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Tyler Wagner, PhD (Former Employee)

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Image Collage of Landsat, pollinator, and volcanologist

Pennsylvania Cooperative Fish and Wildlife Research Unit

The Pennsylvania Cooperative Fish and Wildlife Research Unit, est. 1938, is a partnership among the Pennsylvania Game Commission, Pennsylvania Fish and Boat Commission, Pennsylvania State University, the U.S. Geological Survey, the U.S. Fish and Wildlife Service, and the Wildlife Management Institute.
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Cooperative Research Units
Pennsylvania Cooperative Fish and Wildlife Research Unit

Pennsylvania Cooperative Fish and Wildlife Research Unit

The Pennsylvania Cooperative Fish and Wildlife Research Unit, est. 1938, is a partnership among the Pennsylvania Game Commission, Pennsylvania Fish and Boat Commission, Pennsylvania State University, the U.S. Geological Survey, the U.S. Fish and Wildlife Service, and the Wildlife Management Institute.
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Image: Flathead Catfish

Invasive flathead catfish now top predators in Susquehanna River in Pennsylvania

New study suggests that smallmouth bass and channel catfish are changing what they eat to avoid having to compete with or being eaten by the invader
By
Cooperative Research Units, Chesapeake Bay Activities, New Jersey Water Science Center, Pennsylvania Water Science Center
Invasive flathead catfish now top predators in Susquehanna River in Pennsylvania

Invasive flathead catfish now top predators in Susquehanna River in Pennsylvania

New study suggests that smallmouth bass and channel catfish are changing what they eat to avoid having to compete with or being eaten by the invader
Learn More
Map of study area in the Potomac River Watershed, USA, including sample reaches with smallmouth bass

Wastewater reuse may be detrimental to smallmouth bass abundance in the Shenandoah River Watershed

Issue: Municipal and industrial wastewater effluent is an important source of water for streams and rivers, especially during periods of low flow. The reuse of wastewater effluent may become even more important if climate change exacerbates low streamflow and drought conditions. However, wastewater effluent often contains chemicals that, when chronically present, can affect the health of aquatic...
By
Cooperative Research Units, Chesapeake Bay Activities, Virginia and West Virginia Water Science Center
Wastewater reuse may be detrimental to smallmouth bass abundance in the Shenandoah River Watershed

Wastewater reuse may be detrimental to smallmouth bass abundance in the Shenandoah River Watershed

Issue: Municipal and industrial wastewater effluent is an important source of water for streams and rivers, especially during periods of low flow. The reuse of wastewater effluent may become even more important if climate change exacerbates low streamflow and drought conditions. However, wastewater effluent often contains chemicals that, when chronically present, can affect the health of aquatic...
Learn More
Water quality sensors deployed at Arctic Village

The statistical power to detect regional temporal trends in riverine contaminants in the Chesapeake Bay Watershed

Issue: Chemical contamination of riverine ecosystems is a global concern, with potentially negative effects for human and ecological health. Land management activities (e.g., Best Management Practices; BMPs) are an important tool that can be used to reduce point and non-point sources of pollution. The Chesapeake Bay Program (CBP) has goals for (1) reducing toxic contaminants and (2) reducing...
By
Cooperative Research Units, Chesapeake Bay Activities
The statistical power to detect regional temporal trends in riverine contaminants in the Chesapeake Bay Watershed

The statistical power to detect regional temporal trends in riverine contaminants in the Chesapeake Bay Watershed

Issue: Chemical contamination of riverine ecosystems is a global concern, with potentially negative effects for human and ecological health. Land management activities (e.g., Best Management Practices; BMPs) are an important tool that can be used to reduce point and non-point sources of pollution. The Chesapeake Bay Program (CBP) has goals for (1) reducing toxic contaminants and (2) reducing...
Learn More
Curious smallmouth bass following behind scuba divers in Sparkling Lake, Vilas County, Wis. Photographer: Gretchen Hansen, Wisco

Quantifying the Impacts of Climate Change on Fish Growth and Production to Enable Sustainable Management of Diverse Inland Fisheries

Fisheries managers in Midwestern lakes and reservoirs are tasked with balancing multiple management objectives to help maintain healthy fish populations across a landscape of diverse lakes. As part of this, managers monitor fish growth and survival. Growth rates in particular are indicators of population health, and directly influence the effectiveness of regulations designed to protect...
By
Climate Adaptation Science Centers
Quantifying the Impacts of Climate Change on Fish Growth and Production to Enable Sustainable Management of Diverse Inland Fisheries

Quantifying the Impacts of Climate Change on Fish Growth and Production to Enable Sustainable Management of Diverse Inland Fisheries

Fisheries managers in Midwestern lakes and reservoirs are tasked with balancing multiple management objectives to help maintain healthy fish populations across a landscape of diverse lakes. As part of this, managers monitor fish growth and survival. Growth rates in particular are indicators of population health, and directly influence the effectiveness of regulations designed to protect spawning
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Lake Huran

Fish Habitat Restoration to Promote Adaptation: Resilience of Sport Fish in Lakes of the Upper Midwest

Many Midwestern lakes are experiencing warming water temperatures as a result of climate change. In general, this change is causing coldwater fish species such as cisco and coolwater species such as walleye to decline. Meanwhile, warmer water species such as largemouth and smallmouth bass are increasing as temperatures warm. However, some fish populations are more vulnerable to these...
By
Climate Adaptation Science Centers
Fish Habitat Restoration to Promote Adaptation: Resilience of Sport Fish in Lakes of the Upper Midwest

Fish Habitat Restoration to Promote Adaptation: Resilience of Sport Fish in Lakes of the Upper Midwest

Many Midwestern lakes are experiencing warming water temperatures as a result of climate change. In general, this change is causing coldwater fish species such as cisco and coolwater species such as walleye to decline. Meanwhile, warmer water species such as largemouth and smallmouth bass are increasing as temperatures warm. However, some fish populations are more vulnerable to these changes than
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Maury River, Virginia

FishTail: A Tool to Inform Conservation of Stream Fish Habitats in the Northeast

Human impacts occurring throughout the DOI Northeast Climate Science Center, including urbanization, agriculture, and dams, have multiple effects on streams in the region which support economically valuable stream fishes. Changes in climate are expected to lead to additional impacts in stream habitats and fish assemblages in multiple ways, including changing stream water temperatures. To...
By
Climate Adaptation Science Centers
FishTail: A Tool to Inform Conservation of Stream Fish Habitats in the Northeast

FishTail: A Tool to Inform Conservation of Stream Fish Habitats in the Northeast

Human impacts occurring throughout the DOI Northeast Climate Science Center, including urbanization, agriculture, and dams, have multiple effects on streams in the region which support economically valuable stream fishes. Changes in climate are expected to lead to additional impacts in stream habitats and fish assemblages in multiple ways, including changing stream water temperatures. To manage
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Filter Total Items: 15

Transcriptomic Data for Brook Trout Collected from the Loyalsock Creek Watershed, Pennsylvania in 2016-2017 Transcriptomic Data for Brook Trout Collected from the Loyalsock Creek Watershed, Pennsylvania in 2016-2017

This dataset contains gene expression data for brook trout (Salvelinus fontinalis) collected from the Loyalsock Creek watershed in Pennsylvania. Gene expression was quantified for three genes of interest: elongation factor 1-alpha (EF1), SfontSerpinh1 (a heat shock protein gene), and SfontColdRNA (a gene associated with cold response). The dataset was generated to support investigations...
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Eastern Ecological Science Center

Landscape transcriptomics identify Landscape transcriptomics identify

Rapid heating events, such as heatwaves, are becoming more frequent and intense as a result of climate change. Importantly, such extreme weather events can be more important drivers of extirpation and selection than changes in annual or seasonal averages and they pose a particularly large threat to poikilothermic organisms. In this study, we evaluate the thermal stress response of a...
By
Cooperative Research Units

Microsatellite genotypes for flathead catfish used for analysis of genetic structuring in Pennsylvania rivers Microsatellite genotypes for flathead catfish used for analysis of genetic structuring in Pennsylvania rivers

This dataset provides the microsatellite genotypes for 466 flathead catfish collected in Pennslyvania rivers for an analysis of population genetic structuring of introduced popualtions. Also included is the spatial location of sample sites.
By
Eastern Ecological Science Center

Data describing a predatory fish invasion on a riverine food web Data describing a predatory fish invasion on a riverine food web

Catfishes are opportunistic feeders that are among the world's worst invasive species. Flathead catfish *Pylodictus olivaris* -- a large predatory catfish -- were first detected in the Susquehanna River, Pennsylvania, USA in 2002. Since then, they established a viable and rapidly growing population that is expanding its range throughout the river system. Although the predatory effects of...
By
Cooperative Research Units

Evaluating the effectiveness of joint species distribution modeling for riverine fish communities Evaluating the effectiveness of joint species distribution modeling for riverine fish communities

Species Distribution Models (JSDMs) allow for accounting for both environmental predictors and species dependencies within a single statistical modeling frameworks. However, it is unclear under what conditions incorporating residual species dependencies (conditional predictions) might outperform predictions made using only environmental information (marginal predictions). Here, we...
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Cooperative Research Units

Feeding Habits and Ecological Implications of the Invasive Flathead Catfish, Pylodictis olivaris, in the Susquehanna River Basin, Pennsylvania Feeding Habits and Ecological Implications of the Invasive Flathead Catfish, Pylodictis olivaris, in the Susquehanna River Basin, Pennsylvania

Flathead Catfish _Pylodictis olivaris_ are a prominent aquatic invasive species within the United States and a recent invader in the Susquehanna River Basin, Pennsylvania. Flathead Catfish are piscivores known to consume native and recreationally important fish species. In the northeastern United States, it is unknown how this invader is impacting food webs and which species may be at...
By
Cooperative Research Units

Predicting fish responses to climate change using a joint species, spatially dependent physiologically guided abundance model Predicting fish responses to climate change using a joint species, spatially dependent physiologically guided abundance model

Predicting the effects of warming temperatures on the abundance and distribution of organisms under future climate scenarios often requires extrapolating species-environment correlations to thermal conditions not currently experienced by a species or to temperatures that exceed the range of observed data. For poikilotherms, incorporating species’ thermal physiology to inform...
By
Cooperative Research Units

Accumulated wastewater calculations for smallmouth bass sampling sites in the Shenandoah River Watershed, USA Accumulated wastewater calculations for smallmouth bass sampling sites in the Shenandoah River Watershed, USA

This data release presents calculated accumulated wastewater (ACCWW, as a percent of total streamflow) values for 43 National Hydrologic Dataset Version 2.1 (NHDPlus V2.1) stream segments coinciding with long-term smallmouth bass sampling locations (Table 1) in the Shenandoah River Watershed (encompassing parts of Virginia and West Virginia, USA). Values are calculated for quarter-year...
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Cooperative Research Units

The effects of wastewater reuse on smallmouth bass (Micropterus dolomieu) relative abundance in the Shenandoah River Watershed, USA The effects of wastewater reuse on smallmouth bass (Micropterus dolomieu) relative abundance in the Shenandoah River Watershed, USA

R code to evaluate the effects of wastewater reuse on smallmouth bass (Micropterus dolomieu) relative abundance in the Shenandoah River Watershed, USA
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Cooperative Research Units

Modeling widespread declines in walleye recruitment following zebra mussel invasion in Minnesota lakes Modeling widespread declines in walleye recruitment following zebra mussel invasion in Minnesota lakes

Invasive zebra mussels (Dreissena polymorpha) alter lake ecosystems and can negatively affect first-year growth of walleye (Sander vitreus), potentially lowering walleye recruitment success. We quantified walleye recruitment responses to zebra mussel invasion in Minnesota lakes using data from 1,438 electrofishing surveys across 348 lakes collected between 1993 and 2019 to measure...
By
Cooperative Research Units

Accounting for spatio-temporal variation in catchability in joint species distribution models Accounting for spatio-temporal variation in catchability in joint species distribution models

1: Estimating relative abundance is critical for informing conservation and management efforts and for making inferences about the effects of environmental change on populations. Freshwater fisheries span large geographic regions, occupy diverse habitats, and consist of varying species assemblages. Monitoring schemes used to sample these diverse populations often result in populations...
By
Cooperative Research Units

Per- and Polyfluoroalkyl Substances (PFAS) in U.S. Tapwater: Comparison of Public-Supply and Underserved Private-Well Exposures and Associated Health Implications Per- and Polyfluoroalkyl Substances (PFAS) in U.S. Tapwater: Comparison of Public-Supply and Underserved Private-Well Exposures and Associated Health Implications

This software involves files to fit the statistical models described in Smalling et al. Specifically, there are R scripts and associated stan model files (when appropriate) for comparing PFAS concentrations among public-supply and private-wells and as a function of geospatial predictor variables. There is also an R script for modeling the number of PFAS chemicals detected among water...
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Cooperative Research Units
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Filter Total Items: 124

Model‐based decomposition of spatially varying temporal shifts in seasonal streamflow across north temperate US rivers. Model‐based decomposition of spatially varying temporal shifts in seasonal streamflow across north temperate US rivers.

Anthropogenically forced climate shifts disrupt the seasonal behavior of climatic and hydrologic processes. The seasonality of streamflow has significant implications for the ecology of riverine ecosystems and for meeting societal demands for water resources. We develop a hierarchical Bayesian model of daily streamflow to quantify how the shape of annual hydrographs are changing and to...
Authors
Kevin M. Collins, Erin M. Schliep, Tyler Wagner, Christopher K. Wikle
By
Cooperative Research Units

Invasive predatory fish occupies highest trophic position leading to expansion of isotopic niches in a riverine food web Invasive predatory fish occupies highest trophic position leading to expansion of isotopic niches in a riverine food web

Invasive species are drivers of ecological change with the potential to reshape the structure and function of terrestrial and aquatic ecosystems. The invasive flathead catfish (Pylodictis olivaris) is an opportunistic predator that has established a rapidly growing population in the Susquehanna River, Pennsylvania, USA, since they were first detected in 2002. Although the predatory...
Authors
Olivia C. Hodgson, Sydney Stark, Megan K. Schall, Geoffrey D. Smith, Kelly L. Smalling, Tyler Wagner
By
Cooperative Research Units, Chesapeake Bay Activities, Pennsylvania Water Science Center

Deformity, erosion, lesion, tumor, and parasite (DELT) anomalies in fish communities of the Chesapeake Bay watershed, USA: A regional assessment and potential landscape drivers Deformity, erosion, lesion, tumor, and parasite (DELT) anomalies in fish communities of the Chesapeake Bay watershed, USA: A regional assessment and potential landscape drivers

Fish diseases in freshwater ecosystems pose significant ecological and socioeconomic challenges, yet monitoring them in wild populations is complex due to interactions between pathogens, hosts, and environmental conditions. We examine the prevalence and watershed-scale landscape drivers of external deformity, erosion, lesion, tumor, and parasite (DELT) anomalies in 57 riverine fish...
Authors
Sara E. Breitmeyer, Paul McLaughlin, Vicki S. Blazer, Gregory E. Noe, Kelly L. Smalling, Timothy A. Wertz, Tyler Wagner
By
Cooperative Research Units, Chesapeake Bay Activities, Pennsylvania Water Science Center

Decadal stability in stream fish communities and contemporary ecological drivers of species occupancy in two Appalachian U.S. National Parks Decadal stability in stream fish communities and contemporary ecological drivers of species occupancy in two Appalachian U.S. National Parks

Objective Although conserving fish biodiversity in lotic systems is challenging, protected areas can provide refuge from certain environmental stressors. In the Appalachian region, USA, the National Park Service manages Delaware Water Gap National Recreation Area (DEWA) and New River Gorge National Park & Preserve (NERI), which contain abundant and diverse freshwater resources. To assess...
Authors
Morgan B. Stum, Caleb J. Tzilkowski, Matthew R. Marshall, Frances E. Buderman, Tyler Wagner
By
Cooperative Research Units

Landscape transcriptomic analysis detects thermal stress responses and potential adaptive variation in wild brook trout (Salvelinus fontinalis) during successive heatwaves Landscape transcriptomic analysis detects thermal stress responses and potential adaptive variation in wild brook trout (Salvelinus fontinalis) during successive heatwaves

Extreme weather events, such as heatwaves, are becoming more frequent and intense as a result of climate change. Critically, such extreme weather events can be more important drivers of extirpation and selection than changes in annual or seasonal averages and they pose a particularly large threat to poikilothermic organisms. In this study, we evaluated the transcriptomic response of a...
Authors
Justin Waraniak, Sarah Batchelor, Tyler Wagner, Jason Keagy
By
Cooperative Research Units

Abrupt changes in algal biomass of thousands of US lakes are related to climate and are more likely in low-disturbance watersheds. Abrupt changes in algal biomass of thousands of US lakes are related to climate and are more likely in low-disturbance watersheds.

Climate change is predicted to intensify lake algal blooms globally and result in regime shifts. However, observed increases in algal biomass do not consistently correlate with air temperature or precipitation, and evidence is lacking for a causal effect of climate or the nonlinear dynamics needed to demonstrate regime shifts. We modeled the causal effects of climate on annual lake...
Authors
Patricia A. Soranno, Patrick J. Hanly, Katherine E. Webster, Tyler Wagner, Andrew McDonald, Arnab Shuvo, Erin M. Schliep, Kaitlin L Reinl, Ian M. McCullough, Pang-Ning Tan, Noah R. Lottig, Kendra Spence Cheruvelil
By
Cooperative Research Units

Factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania Factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania

Hyperpigmented melanistic lesions (HPMLs) are a visual anomaly documented on the skin of smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania and in numerous other geographical locations. Currently, there is a lack of information on environmental and fish characteristics that may influence the prevalence of HPMLs associated with a recently described...
Authors
Megan Schall, Geoff Smith, Vicki S. Blazer, Heather L. Walsh, Tyler Wagner
By
Eastern Ecological Science Center

Feeding habits and ecological implications of the invasive Flathead Catfish in the Susquehanna River basin, Pennsylvania Feeding habits and ecological implications of the invasive Flathead Catfish in the Susquehanna River basin, Pennsylvania

Objective Flathead Catfish Pylodictis olivaris are a widespread aquatic invasive species within the United States and a recent invader in the Susquehanna River basin, Pennsylvania. Flathead Catfish are piscivores known to consume native and recreationally important fish species. In the mid-Atlantic United States, it is unknown how this invader is impacting food webs and which species may...
Authors
Sydney Stark, Megan K. Schall, Geoffrey D. Smith, Aaron Maloy, Jason A. Coombs, Tyler Wagner, Julian Avery
By
Cooperative Research Units, Chesapeake Bay Activities, Pennsylvania Water Science Center

Population genetic structure and demographic history reconstruction of introduced flathead catfish (Pylodictis olivaris) in two US Mid-Atlantic rivers Population genetic structure and demographic history reconstruction of introduced flathead catfish (Pylodictis olivaris) in two US Mid-Atlantic rivers

Population genetic analysis of invasive populations can provide valuable insights into the source of introductions, pathways for expansion, and their demographic histories. Flathead catfish (Pylodictis olivaris) are a prolific invasive species with high fecundity, long-distance dispersal, and piscivorous feeding habits that can lead to declines in native fish populations. In this study...
Authors
Justin Waraniak, Michael S. Eackles, Jason Keagy, Geoffrey D. Smith, Megan Schall, Sydney Stark, Shannon L. White, David C. Kazyak, Tyler Wagner
By
Cooperative Research Units, Pennsylvania Water Science Center

Connecting conservation practices to local stream health in the Chesapeake Bay watershed Connecting conservation practices to local stream health in the Chesapeake Bay watershed

The Chesapeake Bay Partnership is implementing conservation practices (CPs) throughout the Chesapeake Bay watershed to reduce nutrient and sediment delivery to the Bay. This study intends to provide an integrated and detailed understanding of how local streams respond to these CP-driven management efforts. Key issue: To what extent do CPs positively affect the health of local streams in...
Authors
Gregory E. Noe, Paul L. Angermeier, Larry B. Barber, Joe Buckwalter, Matthew J. Cashman, Olivia Devereux, Thomas Rossiter Doody, Sally Entrekin, Rosemary Margaret Fanelli, Nathaniel P. Hitt, Molly Elizabeth Huber, Jeramy Roland Jasmann, Kelly O. Maloney, Tristan Gregory Mohs, Sergio Sabat-Bonilla, Kelly L. Smalling, Tyler Wagner, John C. Wolf, Kenneth Hyer
By
Chesapeake Bay Activities, Florence Bascom Geoscience Center

Predicting responses to climate change using a joint species, spatially dependent physiologically guided abundance model Predicting responses to climate change using a joint species, spatially dependent physiologically guided abundance model

Predicting the effects of warming temperatures on the abundance and distribution of organisms under future climate scenarios often requires extrapolating species–environment correlations to climatic conditions not currently experienced by a species, which can result in unrealistic predictions. For poikilotherms, incorporating species' thermal physiology to inform extrapolations under...
Authors
Christopher A. Custer, Joshua S. North, Erin M. Schliep, Michael R. Verhoeven, Gretchen J.A. Hansen, Tyler Wagner
By
Cooperative Research Units

Evaluating the effectiveness of joint species distribution modeling for fresh water fish communities within large watersheds Evaluating the effectiveness of joint species distribution modeling for fresh water fish communities within large watersheds

Accurately predicting species’ distributions is critical for the management and conservation of fish and wildlife populations. Joint Species Distribution Models (JSDMs) account for dependencies between species often ignored by traditional species distribution models. We evaluated how a JSDM approach could improve predictive strength for stream fish communities within large watersheds...
Authors
Paul McLaughlin, Kevin Krause, Kelly O. Maloney, Taylor Woods, Tyler Wagner
By
Cooperative Research Units, Chesapeake Bay Activities, Eastern Ecological Science Center
Filter Total Items: 23

Workflow and analysis for per-and polyfluoroalkyl substances (PFAS) in water and dragonfly larvae in United States protected areas Workflow and analysis for per-and polyfluoroalkyl substances (PFAS) in water and dragonfly larvae in United States protected areas

This code release provides the workflow and analysis code for a study that addresses the prevalence of PFAS on Federally protected lands in water and dragonfly larvae. This study quantifies the prevalence of PFAS in protected areas across the US, identifies ecologically relevant PFAS mixtures, and assesses the potential drivers of PFAS concentration in an effort to better understand...
By
Cooperative Research Units

Accounting for Variable Detection Functions in Temporal Abundance Modeling via Transfer Learning Workflow/Analysis Accounting for Variable Detection Functions in Temporal Abundance Modeling via Transfer Learning Workflow/Analysis

This code release provides the workflow and analysis for our propose approach to (i) learn the effect of environmental covariates on detection probabilities from CR data and (ii) transfer these detection functions to CPUE models for improved inference.
By
Cooperative Research Units

R workflow for quantifying inter-population and inter-individual variation in heat stress response mRNA expression profiles in wild brook trout (Salvelinus fontinalis) populations R workflow for quantifying inter-population and inter-individual variation in heat stress response mRNA expression profiles in wild brook trout (Salvelinus fontinalis) populations

Brook trout are a recreationally important fish species that need cold water for survival. The objective of this study was to quantify within- and among-population variability in HSP47 and CIRBP expression in four wild populations of brook trout (Salvelinus fontinalis) to quantify seasonal changes in gene expression. The code release contains a R script for the analysis of brook trout...
By
Cooperative Research Units

R workflow for the analysis of fish tissue mercury concentrations following the invasion of zebra mussels in Minnesota Lakes R workflow for the analysis of fish tissue mercury concentrations following the invasion of zebra mussels in Minnesota Lakes

Aquatic invasive species can influence mercury methylation and bioaccumulation in lake ecosystems by altering chemical and biological pathways and dynamics. Invasive zebra mussels Dreissena polymorpha, which have invaded lakes and rivers throughout North America, may amplify mercury bioavailability by disrupting food webs and altering biogeochemical processes. This potential...
By
Cooperative Research Units

R code for the workflow and analysis of spatio-temporal analysis of smallmouth bass (Micropterus dolomieu) growth in Pennsylvania Rivers R code for the workflow and analysis of spatio-temporal analysis of smallmouth bass (Micropterus dolomieu) growth in Pennsylvania Rivers

Using a 36-year dataset of smallmouth bass length-at-age, we assess the effect of population density, average critical period temperature, and average spring flow rate on early life growth rate. We also looked at how a disease outbreak in 2004 impacted early life growth rates in reaches with and without the disease. The code in this release provides the R scripts to perform this analysis...
By
Cooperative Research Units

Code for the analysis of fish deformity, erosion, lesion, tumor, and parasite anomalies (DELT) in the Chesapeake Bay Watershed, USA Code for the analysis of fish deformity, erosion, lesion, tumor, and parasite anomalies (DELT) in the Chesapeake Bay Watershed, USA

This repository provides the R scripts and stan files to fit hierarchical logistic regression models, using a regularized horseshoe prior on regression coefficients, to examine spatial drivers of DELT occurrence in fishes in the Chesapeake Bay Watershed, USA.
By
Cooperative Research Units, Chesapeake Bay Activities

Landscape transcriptomics identify Landscape transcriptomics identify

Rapid heating events, such as heatwaves, are becoming more frequent and intense as a result of climate change. Importantly, such extreme weather events can be more important drivers of extirpation and selection than changes in annual or seasonal averages and they pose a particularly large threat to poikilothermic organisms. In this study, we evaluate the thermal stress response of a...
By
Cooperative Research Units

Climate-driven declines in fish abundance workflow and analysis Climate-driven declines in fish abundance workflow and analysis

This repository provides the necessary R and stan scripts to fit a joint species, spatially dependent physiologically guided abundance (jsPGA) model (Custer et al. 2024) to fishes from over 11,000 Midwestern US lakes in an effort to predict the effects of climate change on their abundance, distributions, and extirpation probabilities.
By
Cooperative Research Units

R scripts for the analysis of a predatory fish invasion on a riverine food web R scripts for the analysis of a predatory fish invasion on a riverine food web

Catfishes are opportunistic feeders that are among the world's worst invasive species. Flathead catfish Pylodictus olivaris -- a large predatory catfish -- were first detected in the Susquehanna River, Pennsylvania, USA in 2002. Since then, they established a viable and rapidly growing population that is expanding its range throughout the river system. Although the predatory effects of...
By
Cooperative Research Units

R code for identifying factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania R code for identifying factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania

Hyperpigmented melanistic lesions (HPMLs) are a visual anomaly documented on the skin of smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania and in numerous other geographical locations. Currently, there is a lack of information on environmental and fish characteristics that may influence the prevalence of HPMLs associated with a recently described...
By
Cooperative Research Units

Landscape transcriptomic analysis detects thermal stress responses and potential adaptive variation in wild brook trout during successive heatwaves Landscape transcriptomic analysis detects thermal stress responses and potential adaptive variation in wild brook trout during successive heatwaves

Extreme weather events, such as heatwaves, are becoming more frequent and intense as a result of climate change. Importantly, such extreme weather events can be more important drivers of extirpation and selection than changes in annual or seasonal averages and they pose a particularly large threat to poikilothermic organisms. In this study, we evaluate the thermal stress response of a...
By
Cooperative Research Units

Model-based decomposition reveals spatially varying temporal shifts in seasonal streamflow profiles across north temperate US Rivers Model-based decomposition reveals spatially varying temporal shifts in seasonal streamflow profiles across north temperate US Rivers

Understanding changes in the timing and magnitude of streamflows available to maintain riverine biodiversity and ecological function, while also meeting the increasing societal demands on water resources, is a global priority. A rigorous quantification of seasonal changes in streamflow is needed to inform water management and policy under global change. We introduce a hierarchical...
By
Cooperative Research Units
A Fish Study's Promising Results Highlight Parks' Role in Conservation

A Fish Study's Promising Results Highlight Parks' Role in Conservation

USGS researchers at the Pennsylvania Cooperative Fish and Wildlife Unit are partnering with the National Park Service and Penn State to monitor stream...

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Invasive flathead catfish impacting Susquehanna’s food chain, researchers find

Invasive flathead catfish impacting Susquehanna’s food chain, researchers find

The Pennsylvania State University — by Jeff Mulhollem — October 18, 2024

Read Article

Science and Products

Image Collage of Landsat, pollinator, and volcanologist

Pennsylvania Cooperative Fish and Wildlife Research Unit

The Pennsylvania Cooperative Fish and Wildlife Research Unit, est. 1938, is a partnership among the Pennsylvania Game Commission, Pennsylvania Fish and Boat Commission, Pennsylvania State University, the U.S. Geological Survey, the U.S. Fish and Wildlife Service, and the Wildlife Management Institute.
By
Cooperative Research Units
Pennsylvania Cooperative Fish and Wildlife Research Unit

Pennsylvania Cooperative Fish and Wildlife Research Unit

The Pennsylvania Cooperative Fish and Wildlife Research Unit, est. 1938, is a partnership among the Pennsylvania Game Commission, Pennsylvania Fish and Boat Commission, Pennsylvania State University, the U.S. Geological Survey, the U.S. Fish and Wildlife Service, and the Wildlife Management Institute.
Learn More
Image: Flathead Catfish

Invasive flathead catfish now top predators in Susquehanna River in Pennsylvania

New study suggests that smallmouth bass and channel catfish are changing what they eat to avoid having to compete with or being eaten by the invader
By
Cooperative Research Units, Chesapeake Bay Activities, New Jersey Water Science Center, Pennsylvania Water Science Center
Invasive flathead catfish now top predators in Susquehanna River in Pennsylvania

Invasive flathead catfish now top predators in Susquehanna River in Pennsylvania

New study suggests that smallmouth bass and channel catfish are changing what they eat to avoid having to compete with or being eaten by the invader
Learn More
Map of study area in the Potomac River Watershed, USA, including sample reaches with smallmouth bass

Wastewater reuse may be detrimental to smallmouth bass abundance in the Shenandoah River Watershed

Issue: Municipal and industrial wastewater effluent is an important source of water for streams and rivers, especially during periods of low flow. The reuse of wastewater effluent may become even more important if climate change exacerbates low streamflow and drought conditions. However, wastewater effluent often contains chemicals that, when chronically present, can affect the health of aquatic...
By
Cooperative Research Units, Chesapeake Bay Activities, Virginia and West Virginia Water Science Center
Wastewater reuse may be detrimental to smallmouth bass abundance in the Shenandoah River Watershed

Wastewater reuse may be detrimental to smallmouth bass abundance in the Shenandoah River Watershed

Issue: Municipal and industrial wastewater effluent is an important source of water for streams and rivers, especially during periods of low flow. The reuse of wastewater effluent may become even more important if climate change exacerbates low streamflow and drought conditions. However, wastewater effluent often contains chemicals that, when chronically present, can affect the health of aquatic...
Learn More
Water quality sensors deployed at Arctic Village

The statistical power to detect regional temporal trends in riverine contaminants in the Chesapeake Bay Watershed

Issue: Chemical contamination of riverine ecosystems is a global concern, with potentially negative effects for human and ecological health. Land management activities (e.g., Best Management Practices; BMPs) are an important tool that can be used to reduce point and non-point sources of pollution. The Chesapeake Bay Program (CBP) has goals for (1) reducing toxic contaminants and (2) reducing...
By
Cooperative Research Units, Chesapeake Bay Activities
The statistical power to detect regional temporal trends in riverine contaminants in the Chesapeake Bay Watershed

The statistical power to detect regional temporal trends in riverine contaminants in the Chesapeake Bay Watershed

Issue: Chemical contamination of riverine ecosystems is a global concern, with potentially negative effects for human and ecological health. Land management activities (e.g., Best Management Practices; BMPs) are an important tool that can be used to reduce point and non-point sources of pollution. The Chesapeake Bay Program (CBP) has goals for (1) reducing toxic contaminants and (2) reducing...
Learn More
Curious smallmouth bass following behind scuba divers in Sparkling Lake, Vilas County, Wis. Photographer: Gretchen Hansen, Wisco

Quantifying the Impacts of Climate Change on Fish Growth and Production to Enable Sustainable Management of Diverse Inland Fisheries

Fisheries managers in Midwestern lakes and reservoirs are tasked with balancing multiple management objectives to help maintain healthy fish populations across a landscape of diverse lakes. As part of this, managers monitor fish growth and survival. Growth rates in particular are indicators of population health, and directly influence the effectiveness of regulations designed to protect...
By
Climate Adaptation Science Centers
Quantifying the Impacts of Climate Change on Fish Growth and Production to Enable Sustainable Management of Diverse Inland Fisheries

Quantifying the Impacts of Climate Change on Fish Growth and Production to Enable Sustainable Management of Diverse Inland Fisheries

Fisheries managers in Midwestern lakes and reservoirs are tasked with balancing multiple management objectives to help maintain healthy fish populations across a landscape of diverse lakes. As part of this, managers monitor fish growth and survival. Growth rates in particular are indicators of population health, and directly influence the effectiveness of regulations designed to protect spawning
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Lake Huran

Fish Habitat Restoration to Promote Adaptation: Resilience of Sport Fish in Lakes of the Upper Midwest

Many Midwestern lakes are experiencing warming water temperatures as a result of climate change. In general, this change is causing coldwater fish species such as cisco and coolwater species such as walleye to decline. Meanwhile, warmer water species such as largemouth and smallmouth bass are increasing as temperatures warm. However, some fish populations are more vulnerable to these...
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Climate Adaptation Science Centers
Fish Habitat Restoration to Promote Adaptation: Resilience of Sport Fish in Lakes of the Upper Midwest

Fish Habitat Restoration to Promote Adaptation: Resilience of Sport Fish in Lakes of the Upper Midwest

Many Midwestern lakes are experiencing warming water temperatures as a result of climate change. In general, this change is causing coldwater fish species such as cisco and coolwater species such as walleye to decline. Meanwhile, warmer water species such as largemouth and smallmouth bass are increasing as temperatures warm. However, some fish populations are more vulnerable to these changes than
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Maury River, Virginia

FishTail: A Tool to Inform Conservation of Stream Fish Habitats in the Northeast

Human impacts occurring throughout the DOI Northeast Climate Science Center, including urbanization, agriculture, and dams, have multiple effects on streams in the region which support economically valuable stream fishes. Changes in climate are expected to lead to additional impacts in stream habitats and fish assemblages in multiple ways, including changing stream water temperatures. To...
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Climate Adaptation Science Centers
FishTail: A Tool to Inform Conservation of Stream Fish Habitats in the Northeast

FishTail: A Tool to Inform Conservation of Stream Fish Habitats in the Northeast

Human impacts occurring throughout the DOI Northeast Climate Science Center, including urbanization, agriculture, and dams, have multiple effects on streams in the region which support economically valuable stream fishes. Changes in climate are expected to lead to additional impacts in stream habitats and fish assemblages in multiple ways, including changing stream water temperatures. To manage
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Filter Total Items: 15

Transcriptomic Data for Brook Trout Collected from the Loyalsock Creek Watershed, Pennsylvania in 2016-2017 Transcriptomic Data for Brook Trout Collected from the Loyalsock Creek Watershed, Pennsylvania in 2016-2017

This dataset contains gene expression data for brook trout (Salvelinus fontinalis) collected from the Loyalsock Creek watershed in Pennsylvania. Gene expression was quantified for three genes of interest: elongation factor 1-alpha (EF1), SfontSerpinh1 (a heat shock protein gene), and SfontColdRNA (a gene associated with cold response). The dataset was generated to support investigations...
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Eastern Ecological Science Center

Landscape transcriptomics identify Landscape transcriptomics identify

Rapid heating events, such as heatwaves, are becoming more frequent and intense as a result of climate change. Importantly, such extreme weather events can be more important drivers of extirpation and selection than changes in annual or seasonal averages and they pose a particularly large threat to poikilothermic organisms. In this study, we evaluate the thermal stress response of a...
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Cooperative Research Units

Microsatellite genotypes for flathead catfish used for analysis of genetic structuring in Pennsylvania rivers Microsatellite genotypes for flathead catfish used for analysis of genetic structuring in Pennsylvania rivers

This dataset provides the microsatellite genotypes for 466 flathead catfish collected in Pennslyvania rivers for an analysis of population genetic structuring of introduced popualtions. Also included is the spatial location of sample sites.
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Eastern Ecological Science Center

Data describing a predatory fish invasion on a riverine food web Data describing a predatory fish invasion on a riverine food web

Catfishes are opportunistic feeders that are among the world's worst invasive species. Flathead catfish *Pylodictus olivaris* -- a large predatory catfish -- were first detected in the Susquehanna River, Pennsylvania, USA in 2002. Since then, they established a viable and rapidly growing population that is expanding its range throughout the river system. Although the predatory effects of...
By
Cooperative Research Units

Evaluating the effectiveness of joint species distribution modeling for riverine fish communities Evaluating the effectiveness of joint species distribution modeling for riverine fish communities

Species Distribution Models (JSDMs) allow for accounting for both environmental predictors and species dependencies within a single statistical modeling frameworks. However, it is unclear under what conditions incorporating residual species dependencies (conditional predictions) might outperform predictions made using only environmental information (marginal predictions). Here, we...
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Cooperative Research Units

Feeding Habits and Ecological Implications of the Invasive Flathead Catfish, Pylodictis olivaris, in the Susquehanna River Basin, Pennsylvania Feeding Habits and Ecological Implications of the Invasive Flathead Catfish, Pylodictis olivaris, in the Susquehanna River Basin, Pennsylvania

Flathead Catfish _Pylodictis olivaris_ are a prominent aquatic invasive species within the United States and a recent invader in the Susquehanna River Basin, Pennsylvania. Flathead Catfish are piscivores known to consume native and recreationally important fish species. In the northeastern United States, it is unknown how this invader is impacting food webs and which species may be at...
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Cooperative Research Units

Predicting fish responses to climate change using a joint species, spatially dependent physiologically guided abundance model Predicting fish responses to climate change using a joint species, spatially dependent physiologically guided abundance model

Predicting the effects of warming temperatures on the abundance and distribution of organisms under future climate scenarios often requires extrapolating species-environment correlations to thermal conditions not currently experienced by a species or to temperatures that exceed the range of observed data. For poikilotherms, incorporating species’ thermal physiology to inform...
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Cooperative Research Units

Accumulated wastewater calculations for smallmouth bass sampling sites in the Shenandoah River Watershed, USA Accumulated wastewater calculations for smallmouth bass sampling sites in the Shenandoah River Watershed, USA

This data release presents calculated accumulated wastewater (ACCWW, as a percent of total streamflow) values for 43 National Hydrologic Dataset Version 2.1 (NHDPlus V2.1) stream segments coinciding with long-term smallmouth bass sampling locations (Table 1) in the Shenandoah River Watershed (encompassing parts of Virginia and West Virginia, USA). Values are calculated for quarter-year...
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Cooperative Research Units

The effects of wastewater reuse on smallmouth bass (Micropterus dolomieu) relative abundance in the Shenandoah River Watershed, USA The effects of wastewater reuse on smallmouth bass (Micropterus dolomieu) relative abundance in the Shenandoah River Watershed, USA

R code to evaluate the effects of wastewater reuse on smallmouth bass (Micropterus dolomieu) relative abundance in the Shenandoah River Watershed, USA
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Cooperative Research Units

Modeling widespread declines in walleye recruitment following zebra mussel invasion in Minnesota lakes Modeling widespread declines in walleye recruitment following zebra mussel invasion in Minnesota lakes

Invasive zebra mussels (Dreissena polymorpha) alter lake ecosystems and can negatively affect first-year growth of walleye (Sander vitreus), potentially lowering walleye recruitment success. We quantified walleye recruitment responses to zebra mussel invasion in Minnesota lakes using data from 1,438 electrofishing surveys across 348 lakes collected between 1993 and 2019 to measure...
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Cooperative Research Units

Accounting for spatio-temporal variation in catchability in joint species distribution models Accounting for spatio-temporal variation in catchability in joint species distribution models

1: Estimating relative abundance is critical for informing conservation and management efforts and for making inferences about the effects of environmental change on populations. Freshwater fisheries span large geographic regions, occupy diverse habitats, and consist of varying species assemblages. Monitoring schemes used to sample these diverse populations often result in populations...
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Cooperative Research Units

Per- and Polyfluoroalkyl Substances (PFAS) in U.S. Tapwater: Comparison of Public-Supply and Underserved Private-Well Exposures and Associated Health Implications Per- and Polyfluoroalkyl Substances (PFAS) in U.S. Tapwater: Comparison of Public-Supply and Underserved Private-Well Exposures and Associated Health Implications

This software involves files to fit the statistical models described in Smalling et al. Specifically, there are R scripts and associated stan model files (when appropriate) for comparing PFAS concentrations among public-supply and private-wells and as a function of geospatial predictor variables. There is also an R script for modeling the number of PFAS chemicals detected among water...
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Cooperative Research Units
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Filter Total Items: 124

Model‐based decomposition of spatially varying temporal shifts in seasonal streamflow across north temperate US rivers. Model‐based decomposition of spatially varying temporal shifts in seasonal streamflow across north temperate US rivers.

Anthropogenically forced climate shifts disrupt the seasonal behavior of climatic and hydrologic processes. The seasonality of streamflow has significant implications for the ecology of riverine ecosystems and for meeting societal demands for water resources. We develop a hierarchical Bayesian model of daily streamflow to quantify how the shape of annual hydrographs are changing and to...
Authors
Kevin M. Collins, Erin M. Schliep, Tyler Wagner, Christopher K. Wikle
By
Cooperative Research Units

Invasive predatory fish occupies highest trophic position leading to expansion of isotopic niches in a riverine food web Invasive predatory fish occupies highest trophic position leading to expansion of isotopic niches in a riverine food web

Invasive species are drivers of ecological change with the potential to reshape the structure and function of terrestrial and aquatic ecosystems. The invasive flathead catfish (Pylodictis olivaris) is an opportunistic predator that has established a rapidly growing population in the Susquehanna River, Pennsylvania, USA, since they were first detected in 2002. Although the predatory...
Authors
Olivia C. Hodgson, Sydney Stark, Megan K. Schall, Geoffrey D. Smith, Kelly L. Smalling, Tyler Wagner
By
Cooperative Research Units, Chesapeake Bay Activities, Pennsylvania Water Science Center

Deformity, erosion, lesion, tumor, and parasite (DELT) anomalies in fish communities of the Chesapeake Bay watershed, USA: A regional assessment and potential landscape drivers Deformity, erosion, lesion, tumor, and parasite (DELT) anomalies in fish communities of the Chesapeake Bay watershed, USA: A regional assessment and potential landscape drivers

Fish diseases in freshwater ecosystems pose significant ecological and socioeconomic challenges, yet monitoring them in wild populations is complex due to interactions between pathogens, hosts, and environmental conditions. We examine the prevalence and watershed-scale landscape drivers of external deformity, erosion, lesion, tumor, and parasite (DELT) anomalies in 57 riverine fish...
Authors
Sara E. Breitmeyer, Paul McLaughlin, Vicki S. Blazer, Gregory E. Noe, Kelly L. Smalling, Timothy A. Wertz, Tyler Wagner
By
Cooperative Research Units, Chesapeake Bay Activities, Pennsylvania Water Science Center

Decadal stability in stream fish communities and contemporary ecological drivers of species occupancy in two Appalachian U.S. National Parks Decadal stability in stream fish communities and contemporary ecological drivers of species occupancy in two Appalachian U.S. National Parks

Objective Although conserving fish biodiversity in lotic systems is challenging, protected areas can provide refuge from certain environmental stressors. In the Appalachian region, USA, the National Park Service manages Delaware Water Gap National Recreation Area (DEWA) and New River Gorge National Park & Preserve (NERI), which contain abundant and diverse freshwater resources. To assess...
Authors
Morgan B. Stum, Caleb J. Tzilkowski, Matthew R. Marshall, Frances E. Buderman, Tyler Wagner
By
Cooperative Research Units

Landscape transcriptomic analysis detects thermal stress responses and potential adaptive variation in wild brook trout (Salvelinus fontinalis) during successive heatwaves Landscape transcriptomic analysis detects thermal stress responses and potential adaptive variation in wild brook trout (Salvelinus fontinalis) during successive heatwaves

Extreme weather events, such as heatwaves, are becoming more frequent and intense as a result of climate change. Critically, such extreme weather events can be more important drivers of extirpation and selection than changes in annual or seasonal averages and they pose a particularly large threat to poikilothermic organisms. In this study, we evaluated the transcriptomic response of a...
Authors
Justin Waraniak, Sarah Batchelor, Tyler Wagner, Jason Keagy
By
Cooperative Research Units

Abrupt changes in algal biomass of thousands of US lakes are related to climate and are more likely in low-disturbance watersheds. Abrupt changes in algal biomass of thousands of US lakes are related to climate and are more likely in low-disturbance watersheds.

Climate change is predicted to intensify lake algal blooms globally and result in regime shifts. However, observed increases in algal biomass do not consistently correlate with air temperature or precipitation, and evidence is lacking for a causal effect of climate or the nonlinear dynamics needed to demonstrate regime shifts. We modeled the causal effects of climate on annual lake...
Authors
Patricia A. Soranno, Patrick J. Hanly, Katherine E. Webster, Tyler Wagner, Andrew McDonald, Arnab Shuvo, Erin M. Schliep, Kaitlin L Reinl, Ian M. McCullough, Pang-Ning Tan, Noah R. Lottig, Kendra Spence Cheruvelil
By
Cooperative Research Units

Factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania Factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania

Hyperpigmented melanistic lesions (HPMLs) are a visual anomaly documented on the skin of smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania and in numerous other geographical locations. Currently, there is a lack of information on environmental and fish characteristics that may influence the prevalence of HPMLs associated with a recently described...
Authors
Megan Schall, Geoff Smith, Vicki S. Blazer, Heather L. Walsh, Tyler Wagner
By
Eastern Ecological Science Center

Feeding habits and ecological implications of the invasive Flathead Catfish in the Susquehanna River basin, Pennsylvania Feeding habits and ecological implications of the invasive Flathead Catfish in the Susquehanna River basin, Pennsylvania

Objective Flathead Catfish Pylodictis olivaris are a widespread aquatic invasive species within the United States and a recent invader in the Susquehanna River basin, Pennsylvania. Flathead Catfish are piscivores known to consume native and recreationally important fish species. In the mid-Atlantic United States, it is unknown how this invader is impacting food webs and which species may...
Authors
Sydney Stark, Megan K. Schall, Geoffrey D. Smith, Aaron Maloy, Jason A. Coombs, Tyler Wagner, Julian Avery
By
Cooperative Research Units, Chesapeake Bay Activities, Pennsylvania Water Science Center

Population genetic structure and demographic history reconstruction of introduced flathead catfish (Pylodictis olivaris) in two US Mid-Atlantic rivers Population genetic structure and demographic history reconstruction of introduced flathead catfish (Pylodictis olivaris) in two US Mid-Atlantic rivers

Population genetic analysis of invasive populations can provide valuable insights into the source of introductions, pathways for expansion, and their demographic histories. Flathead catfish (Pylodictis olivaris) are a prolific invasive species with high fecundity, long-distance dispersal, and piscivorous feeding habits that can lead to declines in native fish populations. In this study...
Authors
Justin Waraniak, Michael S. Eackles, Jason Keagy, Geoffrey D. Smith, Megan Schall, Sydney Stark, Shannon L. White, David C. Kazyak, Tyler Wagner
By
Cooperative Research Units, Pennsylvania Water Science Center

Connecting conservation practices to local stream health in the Chesapeake Bay watershed Connecting conservation practices to local stream health in the Chesapeake Bay watershed

The Chesapeake Bay Partnership is implementing conservation practices (CPs) throughout the Chesapeake Bay watershed to reduce nutrient and sediment delivery to the Bay. This study intends to provide an integrated and detailed understanding of how local streams respond to these CP-driven management efforts. Key issue: To what extent do CPs positively affect the health of local streams in...
Authors
Gregory E. Noe, Paul L. Angermeier, Larry B. Barber, Joe Buckwalter, Matthew J. Cashman, Olivia Devereux, Thomas Rossiter Doody, Sally Entrekin, Rosemary Margaret Fanelli, Nathaniel P. Hitt, Molly Elizabeth Huber, Jeramy Roland Jasmann, Kelly O. Maloney, Tristan Gregory Mohs, Sergio Sabat-Bonilla, Kelly L. Smalling, Tyler Wagner, John C. Wolf, Kenneth Hyer
By
Chesapeake Bay Activities, Florence Bascom Geoscience Center

Predicting responses to climate change using a joint species, spatially dependent physiologically guided abundance model Predicting responses to climate change using a joint species, spatially dependent physiologically guided abundance model

Predicting the effects of warming temperatures on the abundance and distribution of organisms under future climate scenarios often requires extrapolating species–environment correlations to climatic conditions not currently experienced by a species, which can result in unrealistic predictions. For poikilotherms, incorporating species' thermal physiology to inform extrapolations under...
Authors
Christopher A. Custer, Joshua S. North, Erin M. Schliep, Michael R. Verhoeven, Gretchen J.A. Hansen, Tyler Wagner
By
Cooperative Research Units

Evaluating the effectiveness of joint species distribution modeling for fresh water fish communities within large watersheds Evaluating the effectiveness of joint species distribution modeling for fresh water fish communities within large watersheds

Accurately predicting species’ distributions is critical for the management and conservation of fish and wildlife populations. Joint Species Distribution Models (JSDMs) account for dependencies between species often ignored by traditional species distribution models. We evaluated how a JSDM approach could improve predictive strength for stream fish communities within large watersheds...
Authors
Paul McLaughlin, Kevin Krause, Kelly O. Maloney, Taylor Woods, Tyler Wagner
By
Cooperative Research Units, Chesapeake Bay Activities, Eastern Ecological Science Center
Filter Total Items: 23

Workflow and analysis for per-and polyfluoroalkyl substances (PFAS) in water and dragonfly larvae in United States protected areas Workflow and analysis for per-and polyfluoroalkyl substances (PFAS) in water and dragonfly larvae in United States protected areas

This code release provides the workflow and analysis code for a study that addresses the prevalence of PFAS on Federally protected lands in water and dragonfly larvae. This study quantifies the prevalence of PFAS in protected areas across the US, identifies ecologically relevant PFAS mixtures, and assesses the potential drivers of PFAS concentration in an effort to better understand...
By
Cooperative Research Units

Accounting for Variable Detection Functions in Temporal Abundance Modeling via Transfer Learning Workflow/Analysis Accounting for Variable Detection Functions in Temporal Abundance Modeling via Transfer Learning Workflow/Analysis

This code release provides the workflow and analysis for our propose approach to (i) learn the effect of environmental covariates on detection probabilities from CR data and (ii) transfer these detection functions to CPUE models for improved inference.
By
Cooperative Research Units

R workflow for quantifying inter-population and inter-individual variation in heat stress response mRNA expression profiles in wild brook trout (Salvelinus fontinalis) populations R workflow for quantifying inter-population and inter-individual variation in heat stress response mRNA expression profiles in wild brook trout (Salvelinus fontinalis) populations

Brook trout are a recreationally important fish species that need cold water for survival. The objective of this study was to quantify within- and among-population variability in HSP47 and CIRBP expression in four wild populations of brook trout (Salvelinus fontinalis) to quantify seasonal changes in gene expression. The code release contains a R script for the analysis of brook trout...
By
Cooperative Research Units

R workflow for the analysis of fish tissue mercury concentrations following the invasion of zebra mussels in Minnesota Lakes R workflow for the analysis of fish tissue mercury concentrations following the invasion of zebra mussels in Minnesota Lakes

Aquatic invasive species can influence mercury methylation and bioaccumulation in lake ecosystems by altering chemical and biological pathways and dynamics. Invasive zebra mussels Dreissena polymorpha, which have invaded lakes and rivers throughout North America, may amplify mercury bioavailability by disrupting food webs and altering biogeochemical processes. This potential...
By
Cooperative Research Units

R code for the workflow and analysis of spatio-temporal analysis of smallmouth bass (Micropterus dolomieu) growth in Pennsylvania Rivers R code for the workflow and analysis of spatio-temporal analysis of smallmouth bass (Micropterus dolomieu) growth in Pennsylvania Rivers

Using a 36-year dataset of smallmouth bass length-at-age, we assess the effect of population density, average critical period temperature, and average spring flow rate on early life growth rate. We also looked at how a disease outbreak in 2004 impacted early life growth rates in reaches with and without the disease. The code in this release provides the R scripts to perform this analysis...
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Cooperative Research Units

Code for the analysis of fish deformity, erosion, lesion, tumor, and parasite anomalies (DELT) in the Chesapeake Bay Watershed, USA Code for the analysis of fish deformity, erosion, lesion, tumor, and parasite anomalies (DELT) in the Chesapeake Bay Watershed, USA

This repository provides the R scripts and stan files to fit hierarchical logistic regression models, using a regularized horseshoe prior on regression coefficients, to examine spatial drivers of DELT occurrence in fishes in the Chesapeake Bay Watershed, USA.
By
Cooperative Research Units, Chesapeake Bay Activities

Landscape transcriptomics identify Landscape transcriptomics identify

Rapid heating events, such as heatwaves, are becoming more frequent and intense as a result of climate change. Importantly, such extreme weather events can be more important drivers of extirpation and selection than changes in annual or seasonal averages and they pose a particularly large threat to poikilothermic organisms. In this study, we evaluate the thermal stress response of a...
By
Cooperative Research Units

Climate-driven declines in fish abundance workflow and analysis Climate-driven declines in fish abundance workflow and analysis

This repository provides the necessary R and stan scripts to fit a joint species, spatially dependent physiologically guided abundance (jsPGA) model (Custer et al. 2024) to fishes from over 11,000 Midwestern US lakes in an effort to predict the effects of climate change on their abundance, distributions, and extirpation probabilities.
By
Cooperative Research Units

R scripts for the analysis of a predatory fish invasion on a riverine food web R scripts for the analysis of a predatory fish invasion on a riverine food web

Catfishes are opportunistic feeders that are among the world's worst invasive species. Flathead catfish Pylodictus olivaris -- a large predatory catfish -- were first detected in the Susquehanna River, Pennsylvania, USA in 2002. Since then, they established a viable and rapidly growing population that is expanding its range throughout the river system. Although the predatory effects of...
By
Cooperative Research Units

R code for identifying factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania R code for identifying factors influencing the prevalence of hyperpigmented melanistic lesions in smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania

Hyperpigmented melanistic lesions (HPMLs) are a visual anomaly documented on the skin of smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania and in numerous other geographical locations. Currently, there is a lack of information on environmental and fish characteristics that may influence the prevalence of HPMLs associated with a recently described...
By
Cooperative Research Units

Landscape transcriptomic analysis detects thermal stress responses and potential adaptive variation in wild brook trout during successive heatwaves Landscape transcriptomic analysis detects thermal stress responses and potential adaptive variation in wild brook trout during successive heatwaves

Extreme weather events, such as heatwaves, are becoming more frequent and intense as a result of climate change. Importantly, such extreme weather events can be more important drivers of extirpation and selection than changes in annual or seasonal averages and they pose a particularly large threat to poikilothermic organisms. In this study, we evaluate the thermal stress response of a...
By
Cooperative Research Units

Model-based decomposition reveals spatially varying temporal shifts in seasonal streamflow profiles across north temperate US Rivers Model-based decomposition reveals spatially varying temporal shifts in seasonal streamflow profiles across north temperate US Rivers

Understanding changes in the timing and magnitude of streamflows available to maintain riverine biodiversity and ecological function, while also meeting the increasing societal demands on water resources, is a global priority. A rigorous quantification of seasonal changes in streamflow is needed to inform water management and policy under global change. We introduce a hierarchical...
By
Cooperative Research Units
A Fish Study's Promising Results Highlight Parks' Role in Conservation

A Fish Study's Promising Results Highlight Parks' Role in Conservation

USGS researchers at the Pennsylvania Cooperative Fish and Wildlife Unit are partnering with the National Park Service and Penn State to monitor stream...

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Invasive flathead catfish impacting Susquehanna’s food chain, researchers find

Invasive flathead catfish impacting Susquehanna’s food chain, researchers find

The Pennsylvania State University — by Jeff Mulhollem — October 18, 2024

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