Skip to main content
U.S. flag

An official website of the United States government

Jonathan Cook, Ph.D.

Jonathan is a research biologist with the Eastern Ecological Science Center (EESC) of the U.S. Geological Survey.

Jonathan's research interests primarily focus on studies related to wildlife health and disease ecology, threatened and endangered species conservation, and the use of decision science to navigate complex decision problems. Most recently, he has focused on developing risk assessments for SARS-CoV-2 spillover to North American wildlife, and on management decision-making surrounding CWD spread in various cervid species.

Professional Experience

  • Jonathan has held research positions focused on field and laboratory work in diverse settings, including aquatic (freshwater, estuarine, marine) and terrestrial systems. 

Education and Certifications

  •  Ph.D. from Michigan State University in Fisheries and Wildlife

  • Master’s degree in Ecology from the University of California – Davis

  • Jonathan has a B.S. in Wildlife, Fish, and Conservation Biology

Science and Products

link
Image: Northern Pintail Ducks

Disease Decision Analysis and Research

The Disease Decision Analysis and Research group is a multi-disciplinary team based out of the Eastern Ecological Science Center whose strengths are in ecology, decision sciences and quantitative modeling.
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Eastern Ecological Science Center
link

Disease Decision Analysis and Research

The Disease Decision Analysis and Research group is a multi-disciplinary team based out of the Eastern Ecological Science Center whose strengths are in ecology, decision sciences and quantitative modeling.
Learn More
link
Image: Black-Footed Ferret

COVID-19 Pathways and Wildlife Dynamics

Below are the USGS 2020 Coronavirus Aid, Relief and Economic Security Act (CARES Act) research projects related to COVID-19 pathways and wildlife dynamics. Select tabs above for related items.
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Eastern Ecological Science Center, Northern Rocky Mountain Science Center, Western Fisheries Research Center
link

COVID-19 Pathways and Wildlife Dynamics

Below are the USGS 2020 Coronavirus Aid, Relief and Economic Security Act (CARES Act) research projects related to COVID-19 pathways and wildlife dynamics. Select tabs above for related items.
Learn More
link
Close up of hibernating bats in a Vermont cave

Decision Science Support for SARS-CoV-2 Risk to North American Bats

The Eastern Ecological Science Center is working closely with federal, state, and tribal partners to help inform decisions that reduce the risk of SARS-CoV-2 transmission from humans to North American wildlife, including bats.
By
Ecosystems Mission Area, Species Management Research Program, Eastern Ecological Science Center
link

Decision Science Support for SARS-CoV-2 Risk to North American Bats

The Eastern Ecological Science Center is working closely with federal, state, and tribal partners to help inform decisions that reduce the risk of SARS-CoV-2 transmission from humans to North American wildlife, including bats.
Learn More
link
Chronic wasting disease

Decision science support for Chronic Wasting Disease

Eastern Ecological Science Center adds the decision analytical skill set to the existing body of USGS expertise on Chronic Wasting Disease (CWD), in support of our sister DOI agencies.
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Eastern Ecological Science Center
link

Decision science support for Chronic Wasting Disease

Eastern Ecological Science Center adds the decision analytical skill set to the existing body of USGS expertise on Chronic Wasting Disease (CWD), in support of our sister DOI agencies.
Learn More

Evaluating management alternatives for Wyoming elk feedgrounds in consideration of chronic wasting disease

Executive SummaryThe authors used decision and modeling analyses to evaluate management alternatives for a decision on whether to permit Cervus canadensis (elk) feeding on two sites on Bridger-Teton National Forest, Dell Creek and Forest Park. Supplemental feeding of elk could increase the transmission of chronic wasting disease (CWD) locally and disease spread regionally, potentially impacting el

Authors
Jonathan D. Cook, Paul C. Cross, Emily M. Tomaszewski, Eric K. Cole, Evan H. Campbell Grant, James M. Wilder, Michael C. Runge
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Northern Rocky Mountain Science Center

Decision making for Centennial Valley Arctic Grayling conservation on Red Rocks Lake National Wildlife Refuge

This report describes a decision analysis process that was conducted in support of a U.S. Fish and Wildlife Service Environmental Assessment on Arctic grayling (Thymallus arcticus) on Red Rocks Lake National Wildlife Refuge in the Centennial Valley, Montana.
Authors
Jonathan D. Cook, Kyle Flynn, Donovan A. Bell, Matthew E. Jaeger, Jeff Warren, Ryan Kreiner, Jarrett Payne, Jaron Andrews, Andrew Brummond, Evan H. Campbell Grant, Sarah Nelson Sells
By
Ecosystems Mission Area, Cooperative Research Units, Eastern Ecological Science Center

Evaluating the risk of SARS-CoV-2 transmission to bats in the context of wildlife research, rehabilitation, and control

Preventing wildlife disease outbreaks is a priority for natural resource agencies, and management decisions can be urgent, especially in epidemic circumstances. With the emergence of SARS-CoV-2, wildlife agencies were concerned whether the activities they authorize might increase the risk of viral transmission from humans to North American bats, but had a limited amount of time in which to make de
Authors
Jonathan D. Cook, Evan H. Campbell Grant, Jeremy T. H. Coleman, Jonathan M. Sleeman, Michael C. Runge
By
Ecosystems Mission Area, National Wildlife Health Center, Eastern Ecological Science Center

Chronic Wasting Disease Modeling for Bridger Teton National Forest Structured Decision Making (cwd-btnf-sdm-v2)

This software release contains the code necessary to run the chronic wasting disease (CWD) and elk habitat selection models used to support the U.S. Forest Service decision on whether to continue to permit supplemental feeding of elk on USFS land. The models allow for four different management alternatives: continued feeding, emergency feeding, phase-out after three years, or no feeding. The CWD m
By
Northern Rocky Mountain Science Center

whitetailedSIRS: A package to project SARS-CoV-2 outbreak dynamics in white-tailed deer

This software release contains several R scripts that generate epidemic projections of SARS-CoV-2 in white tailed deer populations using a Susceptible-Infected-Recovered-Susceptible (SIRS) modeling framework. We provide a workflow of vignettes used in Rosenblatt et al. In Prep and Cook et al. In Prep. Users are able to specify transmission parameters for human-deer and deer-deer transmission to qu
By
Cooperative Research Units

Simulating chronic wasting disease on Wyoming elk feedgrounds RETRACTED see cwd-btnf-sdm-v2

RETRACTED see https://doi.org/10.5066/P9R7XWO1
By
Northern Rocky Mountain Science Center

Decision-Support Tool to Estimate SARS-CoV-2 Human-to-bat Transmission Risk

Source code to run Shiny app of North American bat SARS2 risk model during winter fieldwork
By
Eastern Ecological Science Center
One Health and Structured Decision Making

One Health and Structured Decision Making

November 3 is One Health Day. One Health is the idea that the health of people is connected to the health of animals and our shared environment.

Read Article

Science and Products