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Large wood (LW) plays important geomorphic and ecological roles in rivers and is widely used as a restoration tool. Changes to floodplain land use and historical removal have altered wood dynamics in fluvial systems globally. We know little about the distribution and dynamics of LW in great rivers (approximately >105 km2) like the Upper Mississippi and Illinois Rivers despite its ecosystem importance and use in restoration projects. We assessed LW occurrence data collected by the fisheries component of the Upper Mississippi River Restoration Program's Long Term Resource Monitoring element. We analysed 25 years of data collected across six reaches of the Upper Mississippi and Illinois Rivers that represented contrasting physiographic settings, and across four aquatic area types comprising gradients of hydrology, connectivity and geomorphology. We tested hypotheses on drivers of LW occurrence using generalised linear mixed effects models, where occurrence was predicted by reach‐ and local‐scale environmental variables. Occurrence varied significantly across reaches and aquatic area types. In general, wood occurred more frequently upriver and in side channels compared to other aquatic areas. Large wood was most strongly predicted systemically by reach identity but not local‐scale variables, underscoring the importance of broad‐scale physiographic gradients in defining hydrogeomorphic processes. Floodplain forests and shoreline revetment were consistently important predictors across reaches. Our findings show that the spatial variability of LW occurrence reflects the physical variability of the Upper Mississippi and Illinois Rivers. They also reveal the value in using geomorphic classifications as frameworks for understanding physical processes like LW dynamics because of their ability to contextualise site‐scale conditions. The baseline understanding of LW abundance across different hydrogeomorphic gradients and scales presented here can give insight into how to more effectively target restoration efforts in great rivers and contribute to a broader understanding of LW dynamics where such studies have been lacking. [ABSTRACT FROM AUTHOR]

Scientists and resource managers increasingly use Markdown-based tools to create reproducible reports and manuscripts. These workflows allow people to use standardized methods that are more reproducible, efficient, and transparent than other standard office tools. We present a Quarto template and demonstrate how this template may be used for the Journal of Fish and Wildlife Management. This template may also be readily adapted to other journals that use Microsoft Word-based workflows and for other product types such as annual reports. We also provide a high-level overview of Quarto and other Markdown-based workflows. Last, we provide examples of some features of the Quarto publishing system that may be helpful for authors when customizing Quarto templates for specific journal formatting requirements and other product types. [ABSTRACT FROM AUTHOR]

Natural resource managers commonly use population-level models to aid in understanding the status of target populations or the potential implications of management actions. Sensitivity analyses, specifically, local sensitivity analysis (LSA) and global sensitivity analysis (GSA), exist as tools to improve understanding of these models, the importance of specific parameters to model outcomes, and the assumptions inherent to population models. However, applied ecology and closely related fields such as fisheries and wildlife management rarely use LSA or GSA. Here, we apply LSA and GSA to the Spatially Explicit Invasive Carp Population model, a population-level model used to simulate and compare management actions on the invasive silver carp Hypophthalmichthys molitrix population in the Illinois River. The spatial structure within the model arises from the navigation "pools" that exist between navigation lock-and-dam in the river and are also the focus of fisheries management in the river. We completed LSA and GSA for two reasons: 1) to compare the importance of model input parameters on simulated model populations and 2) to demonstrate the use of LSA and GSA for populationlevel models. In our system, we detected the most important sensitivity values generally in Alton Pool. This pool is the farthest downstream and includes a direct connection with the Mississippi River. These results indicate that the population dynamics in Alton Pool are an important driver of the population dynamics throughout the Illinois River. Management outcomes in this system will, therefore, be strongly dependent on the dynamics of Alton Pool. [ABSTRACT FROM AUTHOR]

Behavioral deterrents of among-pool movement represent a promising tool for controlling invasive fish populations. To date, much of the research in this area has been focused on the direct effectiveness of different methods of deterrence. However, the effect of these structures on populations in spatially complex habitats is unknown. We combine a metacommunity model with movement data of two invasive species (bighead carp and silver carp) in a large river to assess local and river-wide scale population outcomes of deterrent locations. We calculated (1) which potential deterrent locations are most effective at reducing the growth at the invasion front (2) the river-scale population effects at each location, and (3) what, if any, are the risks imposed by altering the current spatial dynamics. We found that the effects on the population dynamics at the invasion front varied with the location of deterrents, ranging from near zero to effects equal to the reduction in an individual's movement across the deterrent. The river-scale population growth rate was slightly increased by all potential deterrent placements because the deterrents tended to concentrate more of the river-scale population into pools with the highest recruitment rates. The short-term, transient dynamics followed a strictly decreasing pattern after deterrent placement suggesting no additional short-term risk. These results suggest that deterrents can be an effective and low-risk intervention for the control of invasive carp, although the population level effect will depend on the interaction of the traits and behavior of the species with the physical character and spatial structure of the habitat. [ABSTRACT FROM AUTHOR]

Effective undergraduate statistical education requires training using real-world data. Textbook datasets seldom match the complexities and messiness of real-world data and finding these datasets can be challenging for educators. Consulting and industrial datasets often have nondisclosure agreements. Academic datasets often require subject area expertise beyond those of a general education or lack connections to real-world applications. Many governments, including the United States, now require the release of data from projects they directly complete or fund though grants and contracts. We show how statistical educators may find datasets and incorporate them into courses. Specifically, we use two examples from the U.S. Geological Survey (USGS) and one example from the ecology literature. We demonstrate the use of these datasets in an upper-level analysis of variance (ANOVA) class. In addition to describing how we found the datasets, we describe how to include them into course work and the course's student assessments. We have used these datasets over multiple semesters and included student feedback from these courses. Although our examples focus on an ANOVA class, the general methods for finding data shared here could be used for statistical classes ranging from high school to graduate education. for this article are available online. [ABSTRACT FROM AUTHOR]

In preparation for his doctoral studies at Stanford University, the late David F. DeSante spent the fall of 1968 studying migratory landbirds at Cabo San Lucas. Although his hopes to capture numerous vagrant warblers were not met, he amassed an impressive list of distributional records for the Baja California Peninsula at a time when few ornithologists were working there. Among these were peninsular firsts for the Ring-necked Duck (Aythya collaris), Broad-billed Hummingbird (Cynanthus latirostris), Broad-winged Hawk (Buteo platypterus), Bobolink (Dolichonyx oryzivorus), and Painted Bunting (Passerina ciris). Another six species, and one subspecies, were found for the first time in Baja California Sur. Venturing away from the immediate confines of Cabo San Lucas, DeSante established the first peninsular record of the Gray-headed Junco (Junco hyemalis caniceps) and first state records for another five species and one subspecies. Although many of these records have been reported previously, the junior authors believe it is appropriate to synthesize them more completely with current context, in Dave’s honor. [ABSTRACT FROM AUTHOR]

Background: Hidden Markov Models (HMMs) are often used to model multi-state capture-recapture data in ecology. However, a variety of HMM modeling approaches and software exist, including both maximum likelihood and Bayesian methods. The diversity of these methods obscures the underlying HMM and can exaggerate minor differences in parameterization. Methods: In this paper, we describe a general framework for modelling multi-state capture-recapture data via HMMs using both maximum likelihood and Bayesian methods. We then apply an HMM to invasive silver carp telemetry data from the Illinois River and compare the results estimated by both methods. Results: Our analysis demonstrates disadvantages of relying on a single approach and highlights insights obtained from implementing both methods together. While both methods often struggled to converge, our results show biologically informative priors for Bayesian methods and initial values for maximum likelihood methods can guide convergence toward realistic solutions. Incorporating prior knowledge of the system can successfully constrain estimation to biologically realistic movement and detection probabilities when dealing with sparse data. Conclusions: Biologically unrealistic estimates may be a sign of poor model convergence. In contrast, consistent convergence behavior across approaches can increase the credibility of a model. Estimates of movement probabilities can strongly influence the predicted population dynamics of a system. Therefore, thoroughly assessing results from HMMs is important when evaluating potential management strategies, particularly for invasive species. [ABSTRACT FROM AUTHOR]

Natural resource managers use tools to control invasive species. In theory, stocking YY males or ZZ females would allow managers to skew sex ratios until populations collapse. In combination with other suppression methods, such as removal, this approach could be incorporated into Integrated Pest Management plans. For example, fishery managers have stocked YY males to control isolated non-native brook trout (Salvelinus fontinalis) populations. However, life histories and demographic factors (e.g., lifespans) vary across species and could affect the feasibility of skewing sex ratios as an effective control strategy for a given population. Likewise, some species may have sex determinations that do not allow population control through sex-skewing methods. We compared five representative aquatic invasive species with global invasion ranges for potential control by skewing the sex ratio through closed population simulations: red swamp crayfish (Procambarus clarkii), zebra mussels (Dreissena polymorpha), lake trout (Salvelinus namaycush), silver carp (Hypophthalmichthys molitrix), and Nile tilapia (Oreochromis niloticus). We determined that Nile tilapia, red swamp crayfish, and zebra mussels would be the most suitable to control through skewing the sex ratio assuming appropriate sex determination exists in the species. Lake trout could be eliminated by stocking YY males but would require either long stocking periods or high stocking numbers because of the long lifespan of the species. Silver carp populations were more difficult to crash because they live longer and produce many recruits. Broadly, these patterns demonstrated that short lived species lend themselves to control by skewing the sex ratio. [ABSTRACT FROM AUTHOR]

Exotic species introductions are a major threat to biodiversity. The first step to their control involves identifying their presence, distribution, and impacts on native species and their habitats, especially in highly diverse regions. We update and document new records of exotic freshwater fauna from the Baja California Mediterranean region. We found 157 locality records of 17 exotic aquatic species; 16 genera and 15 families were recorded. Five species are new records for the region: Malaysian trumpet snail (Melanoides tuberculata), black bullhead catfish (Ameiurus melas), common carp (Cyprinus carpio), spiny softshell turtle (Apalone spinifera), and red-eared slider (Trachemys scripta). The catfish, carp, and softshell turtle have been previously reported from Baja California, but only from the Colorado River and adjacent Mexicali Valley, while the snail and slider represent new state records. Of the 157 locality records, 71 were found in published literature and 86 represent new records from field observations, collected specimens and citizen science observations. Based on discussions with local ranchers and landowners, some exotic species were introduced for food or aesthetic purposes, emphasizing the need for environmental programs to stop these actions. [ABSTRACT FROM AUTHOR]

Invasive species management can benefit from predictive models that incorporate spatially explicit demographics and dispersal to guide resource allocation decisions.We used invasive bigheaded carps (Hypophthalmichthys spp.) in the Illinois River, USA as a case study to create a spatially explicit model to evaluate the allocation of future management efforts. Specifically, we compared additional harvest (e.g. near the invasion front vs. source populations) and enhanced movement deterrents to meet the management goal of reducing abundance at the invasion front.We found additional harvest in lower river pools (i.e. targeting source populations) more effectively limited population sizes upriver at the invasion front compared to allocating the same harvest levels near the invasion front. Likewise, decreasing passage (i.e. lock and dam structures) at the farthest, feasible downriver location limited invasion front population size more than placing movement deterrents farther upriver.Synthesis and applications. Our work highlights the benefits of adopting a multipronged approach for invasive species management, combining suppression of source populations with disrupting movement between source and sink populations thereby producing compounding benefits for control. Our results also demonstrate the importance of considering metapopulation dynamics for invasive species control programs when achieving long‐term management goals. [ABSTRACT FROM AUTHOR]

Metapopulation models include spatial population dynamics such as dispersion and migration between subpopulations. Integral projection models (IPMs) can include demographic rates as a function of size. Traditionally, metapopulation models do not included detailed populaiton models such as IPMs. In some situations, both local population dynamics (e.g. size‐based survival) and spatial dynamics are important.We present a Python package, MetaIPM, which places IPMs into a metapopulation framework, and allow users to readily construct and apply these models that combine local population dynamics within a metapopulation framework.MetaIPM includes an IPM for each subpopulation that is connected to other subpopulations via a metapopulation movement model. These movements can include dispersion, migration or other patterns. The IPM can include for size‐specific demographic rates (e.g. survival, recruitment) as well as management actions, such as length‐based harvest (e.g. gear specific capture sizes, varying slot limits across political boundaries). The model also allows for changes in metapopulation connectivity between locations, such as a fish passage ladders to enhance movement or deterrents to reduce movement. Thus, resource managers can use MetaIPM to compare different management actions such as the harvest gear type (which can be length‐specific) and harvest locations.We demonstrate how MetaIPM may be applied to inform managers seeking to limit the spread of an invasive species in a system with important metapopulation dynamics. Specifically, we compared removal lengths (all length fish versus longer fish only) for an invasive fish population in a fragmented, inland river system. MetaIPM allowed users to compare the importance of harvesting source populations away from the invasion front, as well as species at the invasion front. The model would also allow for future comparisons of different deterrent placement locations in the system.Moving beyond our example system, we describe how MetaIPM can be applied to other species, systems and management approaches. The MetaIPM packages includes Jupyter Notebooks documenting the package as well as a second set of JupyterNotebooks showing the application of the package to our example system. [ABSTRACT FROM AUTHOR]

Missing data are typical yet must be addressed for proper inferences or expanding datasets to guide our limnological understanding and management of aquatic systems. Interpolation methods (i.e., estimating missing values using known values within the dataset) can alleviate data gaps and common problems. We compared seven popular interpolation methods for predicting substantial missingness in a long‐term water quality dataset from the Upper Mississippi River, U.S.A. The dataset included 80,000 sampling sites collected over 30 yr that had substantial missingness for total nitrogen (TN), total phosphorus (TP), and water velocity. For all three interpolated water quality variables, random forests had very high prediction accuracy and outperformed the methods of ordinary kriging, polynomial regressions, regression trees, and inverse distance weighting. TP had a mean absolute error (MAE) of 0.03 mg (L‐TP)−1, TN had a MAE of 0.39 mg (L‐TN)−1, and water velocity had a MAE of 0.10 m s−1. The random forests' error rates were mapped and showed low spatiotemporal variability across the riverscape, indicating high model performance across many habitat types and large spatial scales. In the current era of "big data," interpolation becomes an imperative step prior to ecological analyses yet remains unfamiliar and underutilized. Our research briefly describes the importance of addressing missingness and provides a roadmap to conduct model intercomparisons of other big datasets. We also share adaptable data analysis scripts, which allows others to readily conduct interpolation comparisons for many limnology applications and contexts. [ABSTRACT FROM AUTHOR]

Aquatic invasive species (AIS) present major ecological and economic challenges globally, endangering ecosystems and human livelihoods. Managers and policy makers thus need tools to predict invasion risk and prioritize species and areas of concern, and they often use native range climate matching to determine whether a species could persist in a new location. However, climate matching for AIS often relies on air temperature rather than water temperature due to a lack of global water temperature data layers, and predictive power of models is seldom evaluated. We developed 12 global lake (water) temperature‐derived "BioLake" bioclimatic layers for distribution modeling of aquatic species and compared "climatch" climate matching predictions (from climatchR package) from BioLake with those based on BioClim temperature layers and with a null model. We did this for 73 established AIS in the United States, training the models on their ranges outside of the United States and Canada. Models using either set of climate layers outperformed the null expectation by a similar (but modest) amount on average, but some species were occasionally found in locations with low climatch scores. Mean US climatch scores were higher for most species when using air temperature. Including additional climate layers in models reduced mean climatch scores, indicating that commonly used climatch score thresholds are not absolute but can be context specific and may require calibration based upon climate data used. Although finer resolution global lake temperature data would likely improve predictions, our BioLake layers provide a starting point for aquatic species distribution modeling. Climate matching was most effective for some species that originated at low latitudes or had small ranges. Climatch scores remain useful but limited for predicting AIS risk, perhaps because current ranges seldom fully reflect climatic tolerances (fundamental niches). Managers could consider climate matching as one of a suite of tools that can be used in AIS prioritization. [ABSTRACT FROM AUTHOR]

Objective: The ability to effectively treat parasitic infestations of fish is of high importance for fish culture facilities. However, tools or approved therapies for treating infestations on fish are limited. This paper summarizes results from four separate clinical field studies that evaluated the efficacy of hydrogen peroxide (H2O2; 35% PEROX‐AID) for reducing Gyrodactylus spp. infestation density. Methods: Three species of Gyrodactylus were studied (G. salmonis, hosts: Brook Trout Salvelinus fontinalis and Lake Trout S. namaycush; G. freemani, host: Yellow Perch Perca flavescens; G. hoffmani, host: Fathead Minnow Pimephales promelas) before and after the application of immersion H2O2 therapy. Result: Parasite density was significantly reduced for each parasite × host combination to which H2O2 therapy was applied. Two clinical field studies in salmonids were found to demonstrate substantial effectiveness that enabled 35% PEROX‐AID approval. Conclusion: Further assessments of Gyrodactylus spp. could expand the use of H2O2 for controlling these parasites in aquaculture. Specifically, H2O2 was effective at all levels tested (50 or 75 mg H2O2/L for 60 min for the Yellow Perch and Fathead Minnow clinical field studies; 100 or 150 mg H2O2/L for 30 min regardless of salt pre‐treatment for the Brook Trout study; and 100 mg H2O2/L for 30 min or 50 mg H2O2/L for 60 min for the Lake Trout study). Impact statementThe external parasite species of Gyrodactylus can be very problematic to fish raised in hatchery settings. Having approved and effective treatments to reduce parasite infestations can be helpful to hatcheries. The work summarized in this paper explored the use of hydrogen peroxide as a treatment option for hatcheries to use for reducing Gyrodactylus infestation density on four different species of fish. Hydrogen peroxide was effective at reducing Gyrodactylus infestation densities at all levels tested. [ABSTRACT FROM AUTHOR]

Two medications (one with florfenicol and one with oxytetracycline) that are approved in the United States to control mortality due to furunculosis associated with Aeromonas salmonicida were assessed to determine their efficacy in medicated feeds to treat A. salmonicida‐infected Cisco (also known as Lake Herring) Coregonus artedi. Cisco were subjected to static infection baths containing A. salmonicida or a sham control and then were distributed to replicate test tanks within four treatment groups: (1) fish infected with A. salmonicida and treated with 15 mg florfenicol·kg body weight (BW)−1·d−1, (2) fish infected with A. salmonicida and treated with 83 mg oxytetracycline·kg BW−1·d−1, (3) fish infected with A. salmonicida and treated with a nonmedicated control feed, and (4) uninfected fish treated with a nonmedicated control feed. Medicated and comparative nonmedicated feed rations were administered at 2% BW/d for 10 consecutive days in accordance with the U.S. Food and Drug Administration‐approved drug label, followed by a 7‐d postdosing observation period using only nonmedicated feed. Cisco that were infected with A. salmonicida and treated with florfenicol (79% survival) and oxytetracycline (85% survival) had significantly higher survival than A. salmonicida‐infected fish that received no medicated treatment (3% survival). No statistical difference in Cisco survival between the two medicated feed types was found. Aeromonas salmonicida was not detected in the kidney tissue of any surviving fish treated with medicated feeds at 7 d postdosing using quantitative PCR analysis. Overall, this study demonstrated that florfenicol‐ and oxytetracycline‐medicated feeds were effective A. salmonicida treatments for Cisco. Outcomes may inform ongoing propagation efforts for Cisco restoration within the Great Lakes basin. [ABSTRACT FROM AUTHOR]

Mathematical biology is a wide field of study with many venues that undergraduate students can access through research. However, the topics of study for these students can be overwhelming, and many topics of study yield either only trivial results or abstract outcomes that are nonintuitive and difficult to understand. We have used natural resource modeling, and more specifically, a partnership between academic researchers and federal scientists, as a bridge between undergraduate research and mathematical biology. Our collaboration is an interdisciplinary team that combines biology, mathematics, and statistics professors with government research scientists. As a team, we have mentored students through opportunities such as a Research Experiences for Undergraduates and other projects. In this article, we provide an overview of how we develop questions for undergraduates and outline two case studies, both of which resulted in peer reviewed journal articles. Last, we describe how we also transfer the results from these undergraduate projects to resource managers so the results may be applied to real world problems. [ABSTRACT FROM AUTHOR]

As a generalization of stage-based matrix models, integral projection models (IPMs) have been used to describe the size-based dynamics of wildlife and fisheries populations. Although some matrix models have explicitly included species interactions, few IPMs have expanded beyond single species, which limits their ability to describe the competitive dynamics of co-occuring taxa. We present a coupled system of IPMs where intra- and inter-specific competition may reciprocally affect the life-histories of two species. We investigated the potential role that competition has on two over- lapping fish species in the upper Mississippi River system: the native gizzard shad (Dorosoma cepedianum) and the invasive silver carp (Hypophthalmichthys molitrix). Numerical simulations of this system indicated that the coupled IPMs could exhibit asymptotic behaviors similar to traditional, non-linear competition models. Specifically, by altering the competition coefficients, we demonstrate this model's ability to detect competitive exclusion, species coexistence, and dual extinction outcomes. [ABSTRACT FROM AUTHOR]

Freshwater mussels (order Unionida) play a key role in freshwater systems as ecosystem engineers and indicators of aquatic ecosystem health. The fauna is globally imperilled due to a diversity of suspected factors; however, causes for many population declines and mortality events remain unconfirmed due partly to limited health assessment tools. Mussel-monitoring activities often rely on population-level measurements, such as abundance and age structure, which reflect delayed responses to environmental conditions. Measures of organismal health would enable preemptive detection of declining condition before population-level effects manifest. Metabolomic analysis can identify shifts in biochemical pathways in response to stressors and changing environmental conditions; however, interpretation of the results requires information on inherent variability of metabolite concentrations in mussel populations. We targeted metabolites in the haemolymph of two common mussels, Lampsilis cardium and Lampsilis siliquoidea , from three Indiana streams (USA) using ultra-high-performance liquid chromatography combined with quadrupole time-of-flight mass spectroscopy. The influence of species, stream and sex on metabolite variability was examined with distance-based redundancy analysis. Metabolite variability was most influenced by species, followed by site and sex. Inter- and intraspecies metabolite variability among sexes was less distinct than differences among locations. We further categorized metabolites by occurrence and variability in mussel populations. Metabolites with high occurrence (Categories 1 and 2) included those indicative of energy status (catabolism versus anabolism; arginine, proline, carnitine, nicotinic acid, pantothenic acid), oxidative stress (proline, glutamine, glutamate) and protein metabolism (thymidine, cytidine, inosine). Metabolites with lower occurrence (Category 3) are constituents of assorted metabolic pathways and can be important biomarkers with additional temporal sampling to characterize their variability. These data provide a reference for future temporal (before/after) monitoring and for studies of stressor–metabolite linkages in freshwater mussels. [ABSTRACT FROM AUTHOR]

Metapopulation models may be applied to inform natural resource management to guide actions targeted at location‐specific subpopulations. Model insights frequently help to understand which subpopulations to target and highlight the importance of connections among subpopulations. For example, managers often treat aquatic invasive species populations as discrete populations due to hydrological (e.g., lakes, pools formed by dams) or jurisdictional boundaries (e.g., river segments by country or jurisdictional units such as states or provinces). However, aquatic invasive species often have high rates of dispersion and migration among heterogenous locations, which complicates traditional metapopulation models and may not conform to management boundaries. Controlling invasive species requires consideration of spatial dynamics because local management activities (e.g., harvest, movement deterrents) may have important impacts on connected subpopulations. We expand upon previous work to create a spatial linear matrix model for an aquatic invasive species, Bighead Carp, in the Illinois River, USA, to examine the per capita contributions of specific subpopulations and impacts of different management scenarios on these subpopulations. Managers currently seek to prevent Bighead Carp from invading the Great Lakes via a connection between the Illinois Waterway and Lake Michigan by allocating management actions across a series of river pools. We applied the model to highlight how spatial variation in movement rates and recruitment can affect decisions about where management activities might occur. We found that where the model suggested management actions should occur depend crucially on the specific management goal (i.e., limiting the growth rate of the metapopulation vs. limiting the growth rate of the invasion front) and the per capita recruitment rate in downstream pools. Our findings illustrate the importance of linking metapopulation dynamics to management goals for invasive species control. [ABSTRACT FROM AUTHOR]

Loop-mediated isothermal amplification (LAMP) is a rapid molecular detection technique that has been used as a diagnostic tool for detecting human and animal pathogens for over 20 years and is promising for detecting environmental DNA shed by invasive species. We designed a LAMP assay to detect the invasive carps, silver carp (Hypophthalmichthys molitrix), bighead carp (Hypophthalmichthys nobilis), black carp (Mylopharyngodon piceus), and grass carp (Ctenopharyngodon idella). To determine the sensitivity of the LAMP assay, we determined limit of detection (LOD) for each invasive carp species and compared with the performance of a grass carp quantitative PCR (qPCR) assay in LOD and in a mesocosm study. We used two grass carp densities, 3 juvenile grass carp in one mesocosm and 33 juvenile grass carp in the other. Prior to adding grass carp to the mesocosms, we added 68 kg of fathead minnows (Pimephales promelas) to each mesocosm to simulate farm ponds used for raising bait fish. We filtered 500 mL of water per sample to compare LAMP and qPCR analysis, and we collected 50 mL grab samples that were only analyzed using qPCR to gain additional data using a higher-throughput method to monitor environmental DNA (eDNA) levels throughout the study period. No eDNA for any of the four invasive carp species was detected in water collected from the mesocosms during the three days prior to adding grass carp. Forty-eight hours after grass carp addition to mesocosms, we detected grass carp eDNA in the mesocosm containing 33 grass carp using the LAMP assay. However, we failed to detect any grass carp DNA in the mesocosm containing 3 grass carp with the LAMP assay throughout the study. We analyzed the data using an occupancy model and found that the 500 mL filter samples yielded a higher eDNA capture probability than 50 mL grab samples in the mesocosm containing three grass carp but had similar eDNA capture probability in the mesocosm containing 33 grass carp. Both LAMP and qPCR reliably detected grass carp eDNA 2 days after grass carp addition, but detections were more consistent with qPCR. The LAMP assay may have utility for certain niche uses because it can be used to rapidly analyze eDNA samples and is robust to inhibition, despite having some limitations. [ABSTRACT FROM AUTHOR]

The effect of Parasite‐S® (an aqueous formaldehyde solution) on the nitrification processes of biofilters was evaluated in two recirculating aquaculture systems (RASs). Rearing tanks in the warmwater RAS contained yellow perch (Perca flavescens) and grass carp (Ctenopharyngodon idella) with an initial weight of 166.8 kg and a mean density of 39.5 kg/m3. Rearing tanks in the coldwater RAS contained rainbow trout (Oncorhynchus mykiss) and lake trout (Salvelinus namaycush) with an initial weight of 1377.8 kg at a system density of 41.9 kg/m3. Parasite‐S® was administered to the entire system on four consecutive days in both trials to achieve a nominal concentration of 14.8 mg/L formaldehyde (40 mg/L formalin) at the biofilter. Removal efficiencies for total ammonia nitrogen (TAN) and nitrite nitrogen were measured as indicators of biofilter nitrification processes. The active ingredient in Parasite‐S®, formaldehyde, was measured until it was below the method detection limit of 0.8 mg/L. TAN volumetric removal rate was significantly decreased in both systems after formaldehyde addition and remained below pre‐exposure efficiency in the coldwater RAS. Nitrite nitrogen volumetric removal rate was not significantly different, but the slope and intercepts were less after formaldehyde addition indicating an effect on the nitrifying bacteria. Although removal rates were decreased, no mortality occurred after four consecutive formaldehyde indefinite bath exposures in either system. [ABSTRACT FROM AUTHOR]

Although there are many methods to determine ingestion and absorption of aquafeeds, none exist that are simple, cost‐effective, and quantitative and that can mark fish with a long‐lasting, visible indicator. In addition to aquafeed development, selective baits are needed that can be used for aquatic invasive species removal efforts, including for Grass Carp Ctenopharyngodon idella. Bait incorporated with a pesticide would allow for selective removal of targeted species. A method to quickly assess multiple bait formulations was developed to expediate development for invasive species management. Incorporation of Sudan Black B (SBB) in aquafeeds at concentrations greater than 75 and 120 mg SBB/kg fish resulted in pigmented external soft tissues of Largemouth Bass Micropterus salmoides and Rainbow Trout Oncorhynchus mykiss, respectively, 24 h after consumption. Visual confirmation of consumption was detectable in the gastrointestinal tract at all concentrations tested (≥10 mg SBB/kg) and quantifiable by absorbance measured at 601 nm from extracted SBB in tissues at concentrations less than those required for visual pigmentation. Although SBB was detectable in multiple tissues, fin and mandible tissues yielded the greatest accuracy in estimating consumption from extracted SBB. Compared with other tissues tested, liver tissue accumulated the highest level of SBB but had the greatest variability, while muscle tissue accumulated little detectable SBB. We used the SBB analytical method to compare consumption of six novel baits that were in the initial developmental stages to produce a palatable bait formulation designed to attract Grass Carp for management control. Overwhelming preference of a rapeseed bait formulation was confirmed using SBB as a tracer of consumption in the laboratory; however, use of SBB under natural conditions may be valuable for answering additional questions. Baits incorporated with SBB allowed for the rapid, simultaneous assessment of multiple formulations and could allow for future refinement of management baits, with results available as quickly as 24–72 h after application. [ABSTRACT FROM AUTHOR]

The article presents the discussion on Hooded Grosbeak (Coccothraustes abeillei) being endemic to evergreen montane forests from northern Mexico to northern Central America including pale gray down feathers being present on the head and down feathers also scattered on the back and wings.

Invasive Bighead Carp Hypophthalmichthys nobilis and Silver Carp H. molitrix have infested and caused largescale ecological and economic damage to the Illinois, Mississippi, and Ohio rivers. We compiled demographic data from 42,995 fish from 23 pools in the Illinois, Mississippi, and Ohio rivers, which universities and management agencies previously collected as part of management, monitoring, and research activities. We used this data set to test whether demographic rates (length-weight relations including body condition, mortality, growth curves, and female maturity curves) varied among subpopulations across a gradient of invasion status. We found that length-weight relations and growth curves varied among subpopulations, whereas maturity curves did not. Our findings demonstrated spatial variability in demographic rates for Bighead and Silver carp across a broad geographic area in relation to invasion status and river conditions. Herein, we provide general subpopulation management options and present different hypotheses to explain the observed spatial variability in demographic rates. [ABSTRACT FROM AUTHOR]

Invasive carps are ecologically and economically problematic fish species in many large river basins in the United States and pose a threat to aquatic ecosystems throughout much of North America. Four species of invasive carps: black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella), silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), are particularly concerning for native ecosystems because they occupy and disrupt a variety of food and habitat niches. In response, natural resource agencies are developing integrated pest management (IPM) plans to mitigate invasive carps. Control tools are one key component within a successful IPM program and have been a focal point for development by governmental agencies and academic researchers. For example, behavioural deterrents and barriers that block migratory pathways could limit carps range expansion into new areas, while efficient removal methods could suppress established carp populations. However, control tools are sometimes limited in practice due to uncertainty with deployment, efficacy and availability. This review provides an overview of several emerging modelling approaches and control technologies that could inform and support future invasive carp IPM programs. [ABSTRACT FROM AUTHOR]

Invasive carps are ecologically and economically problematic fish species in many large river basins in the United States and pose a threat to aquatic ecosystems throughout much of North America. Four species of invasive carps: black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella), silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), are particularly concerning for native ecosystems because they occupy and disrupt a variety of food and habitat niches. In response, natural resource agencies are developing integrated pest management (IPM) plans to mitigate invasive carps. Control tools are one key component within a successful IPM program and have been a focal point for development by governmental agencies and academic researchers. For example, behavioural deterrents and barriers that block migratory pathways could limit carps range expansion into new areas, while efficient removal methods could suppress established carp populations. However, control tools are sometimes limited in practice due to uncertainty with deployment, efficacy and availability. This review provides an overview of several emerging modelling approaches and control technologies that could inform and support future invasive carp IPM programs. [ABSTRACT FROM AUTHOR]

Natural resource management and supporting research teams need computational fluency in the data and model‐rich 21st century. Computational fluency describes the ability of practitioners and scientists to conduct research and represent natural systems within the computer's environment. Advancement in information synthesis for natural resource management requires more sophisticated computational approaches, as well as reproducible, reusable, extensible, and transferable methods. Despite this importance, many new and current natural resource practitioners lack computational fluency and no common set of recommended resources and practices exist for learning these skills. Broadly, attaining computational fluency entails moving beyond the simple use of computers to applying sound computational principles and methods and including computational experts (such as computer scientists) on research teams. Our path for computational fluency includes using open‐source tools when possible; reproducible data management, statistics, and modeling; understanding and applying the benefits of basic computer programming to carry out more complex procedures; tracking code with version control; working in controlled computer environments; and using advanced computing resources. Considerations for Resource ManagersNatural resource management increasingly uses computer‐generated results to inform and guide decision making. Open science requires that these data and software be reproducible. In turn, open science promotes computational fluency among natural resource managers, researchers, and educators.Based upon our experiences and perspectives working to support natural resource professionals, many natural resource managers would like to attain computationally fluency, yet lack formal training.We provide a path to computational fluency that emphasizes: using open‐source tools when possible; reproducible data management, statistics, and modeling; understanding and applying the basic computer programming philosophy to carry out both simple and more complex procedures; tracking code with version control; working in controlled computer environments; and using advanced computing resources.Natural resource managers, educators, and researchers can use their computationally fluency skills to promote open science in their own work. [ABSTRACT FROM AUTHOR]

Copyright of Western Birds is the property of Western Field Ornithologists and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

A central challenge in applied ecology is understanding the effect of anthropogenic fatalities on wildlife populations and predicting which populations may be particularly vulnerable and in greatest need of management attention. We used three approaches to investigate the potential effects of fatalities from collisions with wind turbines on 14 raptor species for both current (106 GW) and anticipated future (241 GW) levels of installed wind energy capacity in the United States. Our goals were to identify species at relatively high vs low risk of experiencing population declines from turbine collisions and to also compare results generated from these approaches. Two of the approaches used a calculated turbine‐caused mortality rate to decrement population growth, where population trends were derived either from the North American Breeding Bird Survey or from a matrix model parameterized from literature‐derived demographic values. The third approach was potential biological removal, which estimates the number of fatalities that allow a population to reach and maintain its optimal sustainable population set by management objectives. Different results among the methods reveal substantial gaps in knowledge and uncertainty in both demographic parameters and species‐specific estimates of fatalities from wind turbines. Our results suggest that, of the 14 species studied, those with relatively higher potential of population‐level impacts from wind turbine collisions included barn owl, ferruginous hawk, golden eagle, American kestrel, and red‐tailed hawk. Burrowing owl, Cooper's hawk, great horned owl, northern harrier, turkey vulture, and osprey had a relatively lower potential for population impacts, and results were not easily interpretable for merlin, prairie falcon, and Swainson's hawk. Projections of current levels of fatalities to future wind energy scenarios at 241 GW of installed capacity suggest some species could experience population declines because of turbine collisions. Populations of those species may benefit from research to identify tools to prevent or reduce raptor collisions with wind turbines. [ABSTRACT FROM AUTHOR]

Carbon dioxide (CO2) has been approved by the US Environmental Protection Agency as a new aquatic pesticide to control invasive Asian carps and other aquatic nuisance species in the United States. However, limited CO2 toxicity data could make it challenging for resource managers to characterize the potential risk to nontarget species during CO2 applications. The present study quantified the toxicity of CO2 to 2 native riverine fishes, bluegill (Lepomis macrochirus) and fathead minnow (Pimephales promelas), using 12‐h continuous flow‐through CO2 exposure at 5, 15, and 25 °C water temperatures. Resulting survival indicated that bluegill (median lethal concentration [LC50] range 91–140 mg/L CO2) were more sensitive to CO2 than fathead minnow (LC50 range 235–306 mg/L CO2) across all water temperatures. Bluegill were also more sensitive to CO2 at 5 °C (LC50 91 mg/L CO2, 95% CI 85–96 mg/L CO2) than at 25 °C (LC50 140 mg/L CO2, 95% CI 135–146 mg/L CO2). Fathead minnow showed an opposite response and were less sensitive at 5 °C (LC50 306 mg/L CO2, 95% CI 286–327 mg/L CO2) relative to 25 °C (LC50 235 mg/L CO2, 95% CI 224–246 mg/L CO2). Our results show that CO2 toxicity can differ by species and water temperature. Data from the present study may inform decisions related to the use of CO2 as a control tool. Environ Toxicol Chem 2020;39:2247–2255. Published 2020. This article is a U.S. government work and is in the public domain in the USA. [ABSTRACT FROM AUTHOR]

Natural resource managers use barriers to deter the movement of aquatic invasive species. Research and development of new invasive species barriers is often evaluated in pond and field scales using high‐resolution telemetry data. Telemetry data sets can be a rich source of data about fish movement and behavior but can be difficult to analyze due to the size of these data sets as well as their irregular sampling intervals. Due to the challenges, most barrier studies only use summary endpoints, such as barrier passage counts or average (e.g., mean or median) fish distance from the barrier, to describe the data. To examine more fine‐scale fish movement patterns, we developed a first‐order Markov chain. We then used this model to help understand the impacts of a barrier on fish behavior. For our study system, we used data from a previous study examining how bighead and silver carp (two invasive fish species in the United States) responded to a carbon dioxide (CO2) barrier in a pond. Considerations for management Based upon our findings, management considerations include: Markov chains can be used to describe and quantify movement patterns of aquatic organisms responding to barriers. These models provide insight not possible with previously used summary approaches.The CO2 barrier changed both the locations of fish and movement patterns of fish. The changes in movement were not captured using conventional endpoints.Specifically, fish had less random movement patterns during periods of CO2 exposure. This provides evidence that bighead and silver carp actively avoided areas with CO2 and also shows that our approach can help assess random versus nonrandom movements [ABSTRACT FROM AUTHOR]

Statistical inferences play a critical role in ecotoxicology. Historically, null hypothesis significance testing (NHST) has been the dominant method for inference in ecotoxicology. As a brief and informal definition of NHST, researchers compare (or "test") an experimental treatment or observation against a hypothesis of no relationship (the "null hypothesis") using the collected data to see if the observed values are statistically "significant" given predefined error rates. The resulting probability of observing a value equal to or greater than the observed value assuming the null hypothesis is true is the p value. Criticisms of NHST have existed for almost a century and have recently grown to the point where statisticians, including the American Statistical Association (ASA), have felt the need to clarify the role of NHST and p values beyond their current common use. These limitations also exist in ecotoxicology. For example, a review of the 2010 Environmental Toxicology & Chemistry (ET&C) volume that found many authors did not correctly report p values. We repeated this review looking at the 2019 volume of ET&C. Incorrect reporting of p values still occurred almost a decade later. Problems with NHST and p values highlight the need for statistical inferences besides NHST, something long known in ecotoxicology and the broader scientific and statistical communities. Furthermore, concerns such as these led the executive director of the ASA to recommend against use of "statistical significance" in 2019. In light of these criticisms, ecotoxicologists require alternative methods. We describe some alternative methods including confidence intervals, regression analysis, dose–response curves, Bayes factors, survival analysis, and model selection. Lastly, we provide insights for what ecotoxicology might look like in a post–p value world. Environ Toxicol Chem 2020;39:1657–1669. Published 2020. This article is a U.S. Government work and is in the public domain in the USA. [ABSTRACT FROM AUTHOR]

Zebra mussels (Dreissena polymorpha) have exacerbated the decline of native freshwater mussels (order Unionida) in North America since their arrival in the 1980s. Options for controlling invasive mussels, particularly in unionid mussel habitats, are limited. Previously, carbon dioxide (CO2) showed selective toxicity for zebra mussels, relative to unionids, when applied in cool water (12 °C). We first determined 96‐h lethal concentrations of CO2 at 5 and 20 °C to zebra mussels and responses of juvenile plain pocketbook (Lampsilis cardium). Next, we compared the time to lethality for zebra mussels at 5, 12, and 20 °C during exposure to partial pressure of CO2 (PCO2) values of 110 to 120 atm (1 atm = 101.325 kPa) and responses of juvenile plain pocketbook and fragile papershell (Leptodea fragilis). We found efficacious CO2 treatment regimens at each temperature that were minimally lethal to unionids. At 5 °C, plain pocketbook survived 96‐h exposure to the highest PCO2 treatment (139 atm). At 20 °C, the 96‐h lethal concentration to 10% of animals (LC10) for plain pocketbook (173 atm PCO2, 95% CI 147–198 atm) was higher than the LC99 for zebra mussels (118 atm PCO2, 95% CI 109–127 atm). Lethal time to 99% mortality (LT99) of zebra mussels in 110 to 120 atm PCO2 ranged from 100 h at 20 °C to 300 h at 5 °C. Mean survival of both plain pocketbook and fragile papershell juveniles exceeded 85% in LT99 CO2 treatments at all temperatures. Short‐term infusion of 100 to 200 atm PCO2 at a range of water temperatures could reduce biofouling by zebra mussels with limited adverse effects on unionid mussels. Environ Toxicol Chem 2020;39:1546–1557. Published 2020. This article is a U.S. Government work and is in the public domain in the USA. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. [ABSTRACT FROM AUTHOR]

To the three previous reports of hybrids of the American Coot × Common Gallinule we add two, one from Mountain View, California, in July 1995 and one from Tijuana, Baja California, in December 2019 and January 2020. The hybrids were similar in their coot-like build and intermediate plumage coloration, but they differed in size, bill and leg coloration, extent of lobes on the toes, and some plumage details. The one in Tijuana was larger than either parental species but made vocalizations of both species. Such intergeneric hybrids are rare, but at least 11 examples of Fulica × Gallinula have been reported from the Old World. [ABSTRACT FROM AUTHOR]

Effective natural resources management requires accurate information about species distributions. Environmental DNA (eDNA) analysis is a commonly used method to determine species presence and distribution. However, when understanding eDNA‐based distribution data, managers must contend with imperfect detection in collection samples and subsamples (i.e., molecular analyses) impacting their ability to detect species and estimate occurrence. Occurrence models can estimate 3 probabilities: occurrence, capture, and eDNA detection. However, most occurrence models do not. To quantify imperfect detection in rare versus common species, we examined multiple field capture and detection probabilities. We studied this with 3 objectives: Determine sample sizes required to detect eDNA given imperfect detection, determine sample sizes required to estimate eDNA capture parameters, and examine performance of a 3‐level occurrence model. We found detecting eDNA in ≥1 sample at a site required ≤15 samples per site for common species, but detecting eDNA when looking for rare species required 45 to 90 samples per site. Our occurrence model recovered known parameters unless capture and detection probabilities were <0.2 where >100 samples per site and ≥8 molecular replicates were required. Our findings illustrate the importance of sample size and molecular replication for eDNA‐based work. Integr Environ Assess Manag 2019;15:760–771. Published 2019. This article is a US Government work and is in the public domain in the USA. Key Points: Environmental DNA (eDNA) hold the potential to revolutionize sampling and monitoring programs by allowing passive sampling of biological organisms.Despite this promise, uncertainty exists about how to best design eDNA‐based studies.Our research examined how to design eDNA‐based sampling method.We found that 75 to 100 samples per site may be necessary to detect cryptic, rare, or otherwise difficult to detect species. [ABSTRACT FROM AUTHOR]

The community structures and ecosystem functions of floodplains are primarily driven by variation in flood inundation. However, global changes, such as invasive species and nutrient enrichment, may alter the effects of flooding in these systems. We added nitrogen (N) to correspond with twice the annual atmospheric deposition rate of the south-west Wisconsin, USA region within mature floodplain forest plots and patches of an invasive grass (reed canarygrass, Phalaris arundinacea) along a floodplain elevation gradient in an Upper Mississippi River floodplain forest. We measured soil physicochemical properties and the activity of six extracellular enzymes during 3 months that varied in flooding conditions. Multivariate analyses (distance-based redundancy analysis) revealed that floodplain elevation, month of sampling, and vegetation type were all significant predictors of variation in soil physicochemical properties, while elevation and month were significant predictors of multivariate extracellular enzyme activity (EEA). The best model for predicting EEA consisted of nitrogen availability, soil porosity, and water filled pore space. Although the categorical fertilization and invasion treatments were not significant predictors of EEA, our results suggest that their effects depend on the degree to which they modify N availability and soil moisture. In this system, spatial and temporal patterns in flooding appear to be the main driver of these properties, but N enrichment and invasion may have the potential to further modify them. [ABSTRACT FROM AUTHOR]

Copyright of Western North American Naturalist is the property of Monte L. Bean Life Science Museum and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Environmental DNA (eDNA) samples that are collected from remote locations depend on rapid stabilization of the DNA. The degradation of eDNA in water samples is minimized when samples are stored at ≤ 4 °C. Developing a preservation technique to maintain eDNA integrity at room temperature would allow a wider range of locations to be sampled. We evaluated an ethanol and sodium acetate solution to maintain the integrity of the DNA samples for the time between collection and lab testing. For this evaluation, replicate water samples taken from a tank housing Asian carp were placed on ice or held at room temperature. At both temperatures, water samples were left untreated or were preserved with an ethanol and sodium acetate solution (EtOH-NaAc). Every day for 6 days following collection, a subset of the samples was removed from each preservation method and DNA was extracted and nuclear and mitochondrial markers were assayed with qPCR. Results showed comparable persistence of DNA between iced samples without the EtOH-NaAc treatment and samples that received EtOH-NaAc treatment that were kept at room temperature. We found that DNA can be amplified from preserved samples using an EtOH-NaAc solution after up to 7 days at room temperature. [ABSTRACT FROM AUTHOR]

Common loons (Gavia immer) are at risk of elevated dietary mercury (Hg) exposure in portions of their breeding range. To assess the level of risk among loons in Minnesota (USA), we investigated loon blood Hg concentrations in breeding lakes across Minnesota. Loon blood Hg concentrations were regressed on predicted Hg concentrations in standardized 12‐cm whole‐organism yellow perch (Perca flavescens), based on fish Hg records from Minnesota lakes, using the US Geological Survey National Descriptive Model for Mercury in Fish. A linear model, incorporating common loon sex, age, body mass, and log‐transformed standardized perch Hg concentration representative of each study lake, was associated with 83% of the variability in observed common loon blood Hg concentrations. Loon blood Hg concentration was positively related to standardized perch Hg concentrations; juvenile loons had lower blood Hg concentrations than adult females, and blood Hg concentrations of juveniles increased with body mass. Blood Hg concentrations of all adult common loons and associated standardized prey Hg for all loon capture lakes included in the study were well below proposed thresholds for adverse effects on loon behavior, physiology, survival, and reproductive success. The fish Hg modeling approach provided insights into spatial patterns of dietary Hg exposure risk to common loons across Minnesota. We also determined that loon blood selenium (Se) concentrations were positively correlated with Hg concentration. Average common loon blood Se concentrations exceeded the published provisional threshold. Environ Toxicol Chem 2019;38:524–532. Published 2018 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America. [ABSTRACT FROM AUTHOR]

Zebra mussels (Dreissena polymorpha) are an aquatic invasive species that plague much of North America and are difficult to impossible to eradicate once they become established. Therefore, prevention and monitoring are key elements in the control of these organisms. Traditional microscopy is commonly used in monitoring but requires the presence of larval veligers. This limits the times when resource managers can monitor for the presence in northern lakes. A new monitoring tool, environmental DNA (eDNA), may allow for a more efficient and cost-effective monitoring program for zebra mussels. We developed and tested an environmental DNA assay in the fall and spring for zebra mussels in two Minnesota lakes, one heavily infested and another newly infested. We found that DNA copy numbers tended to be higher near the lake bottom and DNA was more concentrated in softer substrates. We also found that the amount of zebra mussel DNA sampling in winter resulted in similar results to when sampled in fall. This suggests that one could collect and analyze eDNA for zebra mussels during winter months to help inform future efforts in monitoring and control. [ABSTRACT FROM AUTHOR]

Effective behavioral deterrents are needed to prevent aquatic invasive species from entering novel ecosystems. One deterrent strategy that shows promise is elevated carbon dioxide (CO2) concentrations in water which can alter the behavior of freshwater fishes, including invasive bigheaded carps (Hypophthalmichthys spp.). However, few studies have evaluated behavioral responses to elevated CO2 concentrations at different water temperatures. The objective of this study was to quantify CO2 concentrations needed to achieve avoidance (voluntary response) and narcosis (involuntary response observed by loss of equilibrium) behaviors in silver carp (H. molitrix) and bighead carp (H. nobilis) at 5, 15, and 25 °C. Overall, silver carp and bighead carp displayed avoidance and narcosis behaviors to CO2 at each water temperature, however bighead carp responded at higher CO2 concentrations than silver carp. Behavioral avoidance and narcosis were observed at approximately 40% lower CO2 concentrations in 5 °C water relative to 25 °C suggesting considerable influence of water temperature on a CO2 stimulus for both species. Results indicate that fluctuating water temperature (e.g., spatial and temporal variation across management sites) can influence how fish respond to elevated CO2, and may usefully be considered when applying CO2 as a behavioral deterrent. [ABSTRACT FROM AUTHOR]

Biologists and environmental scientists now routinely solve computational problems that were unimaginable a generation ago. Examples include processing geospatial data, analyzing -omics data, and running large-scale simulations. Conventional desktop computing cannot handle these tasks when they are large, and high-performance computing is not always available nor the most appropriate solution for all computationally intense problems. High-throughput computing (HTC) is one method for handling computationally intense research. In contrast to high-performance computing, which uses a single "supercomputer," HTC can distribute tasks over many computers (e.g., idle desktop computers, dedicated servers, or cloud-based resources). HTC facilities exist at many academic and government institutes and are relatively easy to create from commodity hardware. Additionally, consortia such as Open Science Grid facilitate HTC, and commercial entities sell cloud-based solutions for researchers who lack HTC at their institution. We provide an introduction to HTC for biologists and environmental scientists. Our examples from biology and the environmental sciences use HTCondor, an open source HTC system. [ABSTRACT FROM AUTHOR]

Abstract: Florfenicol (Aquaflor®) is the only U.S. Food and Drug Administration (FDA) approved drug for treating diseased fish reared in recirculating aquaculture systems (RAS). Treating diseased fish in RAS is challenging because of the potential to damage nitrifying bacteria in the biofilters. Impaired nitrification can lead to concentrations of ammonia and nitrite that compromise fish welfare. The objective of this study was to determine the effects of a FDA‐approved parasiticide and fungicide, Parasite‐S® (formalin), on biofilter nitrification. Stable biofilters were exposed once to 0, 9.25, 18.5, 37, or 55.5 mg/L formaldehyde. Total ammonia nitrogen (TAN) and nitrite nitrogen were monitored daily before and throughout the study to quantify biofilter function. Formaldehyde concentrations ≥37 mg/L increased TAN and nitrite nitrogen concentrations, and nitrification did not recover to pre‐exposure concentrations up to 8 day postexposure. On the basis of those results, a second trial was conducted. Stable biofilters were exposed once or on four consecutive days to 9.25 or 18.5 mg/L formaldehyde. Biofilters repeatedly exposed to formaldehyde showed signs of impairment and had variable recovery relative to single exposures. Results of this study may help identify formaldehyde concentrations that can be safely applied to RAS when treating diseased fish. [ABSTRACT FROM AUTHOR]

Construction of a water management structure (WMS) in the levee surrounding The Nature Conservancy's Emiquon Preserve (Havana, Illinois, USA) created a new hydrological connection and potential aquatic invasive species pathway between the Illinois River and a large conservation wetland complex. Site managers need a control tool that deters the upstream passage of non-native fishes into the wetland lakes, but does not interfere with normal gate operation and water discharge. This short field study evaluated carbon dioxide (CO2) injected into water as a non-obstructive method to reduce fish abundance near the WMS culverts. We quantified relative fish abundance using underwater sonar with and without injection of CO2 into culverts during three discharge events: no flow (0 m3/s), restricted flow (0.9 m3/s), and unrestricted flow (3.2 m3/s). Overall, CO2 reached or exceeded our target concentration of 100 mg/L during no flow and restricted flow, and fish abundance was 70-95% lower at culvert entrances relative to untreated control days. The target CO2 level was not reached during unrestricted flow and fish abundance was not reduced during CO2 injection. Atmospheric CO2 concentrations were inconsequential and unaffected by CO2 treatments throughout testing. Results from this initial field study provide several considerations for CO2 as a fish deterrent in natural environments. [ABSTRACT FROM AUTHOR]

Every year, migratory species undertake seasonal movements along different pathways between discrete regions and habitats. The ability to assess the relative demographic contributions of these different habitats and pathways to the species’ overall population dynamics is critical for understanding the ecology of migratory species, and also has practical applications for management and conservation. Metrics for assessing habitat contributions have been well‐developed for metapopulations, but an equivalent metric is not currently available for migratory populations. Here, we develop a framework for estimating the demographic contributions of the discrete habitats and pathways used by migratory species throughout the annual cycle by estimating the per capita contribution of cohorts using these locations. Our framework accounts for seasonal movements between multiple breeding and non‐breeding habitats and for both resident and migratory cohorts. We illustrate our framework using a hypothetical migratory network of four habitats, which allows us to better understand how variations in habitat quality affect per capita contributions. Results indicate that per capita contributions for any habitat or pathway are dependent on habitat‐specific survival probabilities in all other areas used as part of the migratory circuit, and that contribution metrics are spatially linked (e.g. reduced survival in one habitat also decreases the contribution metric for other habitats). Our framework expands existing theory on the dynamics of spatiotemporally structured populations by developing a generalized approach to estimate the habitat‐ and pathway‐specific contributions of species migrating between multiple breeding and multiple non‐breeding habitats for a range of life histories or migratory strategies. Most importantly, it provides a means of prioritizing conservation efforts towards those migratory pathways and habitats that are most critical for the population viability of migratory species. [ABSTRACT FROM AUTHOR]

Typically, studies in digestive physiology in fish focus on a few enzymes and provide insight into the specific processes of the enzyme in a targeted species. Comparative studies assessing a wide number of digestive enzymes on fishes that compete for food resources are lacking, especially in the context of an introduced species. It is generally thought that the invasive silver carp (SVC; Hypophthalmichthys molitrix) directly compete for food resources with the native gizzard shad (GZS; Dorosoma cepedianum) in waters where they coexist. We compared 19 digestive enzymes between SVC and GZS throughout a year and in two rivers in the Midwestern United States: Illinois River and Wabash River. All digestive enzymes analyzed were detected in both SVC and GZS in both rivers. However, the profiles of the digestive enzymes varied by species. Alkaline phosphatase, valine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase and N-acetyl-β-glucosaminidase were all much higher in SVC than in GZS. Differences between digestive enzyme profiles were also observed between rivers and months. This study demonstrates the utility of using an ecological approach to compare physiological features in fishes. [ABSTRACT FROM AUTHOR]

Abstract: In this article, we describe ednaoccupancy, an r package for fitting Bayesian, multiscale occupancy models. These models are appropriate for occupancy surveys that include three nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). ednaoccupancy allows users to specify and fit multiscale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model‐selection criteria. We illustrate these features by analysing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species. [ABSTRACT FROM AUTHOR]

Understanding and conserving migratory species requires a method for characterizing the seasonal flow of animals among habitats. Source-sink theory describes the metapopulation dynamics of species by classifying habitats as population sources (i.e. net contributors) or sinks (i.e. net substractors). Migratory species may have non-breeding habitats important to the species (e.g. overwintering or stopover habitats) that traditional source-sink theory would classify as sinks because these habitats produce no individuals. Conversely, existing migratory network models can evaluate the relative contribution of non-breeding nodes, but these models make an equilibrium assumption that is difficult to meet when examining real migratory populations., We extend a pathway-based metric allowing breeding habitats, non-breeding habitats and migratory pathways connecting these habitats to be classified as sources or sinks. Rather than being based on whether place- or season-specific births exceed deaths, our approach quantifies the total demographic contribution from a node or migratory pathway over a flexibly defined yet limited time period across an organism's life cycle. As such, it provides a snapshot of a migratory system and therefore does not require assumptions associated with equilibrium dynamics., We first develop a generalizable mathematical notation and then demonstrate how the metric may be used with two case studies: the common loon ( Gavia immer) and Yellowstone cutthroat trout ( Oncorhynchus clarkii bouvieri). These examples highlight how stressors can impact stopover and wintering habitats (loons) and habitat management targeting migratory pathways can improve population status (trout)., Synthesis and applications. Each of the two case studies presented describes how effects at one location are felt by populations in another through the seasonal flow of individuals. The contribution metric we present should be helpful in allocating regulatory and management attention to times and locations most critical to migratory species persistence. [ABSTRACT FROM AUTHOR]

Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance that comparative analyses are colored by model details rather than general principles. [ABSTRACT FROM AUTHOR]