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Wildlife and natural resource institutions play key roles in invasive species monitoring and management. Paradoxically, the extensive fieldwork undertaken by these institutions and their partners may result in the inadvertent movement and spread of invasive species within and between sensitive ecosystems. In this work, we consider the potential effects of internal guidelines and policies designed to prevent the spread of invasive species by the field activities of management institutions and their partners. Such policies could be high-leverage tools for invasive species prevention, however, as large, complex organizations seek to implement policies to limit the spread of invasive species, it may be challenging to accommodate the wide diversity of potential invasion pathways and mitigation efforts facilitated via the programs, activities, and ecosystems they manage. Prevention policies may also be met with resistance due to the costs of implementation unless concrete benefits can be demonstrated. Assessing and communicating the effects of prevention policies could motivate improved implementation and adherence by institutional units and partners and could help inform adaptive policy changes. However, assessing the effectiveness of invasive species prevention presents a unique set of challenges, including incomplete data on invasive species distribution and pathways, that make it difficult to measure the effects of prevention efforts. In this work, we present a conceptual framework for evaluating institutional policies for invasive species prevention. We describe a flexible, multifaceted approach that considers policy implementation and adherence as well as ecological outcomes. We discuss potential application of this framework using a policy recently implemented by the Pacific Region of the U.S. Fish and Wildlife Service to prevent the introduction and spread of invasive species by service personnel and partners during field activities as a case study. [ABSTRACT FROM AUTHOR]

Background: Prevention of respiratory syncytial virus (RSV) disease in infants is an unmet vaccine need, and maternal immunization is a potential strategy to address this need. This study evaluated concomitant administration of RSV stabilized prefusion F subunit vaccine (RSVpreF) and tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis vaccine adsorbed (Tdap) in healthy, nonpregnant women 18‒49 years of age.Methods: In this phase 2b, multicenter, placebo-controlled, observer-blind, noninferiority study, participants were randomized to receive RSVpreF in a range of doses and formulations with Tdap or alone, or Tdap alone. Safety and immunogenicity were assessed.Results: Local reactions and systemic events were generally similar across vaccine groups. Noninferiority of anti-RSV-A and anti-RSV-B immune responses induced by RSVpreF with Tdap was demonstrated compared to RSVpreF alone. Noninferiority of anti-diphtheria toxoid and anti-tetanus toxoid immune responses after administration of RSVpreF with Tdap was demonstrated compared to Tdap alone; noninferiority was not met for anti-pertussis component responses.Conclusions: RSVpreF was safe and well tolerated when administered with Tdap or alone in nonpregnant women 18‒49 years of age. Immune responses induced by Tdap administered with RSVpreF were noninferior for the tetanus and diphtheria components of Tdap, but not for pertussis.Clinical Trials Registration: NCT04071158. [ABSTRACT FROM AUTHOR]

Occupancy models are often used to analyze long‐term monitoring data to better understand how and why species redistribute across dynamic landscapes while accounting for incomplete capture. However, this approach requires replicate detection/non‐detection data at a sample unit and many long‐term monitoring programs lack temporal replicate surveys. In such cases, it has been suggested that surveying subunits within a larger sample unit may be an efficient substitution (i.e., space‐for‐time substitution). Still, the efficacy of fitting occupancy models using a space‐for‐time substitution has not been fully explored and is likely context dependent. Herein, we fit occupancy models to Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys) catch data collected by two different monitoring programs that use the same sampling gear in the San Francisco Bay‐Delta, USA. We demonstrate how our inferences concerning the distribution of these species changes when using a space‐for‐time substitution. Specifically, we found the probability that a sample unit was occupied was much greater when using a space‐for‐time substitution, presumably due to the change in the spatial scale of our inferences. Furthermore, we observed that as the spatial scale of our inferences increased, our ability to detect environmental effects on system dynamics was obscured, which we suspect is related to the tradeoffs associated with spatial grain and extent. Overall, our findings highlight the importance of considering how the unique characteristics of monitoring programs influences inferences, which has broad implications for how to appropriately leverage existing long‐term monitoring data to understand the distribution of species. [ABSTRACT FROM AUTHOR]

Sturgeons are among the most endangered fishes in the world. Identifying habitat use characteristics to inform restoration projects is crucial for recovery. However, small sample sizes, inadequate replication of studies, and limited spatial extents complicate our ability to effectively apply the findings of single studies to endangered species conservation across the larger riverscape. We synthesized information from amphidromous and anadromous sturgeons in North America to identify species-specific knowledge gaps and conduct a quantitative comparison of species–habitat relationships. We provided a qualitative summary of substrate use and synthesized estimates of depth and velocity during spawning and non-spawning activity. Generalized patterns among species were identified, such as spawning in fast water on hard substrate and then using slow water with soft substrate areas when not spawning. We noted species-specific variability during spawning that may be attributed to historical maximum length, egg characteristics, and watershed features. This study provides some of the first estimates of habitat use that can be adapted for many populations. Results can contribute to empirically grounded decision-support tools used to prioritize information needs for recovery. [ABSTRACT FROM AUTHOR]

Considerable resources have been invested in ecological restoration projects across the globe to restore ecosystem integrity. Restoration strategies are often diverse and have been met with mixed success. In this article, we describe the Chinook salmon (Oncorhynchus tshawytscha) decision‐support models developed by the Central Valley Project Improvement Act Science Integration Team as part of a larger structured decision‐making effort aimed at maximizing natural adult production of Chinook salmon in California's Central Valley, the United States. We then describe the decision‐analytic tools the stakeholder group used to solve the models and explore model results, including stochastic dynamic programming, forward simulation, proportional scoring, relative loss, expected value of perfect information, response profile analyses, and indifference curves. Using these tools, the stakeholder group was able to develop and evaluate restoration strategies for multiple Chinook salmon runs simultaneously, a first for the restoration program. We found that actions targeted at one run were detrimental to others, which was unexpected. Furthermore, information uncovered during this process was used to direct efforts towards targeted research/monitoring to reduce critical uncertainties in salmon demographic rates and make better restoration decisions moving forward. The decision sciences have established a wide range of analytical tools and approaches to simplify complex problems into key components, and we believe the concepts described in this article are of great interest and can be applied by many restoration practitioners that undoubtedly face similar difficulties when implementing restoration strategies for complex systems. [ABSTRACT FROM AUTHOR]

Bull trout (Salvelinus confluentus) are challenging to detect as a result of the species cryptic behavior and coloration, relatively low densities in complex habitats, and affinity for cold, high clarity, low conductivity waters. Bull trout are also closely associated with the stream bed, frequently conceal in substrate, and this concealment behavior is poorly understood. Consequently, population assessments are problematic and biologists and managers often lack quantitative information to accurately describe bull trout distributions, estimate abundance, and assess status and trends; particularly for stream-dwelling populations. During controlled laboratory trials, we recorded concealment, resting, and swimming behavior of juvenile wild bull trout in response to: (1) constant and fluctuating water temperature, (2) presence or absence of light, and (3) substrate size. Light level had the strongest influence on wild fish concealment and more fish concealed as light levels increased from darkness to daylight. Wild fish were 14.5 times less likely to conceal in constant darkness and 4.1 times more likely to conceal in 12 h light x 12 h darkness compared to constant light. Wild fish were 6.2 times less likely to conceal in small (26–51 mm) substrate compared to larger (52–102 mm) substrate. As water temperature increased, fewer wild fish concealed. Knowledge of wild bull trout concealment will improve field sampling protocols and increase detection efficiencies. These data also enhance knowledge of bull trout niche requirements which illuminates ecological differences among species and informs conservation and restoration efforts. [ABSTRACT FROM AUTHOR]

Many frameworks have been used to identify environmental flows for sustaining river ecosystems or specific taxa in the face of widespread flow alteration. However, these frameworks largely focus on identifying suitable flows and often ignore the important links between management actions, resulting flows, and valued ecosystem or social responses. Structured decision making (SDM) could assist the comparison of environmental flows by providing a mature framework to link management actions to objectives via environmental flow science. We describe SDM and illustrate its application using a case study focused on comparing environmental flow scenarios for the mainstem Willamette River, Oregon. In a short timeframe, SDM was applied to identify objectives, develop empirical and expert opinion‐based models, and compare flow scenarios while accounting for interannual flow variability and partial controllability. No scenario was clearly preferred based on available knowledge, largely because river flows could only be partially controlled through dam operations. Participants agreed that SDM was useful for comparing alternative dam operations, but that refined predictive models and additional objectives were needed to better inform basinwide flow decisions. In our view, SDM can provide more realistic comparisons of environmental flows by accounting for partial controllability and uncertainty, which may result in greater implementation of available flow management actions. Research Impact Statement: Structured decision making can support environmental flow implementation decisions by linking management options to ecosystem values while accounting for uncertainty. [ABSTRACT FROM AUTHOR]

Prespawn mortality (PSM) presents a major problem for the recovery of spring Chinook Salmon (Oncorhynchus tshawytscha) populations. In the Willamette River, Oregon, PSM exceeds 90% in some years but factors explaining it are not well understood. We examined intestinal tissue samples using histological slides from over 783 spring Chinook Salmon collected between 2009 and 2021, which included tissues from PSM fish, artificially spawned captive broodstock (BS) and normal river run fish, comprised of trapped (Live) and naturally post‐spawned river (RPS) fish collected from the river. We observed degeneration of the intestinal epithelium and loss of villous structure, with concurrent severe enteritis. A natural progression of decline in epithelial integrity (EI) through the summer and fall until spawning and subsequent death was also observed. Live fish exhibited high EI scores (mean = 68%), BS exhibited variable EI scores (35%) and RPS exhibited severe loss of EI (14%). PSM fish exhibited prominent loss of intestinal epithelium with EI scores (13%), very similar to RPS fish, despite having been collected earlier in the year. Hence, we argue that low EI scores are strongly linked with PSM. Ceratonova shasta and Enterocytozoon schreckii were common in all groups, but neither were linked to either PSM or a decline in EI. [ABSTRACT FROM AUTHOR]

Structured decision making allows reintroduction decisions to be made despite uncertainty by linking reintroduction goals with alternative management actions through predictive models of ecological processes. We developed a decision model to evaluate the trade-offs between six bull trout ( Salvelinus confluentus) reintroduction decisions with the goal of maximizing the number of adults in the recipient population without reducing the donor population to an unacceptable level. Sensitivity analyses suggested that the decision identity and outcome were most influenced by survival parameters that result in increased adult abundance in the recipient population, increased juvenile survival in the donor and recipient populations, adult fecundity rates, and sex ratio. The decision was least sensitive to survival parameters associated with the captive-reared population, the effect of naivety on released individuals, and juvenile carrying capacity of the reintroduced population. The model and sensitivity analyses can serve as the foundation for formal adaptive management and improved effectiveness, efficiency, and transparency of bull trout reintroduction decisions. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Stream ecosystems provide multiple, valued services to society, including water supply, waste assimilation, recreation, and habitat for diverse and productive biological communities. Managers striving to sustain these services in the face of changing climate, land uses, and water demands need tools to assess the potential effectiveness of alternative management actions, and often, the resulting tradeoffs between competing objectives. Integrating predictive modeling with monitoring data in an adaptive management framework provides a process by which managers can reduce model uncertainties and thus improve the scientific bases for subsequent decisions. We demonstrate an integration of monitoring data with a dynamic, metapopulation model developed to assess effects of streamflow alteration on fish occupancy in a southeastern US stream system. Although not extensive (collected over three years at nine sites), the monitoring data allowed us to assess and update support for alternative population dynamic models using model probabilities and Bayes rule. We then use the updated model weights to estimate the effects of water withdrawal on stream fish communities and demonstrate how feedback in the form of monitoring data can be used to improve water resource decision making. We conclude that investment in more strategic monitoring, guided by a priori model predictions under alternative hypotheses and an adaptive sampling design, could substantially improve the information available to guide decision-making and management for ecosystem services from lotic systems. [ABSTRACT FROM AUTHOR]

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 backcalculate 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 °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 °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. [ABSTRACT FROM AUTHOR]

Alvord Chub are small minnows endemic to the Alvord Basin, a endorheic desert basin in southeastern Oregon and northwestern Nevada. Comprehensive distribution surveys were last conducted 30 y ago. Recent, limited surveys raised concern that the range and abundance of Alvord Chub may have contracted. We conducted a comprehensive survey at historically occupied locations in 2013 and obtained mark-recapture population estimates. Despite 2 y of below average precipitation, Alvord Chub were present at the majority of historically occupied drainages, were abundant at many locations, but were restricted in distribution in several drainages. Additionally, we documented current threats, which included water withdrawals, nonnative fishes, grazing, habitat fragmentation, and desiccation. Based on our observations, we suggest a number of management recommendations. [ABSTRACT FROM AUTHOR]

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%. [ABSTRACT FROM AUTHOR]

1. North American freshwater mussels have been subjected to multiple stressors in recent decades that have contributed to declines in the status and distribution of many species. However, considerable uncertainty exists regarding the relative influence of these factors on observed population declines. 2. We used an occupancy modelling approach to quantify relationships between mussel species occurrence and various site- and catchment-level factors, including land cover, stream size, the occurrence of drought and reach isolation due to impoundment for 21 mussel species native to the lower Flint River Basin, Georgia, U.S.A. 3. Our modelling approach accounted for potential biases associated with both incomplete detection and misidentification of species, which are frequently not accommodated as sources of bias in freshwater mussel studies. 4. Modelling results suggested that mussel species were, on average, four times less likely to be present following severe drought, but the negative effects of drought declined rapidly with increasing stream size. Similarly, mussel species were 15 times less likely to occupy small streams that were isolated from mainstem tributaries by impoundments. 5. This study provides insight into the effects of natural and anthropogenic factors on freshwater mussel species. Our findings add to a growing body of literature aimed at improving understanding of the predominant factors influencing freshwater mussel populations and fostering the development of more informed and effective conservation strategies. [ABSTRACT FROM AUTHOR]

In the present study, specimens of the invasive clam, Corbicula fluminea, were collected above and below possible sources of potentially toxic trace elements (As, Cd, Cr, Cu, Hg, Pb, and Zn) in the Altamaha River system (Georgia, USA). Bioaccumulation of these elements was quantified, along with environmental (water and sediment) concentrations. Hierarchical linear models were used to account for variability in tissue concentrations related to environmental (site water chemistry and sediment characteristics) and individual (growth metrics) variables while identifying the strongest relations between these variables and trace element accumulation. The present study found significantly elevated concentrations of Cd, Cu, and Hg downstream of the outfall of kaolin-processing facilities, Zn downstream of a tire cording facility, and Cr downstream of both a nuclear power plant and a paper pulp mill. Models of the present study indicated that variation in trace element accumulation was linked to distance upstream from the estuary, dissolved oxygen, percentage of silt and clay in the sediment, elemental concentrations in sediment, shell length, and bivalve condition index. By explicitly modeling environmental variability, the Hierarchical linear modeling procedure allowed the identification of sites showing increased accumulation of trace elements that may have been caused by human activity. Hierarchical linear modeling is a useful tool for accounting for environmental and individual sources of variation in bioaccumulation studies. [ABSTRACT FROM AUTHOR]

The life history of Cambarus halli, a crayfish endemic to the Tallapoosa River Basin, GA, was studied at four sites within the Tallapoosa River. Two sites had allopatric populations of C. halli, and two sites had populations of C. halli sympatric with C. englishi. Three age classes existed across sites. For Cambarus halli, total number of pleopodal eggs was positively related to carapace length, but egg size was only weakly positively related to carapace length. Cambarus halli were smaller across age classes at sympatric sites, hut had greater growth rates than at allopatric sites. Cambarus halli density estimates were lower at sympatric sites, while proportions of reproductively active age-1 and age-2 individuals were higher at allopatric sites (63% vs. 33%). [ABSTRACT FROM AUTHOR]

We evaluated competing models explaining the occurrence of five stream fishes in an urbanizing watershed to determine the relative importance of (a) impervious surface and other indicators of current land use, (b) historic land use (e.g., agriculture, impoundments), and (c) hydrogeomorphic characteristics (e.g., stream size, elevation, geology). For four of five species, the best-supported models were those that included both current effective impervious cover and historic land use predictor variables, although models with only effective impervious cover were equally well supported for two of those species. For the best-supported models for three species, occurrence probability was predicted to approach zero at levels of development equivalent to about 2%–4% effective impervious cover in the surrounding region. Data were drawn from 357 fish collections made in the Etowah River basin, Georgia, USA, between 1998 and 2003 and analyzed using hierarchical logistic regression accounting for imperfect species detection. This is the first study we know of to examine the response of individual fish species to both increasing impervious cover and historic land use. Such individual species assessments will be increasingly necessary to guide policies for managing urban effects and preventing extirpations of sensitive species. [ABSTRACT FROM AUTHOR]

The article focuses on a study about the sources of variation in detection among wading birds in the Florida Everglades. The study used dual-observer trials for fixed wing aerial surveys of the birds. It explains that the probability of detection depended on the group size and species of the birds, as well as the observer's position in aircraft. It concludes that detection bias should be considered a major factor in the validity of data, and suggests that observers should use dual-observer method for less bias and unexpected factors.

To predict the distributions of breeding birds in the state of Georgia, USA, we built hierarchical models consisting of 4 levels of nested mapping units of decreasing area: 90,000 ha, 3,600 ha, 144 ha, and 5.76 ha. We used the Partners in Flight database of point counts to generate presence and absence data at locations across the state of Georgia for 9 avian species: Acadian flycatcher (Empidonax virescens), brown-headed nuthatch (Sitta pusilla), Carolina wren (Thryothorus ludovicianus), indigo bunting (Passerina cyanea), northern cardinal (Cardinalis cardinalis), prairie warbler (Dendroica discolor), yellow-billed cuckoo (Coccyzus americanus), white-eyed vireo (Vireo griseus), and wood thrush (Hylocichla mustelina). At each location, we estimated hierarchical-level-specific habitat measurements using the Georgia GAP Analysis18 class land cover and other Geographic Information System sources. We created candidate, species-specific occupancy models based on previously reported relationships, and fit these using Markov chain Monte Carlo procedures implemented in OpenBugs. We then created a confidence model set for each species based on Akaike's Information Criterion. We found hierarchical habitat relationships for all species. Three-fold cross-validation estimates of model accuracy indicated an average overall correct classification rate of 60.5%. Comparisons with existing Georgia GAP Analysis models indicated that our models were more accurate overall. Our results provide guidance to wildlife scientists and managers seeking predict avian occurrence as a function of local and landscape-level habitat attributes. [ABSTRACT FROM AUTHOR]

Pteronotropis welaka (Bluenose Shiner) has a fragmented range throughout the Southeast, but its apparent rarity may reflect a low probability of detection during surveys. Our objectives were to obtain up-to-date status information for populations in southwest Georgia and to account for incomplete detection in our estimate of the proportion of sites occupied. We detected Bluenose Shiner at 5 of 39 sites (13%) sampled during 2004 and 2005 and estimated detection probability (p) and the proportion of sites occupied (psi) from seine-haul data. Models containing habitat covariates as predictors of p and psi provided a better description of the data than models without covariates for Bluenose Shiner and three other minnow species. Regardless of the model structure, the probability of detecting Bluenose Shiner during a single seine haul was substantially lower than for the other minnow species (3-8% vs. 13-33%). However, estimates of the proportion of sites occupied (corrected for incomplete detection) were similar to observed occupancy rates for all four species because of the large number of seine hauls we made at each site. The modeling approach we followed increased our confidence in survey results and provided information on where and how much to sample in future surveys. It has broad application to future surveys and monitoring programs for rare aquatic species in the southeastern United States. [ABSTRACT FROM AUTHOR]

Invasions of non-native brook trout (Salvelinus fontinalis) have the potential for upstream displacement or elimination of bull trout (Salvelinus confluentus) and other native species already threatened by habitat loss. We summarized the distribution and number of bull trout in samples from 12 streams with and without brook trout in central Idaho and used hierarchical regression analysis to consider whether brook trout have displaced bull trout along gradients of temperature and elevation. Brook trout generally were observed in higher numbers downstream of bull trout. Brook trout presence, number, and both temperature and elevation were important variables explaining the observed distributions and number of bull trout among streams. Our analyses support the hypothesis that brook trout have displaced bull trout, but results were highly variable and stream dependent. Although brook trout appeared to have displaced bull trout to higher elevations or colder temperatures, there was no clear influence on overall number of bull trout. Brook trout probably do influence bull trout populations and facilitate if not cause local extinctions, but threats probably vary strongly with environmental conditions. Bull trout in smaller streams could be more vulnerable than those in larger streams. [ABSTRACT FROM AUTHOR]

Effective conservation efforts for at-risk species require knowledge of the locations of existing populations. Species presence can be estimated directly by conducting field-sampling surveys or alternatively by developing predictive models. Direct surveys can be expensive and inefficient, particularly for rare and difficult-to-sample species, and models of species presence may produce biased predictions. We present a Bayesian approach that combines sampling and model-based inferences for estimating species presence. The accuracy and cost-effectiveness of this approach were compared to those of sampling surveys and predictive models for estimating the presence of the threatened bull trout (Salvelinus confluentus) via simulation with existing models and empirical sampling data. Simulations indicated that a sampling-only approach would be the most effective and would result in the lowest presence and absence misclassification error rates for three thresholds of detection probability. When sampling effort was considered, however, the combined approach resulted in the lowest error rates per unit of sampling effort. Hence, lower probability-of-detection thresholds can be specified with the combined approach, resulting in lower misclassification error rates and improved cost-effectiveness. [ABSTRACT FROM AUTHOR]

Management of mixed-stock Chinook salmon (Oncorhynchus tshawytscha) fisheries requires balancing fishery access and conservation of vulnerable stocks. Although accurate, timely estimates of stock-specific harvest are crucial in achieving competing objectives, limited numbers of stock assignments (e.g., tag recoveries) can diminish the utility of estimates. We used a flexible simulation approach, applied to both a theoretical and real-world fishery case study, to compare the performance of competing monitoring alternatives and estimators for harvest. We sought to improve accuracy for point estimates of harvest and harvest trajectories over time. Bayesian models provided similarly accurate point estimates to existing models at high levels of data aggregation, generally improved estimates of harvest trajectories at intermediate aggregation, and reliable estimates of uncertainty. Incorporation of time-lagged prior information inconsistently improved estimates of harvest trajectories. Among monitoring alternatives yielding equal increases (33%) in coded wire tag recoveries, increasing tagging rates resulted in the greatest decrease in estimate uncertainty for target stocks (37.5% to 45.3%). Variable performances of mixed-stock harvest estimators suggest their use should considered on a stock- and fishery-specific basis, potentially using a simulation-based approach. [ABSTRACT FROM AUTHOR]

Here, we provide evidence that the freshwater parasitic copepod, Salmincola californiensis, acts as a vector for Aeromonas salmonicida. While investigating the effects of S. californiensis on Chinoook salmon (Oncorhynchus tshawytscha), we tangentially observed that fish infected with the copepod developed furunculosis, caused by A. salmonicida. This occurred despite being reared in pathogen‐free well water in a research facility with no prior history of spontaneous infection. We further investigated the possibility of S. californiensis to serve as a vector for the bacterium via detection of fluorescently labelled A. salmonicida inside the egg sacs from copepods in which the fish hosts were experimentally infected with GFP‐A449 A. salmonicida. We then evaluated copepod egg sacs that were collected from adult Chinook salmon from a freshwater hatchery with A. salmonicida infections confirmed by either culture or PCR. The bacterium was cultured on tryptic soy agar plates from 75% of the egg sacs, and 61% were positive by PCR. These three separate experiments indicate an alternative tactic of transmission in addition to direct transmission of A. salmonicida in captivity. The copepod may play an important role in transmission of the bacterium when fish are more dispersed, such as in the wild. [ABSTRACT FROM AUTHOR]

• Co-infection with Bolbophorus increased odds of Lernaea and Contracaecum infection. • A major marsh restoration project resulted in an increase in infections. • Declines in infections over about 25 days were attributed to parasite-induced host mortality. • Lernaea and Contracaecum might be directly lethal due to the small host sizes. • Recruitment was better in years without Lernaea infections. We used odds ratios and a hurdle model to analyze parasite co-infections over 25 years on >20,000 young-of-the year of endangered Shortnose and Lost River Suckers. Host ecologies differed as did parasite infections. Shortnose Suckers were more likely to be caught inshore and 3–5 times more likely to have Bolbophorus spp. and Contracaecum sp. infections, and Lost River Suckers were more likely to be caught offshore and approximately three times more likely to have Lernaea cyprinacea infections. An observed peak shift seems likely to be due to a lower host size limit for Bolbophorus spp. (13.6 mm) compared with L. cyprinacea (23.4 mm). The large data set allowed us to generate strong hypotheses: (i) that a major marsh restoration project had unintended consequences that resulted in an increase in infections; (ii) that co-infection with Bolbophorus spp. increased the odds of infection by L. cyprinacea and Contracaecum sp.; (iii) that significant declines in the odds of infection over approximately 25 days were due to parasite-induced host mortality; (iv) that the fish's small size relative to L. cyprinacea and Contracaecum sp. might be directly lethal; (v) that the absence of L. cyprinacea infections in the early 1990s was associated with good year-class production of the suckers; and (vi) that parasites might increase the odds of vagrancy from the nursery ground. [ABSTRACT FROM AUTHOR]

Monitoring animal populations is central to wildlife and fisheries management, and the use of N-mixture models toward these efforts has markedly increased in recent years. Nevertheless, relatively little work has evaluated estimator performance when basic assumptions are violated. Moreover, diagnostics to identify when bias in parameter estimates from N-mixture models is likely is largely unexplored. We simulated count data sets using 837 combinations of detection probability, number of sample units, number of survey occasions, and type and extent of heterogeneity in abundance or detectability. We fit Poisson N-mixture models to these data, quantified the bias associated with each combination, and evaluated if the parametric bootstrap goodness-of-fit (GOF) test can be used to indicate bias in parameter estimates. We also explored if assumption violations can be diagnosed prior to fitting N-mixture models. In doing so, we propose a new model diagnostic, which we term the quasi-coefficient of variation (QCV). N-mixture models performed well when assumptions were met and detection probabilities were moderate (i.e., ≥0.3), and the performance of the estimator improved with increasing survey occasions and sample units. However, the magnitude of bias in estimated mean abundance with even slight amounts of unmodeled heterogeneity was substantial. The parametric bootstrap GOF test did not perform well as a diagnostic for bias in parameter estimates when detectability and sample sizes were low. The results indicate the QCV is useful to diagnose potential bias and that potential bias associated with unidirectional trends in abundance or detectability can be diagnosed using Poisson regression. This study represents the most thorough assessment to date of assumption violations and diagnostics when fitting N-mixture models using the most commonly implemented error distribution. Unbiased estimates of population state variables are needed to properly inform management decision making. Therefore, we also discuss alternative approaches to yield unbiased estimates of population state variables using similar data types, and we stress that there is no substitute for an effective sample design that is grounded upon well-defined management objectives. [ABSTRACT FROM AUTHOR]

• Multistate occupancy 'abundance' models can differentiate sites with relatively high and low abundance. • For detecting population trends, the same sites should be surveyed from year to year (fixed-sites). • Multistate occupancy 'abundance' models reliably detect population declines of at least 45% if a fixed-site design is used. • Multistate occupancy 'abundance' models offer advantages compared to assumption sensitive N-mixture models for modeling abundance. • Multistate occupancy 'abundance' models refine the basic occupancy model to improve abundance estimates. Detecting spatiotemporal changes in the abundances of organisms is key to effectively conserving species. While indices of abundance have long been used, there has been a shift toward model-based estimators that account for the detection process. Popular approaches including traditional occupancy models and N-mixture models entail tradeoffs. The traditional occupancy approach requires the researcher coarsen the characterization of abundance to the probability that a site is occupied or unoccupied. Conversely, N-mixture models make use of variation in counts, but perform poorly when individuals have low detectability or move into or out of sites between visits. Multistate occupancy models that differentiate relatively abundant from non-abundant states have the potential to fill this gap but have been underexplored. We conducted a simulation study to test whether multistate occupancy models could capture spatial abundance patterns and detect population declines in the face of low individual detection probability (p ≤ 0.3) and unmodeled heterogeneity (e.g., that arising from individual movement). We considered 10,773 scenarios to examine the effects of differing amounts of heterogeneity as well as alternative study designs, population parameters, and modeling choices. We tracked bias in the proportion of sites estimated to be in the abundant state for single-season models, and power to detect a declining trend across multiple years. We also evaluated data diagnostic metrics to provide guidance to users. Multistate occupancy models were able to differentiate sites with higher abundances from sites with lower abundances when there were at least medium levels of spatial heterogeneity in true abundances. If different sites were randomly selected each year, power to detect even large population declines (65%) was poor (power < 0.8). However, if the same sites were surveyed each year, and a dynamic multistate occupancy was used, multistate occupancy models could detect (power ≥ 0.8) relatively small declines (5-40%) in 20% of scenarios, and frequently detect large declines of 45-60% (mean power = 0.92). Conservation decisions rely on detecting change reliably, rarely needing absolute abundance information. Multistate occupancy models can improve our ability to detect changing abundance while accommodating low individual detection probability and heterogeneity in count monitoring data. [ABSTRACT FROM AUTHOR]

Pacific salmon experience prolonged elevation in corticosteroid hormones during important life history events including migration, reproduction, and senescence. These periods of elevated corticosteroids correspond with changes to immunity and energy metabolism; therefore, fish may be particularly vulnerable to mortality at these times. Recent studies found that stress-induced cortisol release associated with microbial community shifts in salmonids, raising the question of how longer-term corticosteroid dynamics that accompany life history transitions affect salmonid microbiomes. In this work, we experimentally evaluated the relationships between gut microbiome composition, chronically elevated corticosteroids, and mortality in juvenile Chinook salmon (Oncorhynchus tshawytscha). We found that treatment with slow-release implants of the corticosteroids cortisol or dexamethasone resulted in changes to the gut microbiome. Morbidity was also associated with microbiome composition, suggesting that the gut microbiome reflects individual differences in susceptibility to opportunistic pathogens. Additionally, we analyzed a small number of samples from adult fish at various stages of senescence. Results from these samples suggest that microbiome composition associated with gut integrity, and that the microbial communities of corticosteroid treated juveniles shift in composition toward those of senescent adults. Overall, findings from this work indicate that the gut microbiome correlates with mortality risk during periods of chronic corticosteroid elevation. [ABSTRACT FROM AUTHOR]

Pseudoloma neurophilia is a critical threat to the zebrafish (Danio rerio) model, as it is the most common infectious agent found in research facilities. In this study, our objectives were two‐fold: (1) compare the application of diagnostic tools for P. neurophilia and (2) track the progression of infection using PCR and histology. The first experiment showed that whole‐body analysis by qPCR (WB‐qPCR) can be a standardized process, providing a streamlined diagnostic protocol, without the need for extraction of specific tissues. Evaluating the course of infection in experimentally infected fish, we showed key dynamics in infection. Starting with a low dose exposure of 8000 spores/fish, the prevalence remained low until 92 days post‐exposure (dpe), followed by a 30%–40% prevalence by histology or 40%–90% by PCR until the end of the experiment at 334 dpe. WB‐qPCR positively detected infection in more fish than histology throughout the study, as WB‐qPCR detected the parasite as early as 4 dpe, whereas it was undetected by histology until 92 dpe. We also added a second slide for histologic analyses, showing an increase in detection rate from 24% to 26% when we combined all data from our experiments, but this increase was not statistically significant. [ABSTRACT FROM AUTHOR]

Improved understanding of angling behavior in recreational fisheries can help managers account for partial controllability in systems in which angling effort is not directly regulated. Relevant aspects of angling behavior include fishing participation, site choice, and catch-and-release actions and can be considered at scales of both aggregate fishing effort and individual-decision-making. Using creel survey data collected across eight fishery seasons, we predicted aggregate angling effort (e.g., daily number of boating trips engaged in fishing) and characterized influences of individual trip-based site choice for recreational fisheries acting on fall-run Chinook salmon and coho salmon near the mouth of the Columbia River, United States of America. We applied an overdispersed Poisson likelihood-based generalized linear model with an autoregressive structure to aggregate boating effort and a multinomial logit model to trip-based site choice decisions among separate ocean and estuary fishing zones. Predictive models explained 71% and 79% of out-of-sample and in-sample variability in aggregate effort, respectively, and included the covariates weekend status, Chinook salmon catch rate, tidal range, and pre-season expectations of fish abundance. In addition to reinforcing the importance of Chinook salmon catch rate and tidal range, site choice model selection revealed influences of weather, fishery restrictions, expected fishery season lengths, and the individual-specific characteristics of boat length and guide status on decision-making. Model results provide predictive models for short-term fishery planning, highlight heterogeneity in individual decision-making, and illustrate the value of standardized creel data for evaluating angling behavior. • Historical creel survey data can improve understanding of angler dynamics in recreational fisheries. • Phenomenological models of angling effort in a Pacific salmon recreational fishery predicted effort trends using creel data. • Predictors of angling effort included weekend status, lagged catch rates, tidal range, and pre-season fishery expectations. • Mechanistic site choice models revealed both fishery- and individual-based influences on trip-specific decision-making. • Comparison of effort and site choice models revealed complex interactions of fishery attributes on angling behavior. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Mitochondrial disease diagnosis requires interrogation of both nuclear and mitochondrial (mtDNA) genomes for single-nucleotide variants (SNVs) and copy number alterations, both in the proband and often maternal relatives, together with careful phenotype correlation. We developed a comprehensive mtDNA sequencing test ('MitoGenome') using long-range PCR (LR-PCR) to amplify the full length of the mtDNA genome followed by next generation sequencing (NGS) to accurately detect SNVs and large-scale mtDNA deletions (LSMD), combined with droplet digital PCR (ddPCR) for LSMD heteroplasmy quantification. Overall, MitoGenome tests were performed on 428 samples from 394 patients with suspected or confirmed mitochondrial disease. The positive yield was 11% (43/394), including 34 patients with pathogenic or likely pathogenic SNVs (the most common being m.3243A > G in 8/34 (24%) patients), 8 patients with single LSMD, and 3 patients with multiple LSMD exceeding 10% heteroplasmy levels. Two patients with both LSMD and pathogenic SNV were detected. Overall, this LR-PCR/NGS assay provides a highly accurate and comprehensive diagnostic method for simultaneous mtDNA SNV detection at heteroplasmy levels as low as 1% and LSMD detection at heteroplasmy levels below 10%. Inclusion of maternal samples for variant classification and ddPCR to quantify LSMD heteroplasmy levels further enables accurate pathogenicity assessment and clinical correlation interpretation of mtDNA genome sequence variants and copy number alterations. [ABSTRACT FROM AUTHOR]

1. Colonisation and population recovery are crucial to species persistence in environmentally variable ecosystems, but are poorly understood processes. After documenting movement rates for several species of stream fish, we predicted that this variable would influence colonisation rates more strongly than local abundance, per cent occupancy, body size and taxonomic family. We also predicted that populations of species with higher movement rates would recover more rapidly than species with lower movement rates and that assemblage structure would change accordingly. 2. To test these predictions, we removed fishes from a headwater and a mainstem creek in southwest Virginia and monitored colonisation over a 2-year period. Using an information–theoretic approach, we evaluated the relative plausibility of 15 alternative models containing different combinations of our predictor variables. Our best-supported model contained movement rate and abundance and was 41 times more likely to account for observed patterns in colonisation rates than the next-best model. Movement rate and abundance were both positively related to colonisation rates and explained 88% of the variation in colonisation rates among species. 3. Population recovery, measured as the per cent of initial abundance restored, was also positively associated with movement rate. One species recovered within 3 months, most recovered within 2 years, but two species still had not recovered after 2 years. Despite high variation in recovery, the removal had only a slight impact on assemblage structure because species that were abundant in pre-removal samples were also abundant in post-removal samples. 4. The significance of interspecific variation in colonisation and recovery rates has been underappreciated because of the widely documented recovery of stream fish assemblages following fish kills and small-scale experimental defaunations. Our results indicate that recovery of the overall assemblage does not imply recovery of each component species. Populations of species that are rare and less mobile will recover more slowly and will be more vulnerable to extinction in systems where chemical spills, hydrological alteration, extreme droughts and other impacts are frequent. [ABSTRACT FROM AUTHOR]

Pacific salmon (Oncorhynchus spp.) rearing in lakes and reservoirs above dams have been known to become heavily infected with an ectoparasitic copepod (Salmincola californiensis). Little is known about the factors that affect the parasite infection prevalence and intensity. However, previous research suggests that the parasite may negatively affect the fitness and survival of the host fish. The effect of water temperature, confinement and the density of the free‐swimming infectious stage of S. californiensis, the copepodid, on infection prevalence and intensity was evaluated by experimentally exposing juvenile Chinook Salmon (O. tshawytscha). Infection rates observed in wild populations were achieved under warm water (15–16°C) and high copepodid density (150–300/L) treatment conditions. Infection prevalence and intensity were also significantly higher in larger fish. During the infection experiment, 4.5% of infected fish died within 54 days with mortality significantly related to copepod infection intensity. The potential for autoinfection was compared to cross‐infection by cohabitation of infected fish with naïve fish. Previously infected fish had significantly greater infection intensity compared with naïve fish, indicating that infected fish can be reinfected and that they may be more susceptible than naïve fish. [ABSTRACT FROM AUTHOR]

Human 4-hydroxyphenylpyruvate dioxygenase-like (HPDL) is a putative iron-containing non-heme oxygenase of unknown specificity and biological significance. We report 25 families containing 34 individuals with neurological disease associated with biallelic HPDL variants. Phenotypes ranged from juvenile-onset pure hereditary spastic paraplegia to infantile-onset spasticity and global developmental delays, sometimes complicated by episodes of neurological and respiratory decompensation. Variants included bona fide pathogenic truncating changes, although most were missense substitutions. Functionality of variants could not be determined directly as the enzymatic specificity of HPDL is unknown; however, when HPDL missense substitutions were introduced into 4-hydroxyphenylpyruvate dioxygenase (HPPD, an HPDL orthologue), they impaired the ability of HPPD to convert 4-hydroxyphenylpyruvate into homogentisate. Moreover, three additional sets of experiments provided evidence for a role of HPDL in the nervous system and further supported its link to neurological disease: (i) HPDL was expressed in the nervous system and expression increased during neural differentiation; (ii) knockdown of zebrafish hpdl led to abnormal motor behaviour, replicating aspects of the human disease; and (iii) HPDL localized to mitochondria, consistent with mitochondrial disease that is often associated with neurological manifestations. Our findings suggest that biallelic HPDL variants cause a syndrome varying from juvenile-onset pure hereditary spastic paraplegia to infantile-onset spastic tetraplegia associated with global developmental delays. [ABSTRACT FROM AUTHOR]

• Model for integrating pinniped survey data from aerial counts with sightings-at-sea • Allows for the estimation of abundance, distribution, attendance at sites • Applied to Steller sea lions in Glacier Bay, Alaska • Estimates were biologically reasonable and comparable to previous studies • The modelling framework is generalizable to other species and systems Pinnipeds are commonly monitored using aerial photographic surveys at land- or ice-based sites, where animals come ashore for resting, pupping, molting, and to avoid predators. Although these counts form the basis for monitoring population change over time, they do not provide information regarding where animals occur in the water, which is often of management and conservation interest. In this study, we developed a hierarchical model that links counts of pinnipeds at terrestrial sites to sightings-at-sea and estimates abundance, spatial distribution, and the proportion of time spent on land (attendance probability). The structure of the model also allows for the inclusion of predictors that may explain variation in ecological and observation processes. We applied the model to Steller sea lions (Eumetopias jubatus) in Glacier Bay, Alaska using counts of sea lions from aerial photographic surveys and opportunistic in-water sightings from vessel surveys. Glacier Bay provided an ideal test and application of the model because data are available on attendance probability based on long-term monitoring. We found that occurrence in the water was positively related to proximity to terrestrial sites, as would be expected for a species that engages in central-place foraging. The proportion of sea lions in attendance at terrestrial sites and overall abundance estimates were consistent with reports from the literature and monitoring programs. The model we describe has benefit and utility for park managers who wish to better understand the overlap between pinnipeds and visitors, and the framework that we present has potential for application across a variety of study systems and taxa. [ABSTRACT FROM AUTHOR]

Warner Sucker ( Catostomus warnerensis), endemic to the lakes and tributaries of the Warner basin, southeastern Oregon, USA, was listed as threatened by the US Fish and Wildlife Service in 1985 because of habitat fragmentation and threats from introduced nonnative fish. To determine progress towards recovery and document factors that may prevent recovery, we evaluated the distribution, abundance, and movements of this species between 2006 and 2013. The species exhibits 2 distinct life-history types, a lake morph and a stream morph. The abundance of suckers in the Warner Valley lakes has decreased since the mid-1990s, and the lake fish assemblages were dominated by nonnative predatory fishes. The basin experienced drought conditions from 2007 through 2010, and the lakes partially dried which affected both sucker distribution and movement. During the drought, when lake levels were low and receding, we found little evidence of sucker recruitment in the lake populations. In 2011, stream discharge was high and the lakes refilled, and in 2012 we documented successful sucker recruitment. Warner Suckers in the tributaries were widely distributed and relatively abundant, and the stream habitat was in good condition. We did not document substantial downstream movement of suckers during the spring and summer months and found little evidence of mixing between the stream and lake populations. We documented the upstream movement of large numbers of suckers in 2 tributary streams during the spawning season. We also described associations between sucker distribution and habitat characteristics in the tributaries. Our analysis indicated support for the threatened listing and suggests that recovery efforts would be most effective by focusing on improvements to both upstream and downstream passage at irrigation diversion dams and on irrigation efficiencies. [ABSTRACT FROM AUTHOR]

In semelparous Pacific salmon, increased cortisol levels accompany sexual maturation and may be related to the rapid senescence and death that occur after spawning. In fish with extremely high cortisol, pre-spawning mortality is more likely. This may be because elevated cortisol is accompanied by energy depletion and reduces the immune capacity of sexually maturing individuals, thus increasing their susceptibility to parasites and pathogens. Several studies have measured cortisol levels in Pacific salmon during the last few weeks prior to spawning, but there is a lack of information regarding longer-term changes in resting and stressed cortisol levels of migrating adult Pacific salmon. A better understanding of the scope of the cortisol response during sexual maturation could contribute to understanding the extremely high pre-spawning mortality experienced by some threatened populations of Pacific salmon. The objective of this study was to determine the scope of the cortisol stress response in spring Chinook salmon as well as the dynamics of resting cortisol during maturation. We conducted a laboratory experiment in which plasma cortisol in adult Chinook salmon was measured before and after application of a standardized stressor applied at monthly intervals during the last three months prior to spawning. We found that resting and stressed cortisol levels increased during the last three months prior to spawning. We also found that sexually maturing Chinook salmon are able to mount a cortisol response to acute stressors when resting levels are elevated during maturation. Additionally, the effects of stress and time on cortisol dynamics differed between males and females as well as between individuals, which has implications for population resilience to anthropogenic stressors in wild populations. [ABSTRACT FROM AUTHOR]

• We illustrate how estimates from disjunct monitoring data can be used to inform adaptive water management. • Larger may flow pulses than are currently being allocated are projected to be optimal for increasing Chinook salmon smolt survival through the south delta. • Water temperature and smolt outmigration timing drive optimal water distribution but sensitivity analysis indicates water allocation changes little with temperature uncertainty indicating future monitoring should focus on outmigration timing. • We suggest using current data to start informing decisions for complex problems despite far from perfect knowledge about system responses. Monitoring is usually among the first actions taken to help inform recovery planning for declining species, but these data are rarely used formally to inform conservation decision making. For example, Central Valley Chinook salmon were once abundant, but anthropogenic activities have led to widespread habitat loss and degradation resulting in significant population declines. Monitoring data suggest survival through the southern Sacramento-San Joaquin River Delta, in particular, may be a limiting factor for juvenile Chinook salmon outmigrating from the San Joaquin River and its tributaries. However, survival and routing monitoring data have not been formally used to inform water management in a decision analytic framework. Here, we illustrate how estimates derived from disjunct monitoring data can be used to inform water management and as a basis for adaptively managing flows. We aggregated a meta-analysis of Chinook salmon smolt survival and routing estimates through the south Delta with other sources of data to develop a survival and routing simulation model to estimate optimal flows for the San Joaquin River during smolt outmigration from February–May. We found that large flow pulses at predictable times during the spring are projected to be optimal for increasing Chinook salmon smolt survival to the San Francisco Bay and that optimal scenarios differed somewhat with water year type. Sensitivity analysis revealed temperature and smolt outmigration timing are driving optimal pulse distribution and that water allocation changes little with parameter uncertainty. This case study highlights the utility of the decision-analytic framework for solving conservation problems. [ABSTRACT FROM AUTHOR]

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, cortisol and 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Perfluoroalkyl acids (PFAAs) are widespread contaminants emanating from, among other sources, the production/degradation of fluorinated chemicals used in surface repellant applications, such as carpet manufacturing. The goal of the present study was to assess the concentrations of PFAAs, including perfluorooctane sulfonate (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), perfluoroundecanoic acid (PFUA), and perfluorooctane sulfonamide (PFOSA), in surface waters both near a wastewater land application system (LAS) in Dalton (GA, USA), home to North America's largest carpet manufacturing site, and distant to this location (Altamaha River, GA, USA) to understand the fate of PFAAs in freshwater. Levels of PFAAs were high in the Conasauga River (GA, USA) downstream of the LAS (PFOA, 253-1,150 ng/L; PFOS, 192-318 ng/L; PFNA, 202-369 ng/L; PFDA, 30.1-113 ng/L; PFUA, 58.0-99.2 ng/L; PFOSA, 162-283 ng/L) and in streams and ponds in Dalton (PFOA, 49.9-299 ng/L; PFOS, 15.8-120 ng/L), and were among the highest measured at a nonspill or direct-lease location. Perfluoroalkyl acids in the Altamaha River were much lower (PFOA, 3.0-3.1 ng/L; PFOS, 2.6-2.7 ng/L), but were a source of PFAAs to Georgia's estuaries. A preliminary hazard assessment indicated that concentrations of PFOS at two sites in the Conasauga River exceeded the threshold effect predicted for birds consuming aquatic organisms that are exposed continuously to the PFOS levels at these sites. Assuming that toxicity for all PFAAs quantified is equal to that of PFOS, the sum total PFAAs at two sites within the Conasauga River exceeded PFOS thresholds for aquatic and avian species, warranting additional research. [ABSTRACT FROM AUTHOR]

We used strong inference with Akaike's Information Criterion (AIC) to assess the processes capable of explaining long-term (1984-1995) variation in the per capita rate of change of mottled sculpin (Cottus bairdi) populations in the Coweeta Creek drainage (USA). We sampled two fourth- and one fifth-order sites (BCA [uppermost], BCB, and CC [lowermost]) along a downstream gradient, and the study encompassed extensive flow variation. Physical habitat availability varied significantly both within and among the sites. Sculpin densities in all sites were highly stable (coefficients of variation = 0.23-0.41) and sampling variability was low (coefficients of variation = 0.11-0.15). Population stability was positively associated with habitat stability, and the only significant correlations of population parameters among sites involved juveniles. Sculpin densities were significantly higher in BCB than in CC. The data suggest that, despite their proximity, the dynamics of populations within the sites are being determined by small-scale (i.e., 30-50 m) rather than broad-scale spatial processes. Both AIC and Dennis and Taper analyses indicated that simple density dependence had the greatest ability to explain variation in r for all life-history classes in all sites (AIC, seven of nine cases; Dennis and Taper, nine of nine cases). Multiprocess models had little explanatory power. When adults were removed from two sites, juvenile sculpin shifted into microhabitats formerly occupied by adults. No shifts occurred in control sites. Consequently, it is likely that the patterns of density dependence observed in all three sites were a consequence of intraspecific competition for space. Our findings argue for a multitiered approach to the study of population variation, one that encompasses long-term monitoring, spatial variation, and experimental testing of potential mechanisms. [ABSTRACT FROM AUTHOR]