevalence unadjusted for test sensitivity, confirming that prevalence unadjusted for test sensitivity was negatively biased. The modeling approach provided an analytical approach for using hierarchically structured pathogen detection data from lower sensitivity diagnostic tests, such as histology, to obtain unbiased pathogen prevalence estimates with associated uncertainties. Accounting for test sensitivity using within host replicate samples also required fewer individual fish to be sampled. This approach is useful for evaluating pathogen or microbe community dynamics when test sensitivity is <100%.

PLoS ONE↗
USGS2015

Evaluation of methods for assessing physiological biomarkers of stress in freshwater mussels

Freshwater mussel populations are highly susceptible to environmental alterations because of their diminished numbers and primarily sessile behaviors; nonlethal biomonitoring programs are needed to evaluate the health of populations prior to mass mortality events. Our objectives were to determine ( i ) which biochemical parameters in freshwater mussel hemolymph could be consistently quantified, ( ii ) how hemolymph parameters and tissue glycogen respond to a thermal stress gradient (25, 30, and 35 &deg;C), and ( iii ) the effects of tissue and hemolymph extraction on long-term growth and survival of smaller- and larger-bodied mussel species. Glucose exhibited elevated expression in both species with increasing water temperature. Two transaminase enzymes had elevated expression in the 30 &deg;C treatment. The effects of hemolymph extraction and tissue biopsies were evaluated with a large-bodied species, Elliptio crassidens , and a smaller species, Villosa vibex . Individuals were monitored for 820 to 945 days after one of four treatments: hemolymph extraction, tissue biopsy, tissue and hemolymph extraction, and control. Hemolymph extraction and tissue biopsy adversely affected survival of V. vibex , suggesting that these extraction methods may add some risk of reduced survival to smaller-bodied species. Survival of E. crassidens was not impaired by any of the treatments, supporting the use of these techniques in nonlethal biomonitoring programs for larger-bodied mussel species.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2015

Non-lethal assessment of freshwater mussel physiological response to changes in environmental factors

The development of effective nonlethal biomonitoring techniques is imperative for the preservation of imperiled freshwater mussel populations. Changes in hemolymph chemistry profiles and tissue glycogen are potential biomarkers for nonlethally monitoring stress in mussels. We sampled three species in the Flint River Basin over 2 years to evaluate how these hemolymph and tissue biomarkers responded to environmental changes. We used hierarchical linear models to evaluate the relationships between variation in the biomarkers and environmental factors and found that the responses of the hemolymph and tissue parameters were strongly related to stream discharge. Shifts in alanine aminotransferase and glycogen showed the largest relations with discharge at the time of sampling, while magnesium levels were most explained by the discharge for 5 days prior to sampling. Aspartate aminotransferase, bicarbonate, and calcium showed the strongest relations with mean discharge for 15 days prior to sampling. The modeling results indicated that biomarker responses varied substantially among individuals of different size, sex, and species and illustrated the value of hierarchical modeling techniques to account for the inherent complexity of aquatic ecosystems.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2015

A formalized approach to making effective natural resource management decisions for Alaska National Parks

A fundamental goal of the National Park Service (NPS) is the long-term protection and management of resources in the National Park System. Reaching this goal requires multiple approaches, including the conservation of essential habitats and the identification and elimination of potential threats to biota and habitats. To accomplish these goals, the NPS has implemented the Alaska Region Vital Signs Inventory and Monitoring (I&M) Program to monitor key biological, chemical, and physical components of ecosystems at more than 270 national parks. The Alaska Region has four networks—Arctic, Central, Southeast, and Southwest. By monitoring vital signs over large spatial and temporal scales, park managers are provided with information on the status and trajectory of park resources as well as a greater understanding and insight into the ecosystem dynamics. While detecting and quantifying change is important to conservation efforts, to be useful for formulating remedial actions, monitoring data must explicitly relate to management objectives and be collected in such a manner as to resolve key uncertainties about the dynamics of the system (Nichols and Williams 2006). Formal decision making frameworks (versus more traditional processes described below) allow for the explicit integration of monitoring data into decision making processes to improve the understanding of system dynamics, thereby improving future decisions (Williams 2011).

Alaska↗
USGS2014

The effects of flow and stream characteristics on the variation in freshwater mussel growth in a Southeast US river basin

Summary The evaluation of the age and growth of animal populations is essential for understanding and predicting how populations will respond to changes in environmental conditions and anthropogenic stressors. We used a novel, von Bertalanffy hierarchical modelling approach to quantify relationships between the growth of three freshwater mussel species and various site- and watershed-level factors including seasonal discharge, land cover and stream size in the lower Flint River Basin, Georgia, U.S.A. Our modelling approach quantified the mussel-to-mussel variation in the von Bertalanffy parameters and accounted for biases associated with multiple measurements made on each mussel specimen, which are generally not accounted for as sources of bias in age and growth studies. Modelling results suggested that maximum shell size parameter and the Brody growth coefficient varied across species, on average, 19 and 33%, respectively, among individual mussels within sample sites. The variation was related to short-term high streamflows during the spring season, stream size, channel geomorphology and land cover in the watershed. This study provides insight to the factors affecting the growth of stream-dwelling freshwater mussels. Although hierarchical von Bertalanffy growth models are rarely used for freshwater mussel age and growth studies, this approach can provide important information regarding the ecology of freshwater mussels.

Georgia↗
USGS2014

An evaluation of the relations between flow regime components, stream characteristics, species traits and meta-demographic rates of warmwater stream fishes: Implications for aquatic resource management

Fishery biologists are increasingly recognizing the importance of considering the dynamic nature of streams when developing streamflow policies. Such approaches require information on how flow regimes influence the physical environment and how those factors, in turn, affect species-specific demographic rates. A more cost-effective alternative could be the use of dynamic occupancy models to predict how species are likely to respond to changes in flow. To appraise the efficacy of this approach, we evaluated relative support for hypothesized effects of seasonal streamflow components, stream channel characteristics, and fish species traits on local extinction, colonization, and recruitment (meta-demographic rates) of stream fishes. We used 4&thinsp;years of seasonal fish collection data from 23 streams to fit multistate, multiseason occupancy models for 42 fish species in the lower Flint River Basin, Georgia. Modelling results suggested that meta-demographic rates were influenced by streamflows, particularly short-term (10-day) flows. Flow effects on meta-demographic rates also varied with stream size, channel morphology, and fish species traits. Small-bodied species with generalized life-history characteristics were more resilient to flow variability than large-bodied species with specialized life-history characteristics. Using this approach, we simplified the modelling framework, thereby facilitating the development of dynamic, spatially explicit evaluations of the ecological consequences of water resource development activities over broad geographic areas. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Georgia↗
USGS2014

A multi-scaled approach to evaluating the fish assemblage structure within southern Appalachian streams USA.

There is considerable uncertainty about the relative roles of stream habitat and landscape characteristics in structuring stream-fish assemblages. We evaluated the relative importance of environmental characteristics on fish occupancy at the local and landscape scales within the upper Little Tennessee River basin of Georgia and North Carolina. Fishes were sampled using a quadrat sample design at 525 channel units within 48 study reaches during two consecutive years. We evaluated species&ndash;habitat relationships (local and landscape factors) by developing hierarchical, multispecies occupancy models. Modeling results suggested that fish occupancy within the Little Tennessee River basin was primarily influenced by stream topology and topography, urban land coverage, and channel unit types. Landscape scale factors (e.g., urban land coverage and elevation) largely controlled the fish assemblage structure at a stream-reach level, and local-scale factors (i.e., channel unit types) influenced fish distribution within stream reaches. Our study demonstrates the utility of a multi-scaled approach and the need to account for hierarchy and the interscale interactions of factors influencing assemblage structure prior to monitoring fish assemblages, developing biological management plans, or allocating management resources throughout a stream system.

Georgia, North Carolina, Tennessee↗