Geology topics

Richard A. Erickson

Publications and source records attributed to Richard A. Erickson.

At least 37 records · Page 2Linked to original sources

USGS2023

BioLake: A first assessment of lake temperature-derived bioclimatic predictors for aquatic invasive species

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.

Ecosphere↗

USGS2023

Targeted metabolomics characterizes metabolite occurrence and variability in stable freshwater mussel populations

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.

Indiana↗

USGS2023

MetaIPM: Placing integral projection models into a metapopulation framework

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.

Methods in Ecology and Evolution↗

USGS2023

Reconstructing missing data by comparing interpolation techniques: Applications for long-term water quality data

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.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗

USGS2023

Obtaining and applying public data for training students in technical statistical writing: Case studies with data from U.S. Geological Survey and general ecological literature

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. Supplementary materials for this article are available online.

Journal of Statistics and Data Science Education↗

USGS2023

Efficacy of hydrogen peroxide to reduce Gyrodactylus species infestation density on four fish species

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 (H 2 O 2 ; 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 H 2 O 2 therapy. Result Parasite density was significantly reduced for each parasite × host combination to which H 2 O 2 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 H 2 O 2 for controlling these parasites in aquaculture. Specifically, H 2 O 2 was effective at all levels tested (50 or 75 mg H 2 O 2 /L for 60 min for the Yellow Perch and Fathead Minnow clinical field studies; 100 or 150 mg H 2 O 2 /L for 30 min regardless of salt pre-treatment for the Brook Trout study; and 100 mg H 2 O 2 /L for 30 min or 50 mg H 2 O 2 /L for 60 min for the Lake Trout study).

Journal of Aquatic Animal Health↗

USGS2023

Efficacy of florfenicol and oxytetracycline administered in feed to control cisco mortality associated with Aeromonas salmonicida infections

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.

North American Journal of Aquaculture↗

USGS2023

An integral projection model for gizzard shad (Dorosoma cepedianum) utilizing density-dependent age-0 survival

Gizzard shad (Dorosoma cepedianum) is a common freshwater fish species found throughout the central and eastern portions of North America. Within these regions, gizzard shad play several critical roles in the freshwater community such as serving as prey for other fish species and translocating nutrients from substrates into the water column. Because of this, it is important to understand gizzard shad population dynamics. Here, we introduce an integral projection model (IPM) for gizzard shad that incorporates empirical information from sources including Long Term Resource Monitoring (LTRM) upper Mississippi River restoration data. IPMs are a generalization of stage-based, matrix population models that have been used to describe a wide range of organisms, and as such are a natural choice for gizzard shad because many aspects of their life cycle have been studied. We tested model outputs against empirical patterns reported for gizzard shad from a different location along the Illinois River (La Grange Reach). Results of our work indicate that our model could serve as an important tool for predicting patterns within gizzard shad populations.

Ecological Modelling↗

USGS2023

Using integral projection models to explore management strategies for silver carp (Hypophthalmichthys molitrix)

Silver carp ( Hypophthalmichthys molitrix ) are planktivorous fish that were originally introduced to the United States for use in fish production ponds and have since escaped these enclosures and are invading the Mississippi River Basin. The silver carp invasion of the Illinois River has a myriad of negative effects on native ecosystems. In this paper, we introduce key dependencies that are likely important in the population dynamics of silver carp: length-dependent egg production and density-dependent growth. Using movement data between two adjacent pools of the Illinois River, we conduct numerical simulations to explore the theoretical effect of harvesting and the use of movement barriers. Results of our model provide insights on how the number of silver carp may respond to movement barriers placed between adjacent harvesting sites.

SPORA↗

USGS2023

Bridging the gap between mathematical biology and undergraduate education using applicable natural resource modeling

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 diffcult 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.

Letters in Biomathematics↗

USGS2023

Using a coupled integral projection model to investigate interspecific competition during an invasion: An application to silver carp (Hypophthalmichthys molitrix) and gizzard shad (Dorosoma cepedianum)

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 overlapping 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.

Letters in Biomathematics↗

USGS2022

Analysis of per capita contributions from a spatial model provides strategies for controlling spread of invasive carp

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.

Illinois↗

USGS2022

Validation of a portable eDNA detection kit for invasive carps

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.

Fishes↗

USGS2022

Effects of formaldehyde (Parasite-S®) on biofilter nitrification from a cold- and a warm freshwater RAS

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/m 3 . 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/m 3 . 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.

Aquaculture Research↗

USGS2022

Quantitative method development to determine feed consumption using a dye

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.

North American Journal of Aquaculture↗

USGS2022

Climate matching with the climatchR R package

Climate matching allows comparisons of climatic conditions between different locations to understand location and species range climatic suitability. The approach may be used as part of horizon scanning exercises such as those conducted for invasive species. We implemented the CLIMATCH algorithm into an R package, climatchR . The package allows automated and scripted climate matching exercises across all steps from downloading data to summarizing species climate matches. We also show how climatchR may be used with high-throughput computing to process many species. For example, we were able to calculate climate scores for over 8,000 species in less than 3 days using this package. This automation allows high-throughput processing of species data, a new development for improving the efficiency and speed of climate matching and horizon scanning.

Environmental Software & Modeling↗

USGS2022

FishStan: Hierarchical Bayesian models for fisheries

Fisheries managers and ecologists use statistical models to estimate population-level relations and demographic rates (e.g., length-maturity curves, growth curves, and mortality rates). These relations and rates provide insight into populations and inputs for other models. For example, growth curves may vary across lakes showing fish populations differ due to management actions or underlying environmental conditions. A fisheries manager could use this information to set lake-specific harvest limits or an ecologist could use this information to test scientific hypotheses about fish populations. The above example also demonstrates how populations exist within hierarchical structures where sub-populations may be nested within a meta-population. More generally, these hierarchical structures may be both biological (e.g., different lakes or river pools) and statistical (e.g., correlated error structures). Currently, limited options exist for fitting these hierarchical models and people seeking to use them often must program their own implementations. Furthermore, many fisheries managers and researchers may not have Bayesian programming skills, but many can use interactive languages such as R. Additionally, programs such as JAGS often require long run times (e.g., hours if not days) to fit hierarchical models and programs such as Stan can be more difficult to program because it is a compiled language. We created fishStan to share hierarchical models for fisheries and ecology in an easy-to-use R package.

Journal of Open Source Software↗

USGS2021

Paths to computational fluency for natural resource educators, researchers, and managers

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.

Natural Resource Modelling↗