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Upper Midwest Environmental Sciences Center

May 2016 Activity Highlights
Upper Midwest Environmental Sciences Center
La Crosse, Wisconsin

Topics covered in the May activity report.

Collaborative Research Activities

Sea Lamprey Population Estimation using Environmental DNA

Nick Schloesser, Chris Merkes (UMESC), USGS staff from the Hammond Bay Biological Station (HBBS) and U.S. Fish and Wildlife Service set up the testing system for a study to see if environmental DNA (eDNA) samples could be used to estimate the densities of larval sea lamprey in tributaries to the Great Lakes, May 9-13, 2016, at the HBBS in Millersburg, MI. Aquariums filled with water, sand, and varying densities of larval sea lamprey will be used to see if the amount of eDNA collected can be used to estimate the density of lamprey.  If successful, using eDNA to estimate population densities will help reduce the cost, and increase efficiency, of conducting annual sea lamprey assessments in Great Lakes tributaries.  The Great Lakes Fisheries Commission is funding this study.

National Institute for Mathematical and Biological Synthesis – Habitat for Migratory Birds

Richard Erickson and Wayne Thogmartin (UMESC) participated in the National Institute for Mathematical and Biological Synthesis (NIMBioS) Working Group on Habitat for Migratory Species, May 17-20, 2016.  Thogmartin is an organizer and co-PI for the working group.  The working group is developing quantitative frameworks and mathematical models for assigning value to habitat used by migratory species such as waterfowl and Monarch butterflies. Other USGS participants include, Jay Diffendorfer, Darius Semmens (GECSC), and Mike Runge (PWRC).  NIMBioS is a National Science Foundation funded Synthesis Center housed at the University of Tennessee, Knoxville. Additional information is available at,

Monitoring Zika Virus using a portable hand-held DNA Detection Tool

Jon Amberg and Chris Merkes (UMESC) initiated a collaboration with representatives of Lucigen Corporation to transfer Lucigen’s technology for diagnosing Zika virus in patients to monitoring mosquito populations using a portable hand-held near real-time DNA detection tool. The team will submit a request for funding through USAID Zika Grand Challenge on May 20, 2016. 

Great Smoky Mountains National Park Vegetation Mapping Project

Andrew Strassman, Kevin Hop, Erin Hoy, and Stephanie Sattler (UMESC) joined Tom Remaley, Troy Evans, and other GRSM staff (NPS-GRSM), and Rickie White (NatureServe) May 19-27th, 2016 to conduct a field reconnaissance of the vegetation within the North Carolina-side of Great Smoky Mountains (GRSM) National Park for the Great Smoky Mountains National Park Vegetation Mapping Project (part of the NPS Vegetation Mapping Inventory (VMI) Program).  Field work was centered around Cherokee, NC and Maggie Valley, NC and involved the comparison of aerial imagery signatures to ground conditions while simultaneously testing the key to vegetation for functionality and consistency. 

Jean LaFitte National Historical Park and Preserve Vegetation Mapping Project

Erin Hoy, Stephanie Sattler (UMESC), Rickie White, and Milo Pyne (NatureServe) conducted a mid-season field visit for the Jean LaFitte National Historical Park and Preserve (JELA) Vegetation Mapping Project, May 31-June 3, 2016, at the Barataria Preserve in Marrero, LA.  This field visit provided an opportunity for UMESC and NatureServe staff to assess field data collection procedures and make sure regional botanists are following collection protocols and collecting all needed data. These regional botanists participated in an initial meeting and training session in April in vegetation data collection for the accuracy assessment of the JELA Vegetation Mapping Project, a mapping effort conducted under the National Park Service (NPS) Vegetation Mapping Inventory Program. Accuracy assessment data collection involves the recording of spatial, temporal, and vegetative data (by strata) at predetermined locations within the Park.  Additional participants include, Al Schotz (Alabama Natural Heritage Program), Julie Whitbeck, and Dusty Pate (NPS).  Accuracy assessment data collection will continue through October, 2016.

Great Lakes Restoration Initiative (GLRI)

GLRI Project 80 - Birds as Indicators of Contaminant Exposure in the Great Lakes

Chris and Tom Custer, and Paul Dummer began field work at all tree swallow study sites on Lakes Superior, Michigan, and Erie for Great Lakes Restoration Initiative project, “Birds as Indicators of Contaminant Exposure and Effects.” Work this year includes the Areas of Concern (AOCs) focused sites, as well as, sites to study contaminants of emerging concern (CECs).  Field work is a collaboration between the National Wildlife Health Center (Diana Goldberg and Chris Franson) and UMESC personnel at >30 study sites.  The CEC work is a multi-agency effort (EPA, NOAA, USACE, and USFWS) to study CECs at all levels of biological organization and developing/assessing effects using new tools such as metabolomic and transcriptomic assays.


Elementary Schools Learn about Aquatic Invertebrates

Erin Hoy (UMESC) and Kirsten Cahow-Scholtes (WI-DNR) helped 1st-5th grade students from Coulee Montessori and Northside Elementary in La Crosse, WI, learn more about aquatic invertebrates during the annual Coulee Montessori/Northside Elementary School day in the park at Perrot State Park in Trempealeau, WI, May 27th, 2016. Students worked on their identification skills while observing live aquatic invertebrates and learning about the importance of these tiny creatures in healthy ecosystems.

Partner Meetings

Great Smoky Mountains National Park Vegetation Mapping Project

Andrew Strassman, Kevin Hop, Erin Hoy, and Stephanie Sattler (UMESC) joined Tom Remaley and Troy Evans (NPS-GRSM), and Rickie White (NatureServe) for the Vegetation Classification Meeting for the Great Smoky Mountains (GRSM) National Park Vegetation Mapping Project (part of the NPS Vegetation Mapping Inventory (VMI) Program) at the Oconaluftee Vistior Center in Cherokee, NC on May 17-18th, 2016.  This meeting reviewed the vegetation classification and key to vegetation in the park and provided an opportunity for input on the summer’s fieldwork at the park.

UMRBA and UMRCC Quarterly Meetings

Jennifer Sauer and Jeff Houser (UMESC) participated in the May quarterly meetings of the Upper Mississippi River Basin Association (UMRBA) and the Upper Mississippi River Restoration (UMRR)-Coordinating Committee (UMRR-CC), May 24-25, in St. Louis, MO. Presentations include:

The UMRR is a U.S. Army Corps of Engineers’ research and restoration program for the Upper Mississippi River System. The Upper Midwest Environmental Sciences Center (UMESC) implements the LTRM element of the UMRR, combing environmental monitoring, research, systemic data acquisition, and modeling in an effort to provide a solid scientific foundation upon which resource managers and policy makers base management actions and develop environmental policy on the Upper Mississippi River System.

Water Level Management Task Force

Teresa Newton, Kevin Kenow (UMESC), and members of the multi-agency Water Level Management Task Force met with mayors from cities and towns in the Upper Mississippi River basin aboard the “Cal Fremling Interpretative Center and Classroom,” a 60-foot vessel used by Winona State University as a floating interpretive center and classroom.  The purpose of the excursion was to brief the mayors on the costs and benefits of using water level management as a tool to mimic the River’s natural hydrograph, to restore aquatic vegetation and biota.  The meeting was held May 24, 2016, on the Mississippi River near Winona, MN.


Factors affecting Henslow's Sparrow nest survival in southern Indiana

Wayne Thogmartin (UMESC) and colleagues with the U.S. Fish and Wildlife Service recently published, “Factors affecting Henslow's Sparrow nest survival in southern Indiana,” in the Wilson Journal of Ornithology. Prior to the advent of the Conservation Reserve Program, Henslow's Sparrows were the fastest declining landbird in North America, largely due to loss of grassland habitat and associated benefits to reproduction. Henslow's Sparrows prefer tall, dense grass with a well-developed litter layer and standing dead vegetation. Therefore, burning of grassland may negatively affect nesting. The authors used a mixed-effects implementation of the logistic exposure model to predict daily nest survival as a function of time since burn and other covariates. The authors found only nominal support for time since burn influencing nest survival; instead, nest age and standing dead vegetation were the principal factors associated with nest survival. The authors suggest positive benefits of burning, such as increased invertebrate density, may offset the negative consequences of burning for Henslow's Sparrows in this location.  A copy of the paper is available online, at

Measuring spatial variation in secondary production and food quality using a common consumer approach in Lake Erie

Scientists from UMESC, GLSC, and the National Oceanic and Atmospheric Administration recently published an article investigating spatial variation in secondary production and food quality across hydrologic and cyanobacterial gradients in the western basin of Lake Erie.  This researched used caged unionid mussels from a single initial cohort to quantify differences in growth and tissue composition to compare sites across these gradients.  We found secondary production was highest within the Maumee rivermouth and lowest in the open waters of the lake. Mussel tissues in the Maumee rivermouth also included more eicosapentaenoic and docosapentaenoic fatty acids (EPA and DPA, respectively), but fewer bacterial FAs, suggesting more algae at the base of the food web in the Maumee rivermouth compared to open lake sites. The satellite-derived estimate of cyanobacterial abundance was not correlated to secondary production, but was positively related to EPA and DPA content in the mussels, suggesting more of these important FAs in locations with more cyanobacteria. These results suggest that growth of secondary consumers and the availability of important fatty acids in the western basin are centered on the Maumee rivermouth. The paper is available online at, The data release is available at,

Developing population models with data from marked individuals – Landbird Examples

Wayne Thogmartin (UMESC) and colleagues from Stony Brook University, the University of Wisconsin, Madison, and the U.S. Fish and Wildlife Service recently published the article titled, “Developing population models with data from marked individuals.” Population viability analysis is a powerful tool for biodiversity assessments, but its use has been limited because of requirements for fully specified population models such as demographic structure, density-dependence, environmental stochasticity, and specification of uncertainties. The authors present a general method estimating all the key parameters required to specify a stochastic, matrix-based population model, with examples constructed using long-term mark–recapture data for 9 landbird species from the Monitoring Avian Productivity and Survivorship (MAPS). Unlike standard mark–recapture analyses, this approach provides estimates of true survival rates and fecundities, their respective natural temporal variabilities, and density-dependence functions, making it possible to construct a population model for long-term projection of population dynamics. This method is expected to greatly enhance our understanding of the processes underlying population dynamics and our ability to analyze viability and project trends for species of conservation concern. The research is a result of a NASA-funded collaboration examining consequences of extreme weather and climate on avian occurrence, abundance, and demography. The paper is available online at,

The pace of past climate change vs. potential bird distributions and land use in the United States

Wayne Thogmartin (UMESC) and colleagues from the University of Wisconsin-Madison, U.S. Fish and Wildlife Service, and James Cook University in Australia published research in Global Change Biology describing the race of species to keep pace with a changing climate. On Tuesday, May 10, 2016, this research was be featured in an episode of Yale Climate Connections titled, “Birds Adapting to Global Warming." Climate Connections consists of 90-second stories about how people are responding to our warming world. The show airs 5 days a week on approximately two hundred radio stations as well as online via subscription.  More information, including the episode in which this research is featured and a link to subscribe to the podcast, see

Scientific Meetings, Conferences, and Workshops

Unmanned Aerial Systems Conference

Larry Robinson (UMESC) participated in XPONENTIAL 2016, the largest and most influential Unmanned Aerial Systems (UAS) event dedicated to unmanned systems, drones, and intelligent robotics. The conference offered over 200 educational sessions on future of unmanned system policies, regulations, and technology.  UMESC’s Geospatial Sciences and Technology Branch is planning to purchase a UAS in the near future.  The exhibit hall’s 600+ vendor displays gave Robinson the opportunity to meet with numerous UAS vendors and discuss the capabilities of their products.  Xponential 2016 was held May 2-6, 2016, in New Orleans, LA, hosted by the Association for Unmanned Vehicle Systems International (UAVSI).

Great Lakes Law Enforcement Training for use of eDNA Detectors

Chris Merkes and Emily Ziegler (UMESC) trained law enforcement officers in Vickery, OH, May 3, 2016, on use of a portable eDNA detector for the detection of invasive bighead carp and silver carp.  Working with private industry last year, USGS developed and validated a loop-mediated isothermal amplification (LAMP) assay for the detection of bighead and silver carp eDNA from water samples in the field.  Conservation officers from Illinois, Michigan, and Ohio Departments of Natural Resources participated in the training, and this year they will implement a pilot study using the LAMP assay to inspect tanks at bait dealers for invasive bigheaded carps.  Law enforcement’s use of this technology will help spread awareness about invasive species moving through the bait trade.  Results and feedback from the pilot study will help guide the use of this technology by law enforcement in the future.  Conservation officers from Department of Fisheries and Oceans Canada and a fisheries manager from Wisconsin Department of Natural Resources will also attend the training in preparation for potential future use of this technology in their jurisdictions.

Monarch Conservation Science Partnership Workshop

Jason Rohweder (UMESC) participated in a Structured Decision Making workshop for the Monarch Conservation Science Partnership, May 2-6, 2016, in Chicago, IL.  The goal of this workshop was to evaluate how states and other partners can strategically coordinate efforts, at multiples scales and across management jurisdictions, to ensure that biological targets for monarch butterflies are achieved through collective actions.  Jason assisted the workshop providing GIS support and utilizing tools developed by the Monarch Conservation Science Partnership.

Geospatial and Hydrodynamic Model Presentations

Molly Van Appledorn (UMESC) presented, “Floods and Forests: disentangling complex relationships in bottomland ecosystems,” for the USGS Eastern Geographic Science Center and the National Research Programs May 17, 2016, in Reston, VA. The seminar will explore multi-scalar eco-hydraulic interactions using novel applications of geospatial and hydrodynamic models.

Geospatial North America Conference

Enrika Hlavacek (UMESC) attended the Free and Open Source Software for Geospatial (FOSS4G) North America Conference in Raleigh, NC, May 2-5, 2016. The conference brought together the open source community for technical sessions, workshops, and collaboration on the latest geospatial topics, such as web mapping, spatial databases, and geoprocessing.

Asian Carp Complex Sound Workshop

Brent Knights, Marybeth Brey (UMESC), and cooperators from the U.S. Fish and Wildlife Service, U.S. Army Corps of Engineers, Minnesota Department of Natural Resources, and Kentucky Department of Fish and Wildlife, held a Complex Sound Workshop at the Upper Midwest Environmental Sciences Center, May 17-18, 2016.  This “state of the science” workshop and discussion forum was organized for management agencies interested in using complex sounds as a deterrent for invasive bigheaded carp.  Researchers conducting “complex sound” studies on invasive carps and native fish species presented their latest results, on-going research, and planned next steps; and answered questions regarding the efficacy, limitations, and information gaps in the use of complex sound as a deterrent to invasive carps. Managers from the Great Lakes and Mississippi River basins discussed their interests and research needs to support deployment and evaluation of sound deterrent barriers. The desired outcome of the meeting was to develop a common understanding of current knowledge, efficacy, limitations, and ongoing research into using complex noise as a deterrent for invasive carp; and to collaboratively identify (1) highest priority research needs in support of field deployment, (2) considerations for evaluating specific locations within each basin for field deployment of sound barrier technology, and (3) next steps for advancing research, field deployment, and evaluation.

HTCondor Conference

Richard Erickson (UMESC) presented a case study of how UMESC is using HTCondor technology to develop new models for estimating trends from available long term fish and vegetation data for the Upper Mississippi River, during HTCondor Week in Madison, WI, May 17-20, 2016.  The conference brings together a wide variety of data scientists from organizations such as CERN, Fermilab, and Brookhaven National Laboratory to find innovative ways to process data. Activities include presentations and tutorials on high-throughput computing and cycle scavenging to process large data sets.  S. Grace McCalla will also attend to gain insights on processing large DNA databases, Jon Knudson and Mel Bower will be looking for technical pointers on how to administer and maintain HTCondor systems.


Richard Erickson (UMESC) presented, “Detecting seasonal trends in eDNA with occupancy modeling,” and lead the workshop, “R-Bootcamp: An interactive introduction to R,” at the 2016 Midwest Mathematical Biology Conference at the University of Wisconsin-La Crosse, May 21-22, 2016.

Upper Midwest Geospatial Conference

Enrika Hlavacek, Janis Ruhser, Jayme Stone, Jenny Hanson, Larry Robinson, and Stephanie Sattler (UMESC) attended the 2016 Upper Midwest Geospatial Conference (UMGEOCON) at the University of Wisconsin-La Crosse, May 25-26, 2016. UMGEOCON provided a forum for geospatial professionals from the Midwest region to share the latest updates on emerging geospatial topics including open data policies, cloud computing, and mobile and drone technologies. Participants included geospatial community leaders, providing a platform for attendees to discuss the challenges in addressing policy and regulation changes to the GIS industry. The event offered a variety of presentations, free workshops, hands-on training seminars, and an exhibition hall showcasing new technology, equipment, and services.


NatureServe's Core Methodology Training

Kevin Hop (UMESC) attended NatureServe's Core Methodology Training 2016 in Arlington, VA, May 3-5, 2016. Core Methodology Training provides an understanding of the fundamental or core concepts that NatureServe’s primary work is built on - the work of documenting and managing information on species and ecosystems in a standard way. The training also touched on ways in which data are being used, from modeling to visualization products. While at UMESC, Kevin has a 20-year collaborative relationship with NatureServe, developing vegetation classification and mapping products for the National Park Service Vegetation Mapping Inventory Program. This training will aid him in greater understanding of the core methods NatureServe has adopted to develop their standard products.


AOC – Area of Concern
CEC – Contaminants of Concern
DNR – Department of Natural Resources
DPA – eicosapentaenoic fatty acids
eDNA – environmental DNA
EPA – Environmental Protection Agency
EPA – eicosapentaenoic fatty acids
GECSC – Geosciences and Environmental Change Science Center
GIS – Geographic Information System
GLSC – Great Lakes Science Center
GLRI – Great Lakes Restoration Initiative
GRSM – Great Smokey Mountains
HBBS – Hammond Bay Biological Station
JELA – Jean LaFitte National Historical Park and Preserve
LAMP – loop-mediated isothermal amplification
LTRM – Long Term Resource Monitoring
MAPS – Monitoring Avian Productivity and Survivorship
NASA – National Aeronautics and Space Administration
NIMBioS – National Institute for Mathematical and Biological Synthesis
NOAA – National Oceanic and Atmospheric Administration
NPS – National Park Service
NPWRC – Northern Prairie Wildlife Research Center
PWRC – Patuxent Wildlife Research Center
UAS – Unmanned Arial Systems
UMESC – Upper Midwest Environmental Sciences Center
UMRBA – Upper Mississippi River Basin Association
UMRR – Upper Mississippi River Restoration
USACE – U.S. Army Corps of Engineers
USFWS – U.S. Fish and Wildlife Service
USGS – U.S. Geological Survey
VMI – Vegetation Mapping Inventory

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