Prairie Research Institute

Illinois Natural History Survey

Two hundred years ago Illinois was home to vast prairies, dotted with forests, savannas, and wetlands. Now few remnant natural areas remain. To protect and enhance Illinois’ natural heritage, agencies and interest groups must not only preserve the natural areas that remain but also restore degraded lands and try to reconstruct natural habitats and plant communities on sites that were formerly used for agriculture or industry.

INHS botanists support these efforts by:

  • surveying plant communities and assessing habitat quality at sites across Illinois;
  • tracking the success of management and restoration efforts by monitoring changes in plant community composition and quality over time; 
  • collecting the distribution, status, life history, and threat information needed for rare, threatened, and endangered plant conservation plans;
  • gathering invasive plant distribution data to inform targeted control measures; and
  • studying the interactions between plants and insects.

Surveys and habitat assessments

INHS botanists document the occurrence and/or abundance of individual plant species—particularly rare, imperiled, and invasive species—and survey plant communities at sites across Illinois and beyond.

For instance, Critical Trends Assessment Program (CTAP) botanists have surveyed plant communities at over 600 randomly selected grassland, forest, and wetland sites in Illinois since the program’s inception in 1997. The herbaceous and woody vegetation data collected can be used to assess the occurrence or abundance of individual plant species, site quality, and changes in a site’s ecological conditions over time, and can serve as a baseline from which to compare regional and site-specific patterns throughout Illinois.


INHS botanists employ a variety of sampling techniques to survey Illinois’ flora, selecting the methods that best address the goals of their research project. For instance, ecologically informed meander surveys are often used in studies that require determining the presence/absence of a species or assembling site species lists. When more detailed information is required on plant populations (like size and density) or on plant communities (like diversity and coverage), other systematic approaches are used, like setting transects, plots, and quadrats.

Governmental agencies and conservation groups often call on INHS scientists not only to collect plant community data but also to assess the quality and ecological integrity of sites for the prioritization of land acquisition, protection, and/or stewardship.

INHS botanists are at the forefront of validating and refining the Floristic Quality Assessment (FQA) as a tool to rapidly and qualitatively assess the ecological integrity of natural areas. FQA uses coefficients of conservatism values assigned to plants in a region to obtain a Floristic Quality Index for a given land area. Originally co-developed by retired INHS botanist John Taft, FQA has become a popular tool for identifying high-quality natural areas, comparing floristic quality among sites regardless of community type, monitoring natural areas, and tracking the success of restoration activities.

Currently, INHS botanists Jason Bried, Suneeti Jog, and Greg Spyreas are working on a variety of projects evaluating shortcuts to traditional FQA, including the use of indicator species, dominant species, and/or stressor checklists. They are also exploring how taxonomic distinctness intersects with FQAs and the significance of including non-native species in FQAs. The aim of their work is to help provide practitioners with the most effective and efficient site quality assessment tools possible.

Land management and restoration

INHS botanists assist with land management and restoration initiatives led by governmental agencies and conservation groups by gathering baseline data on plant communities and/or monitoring those communities for composition and quality changes over time. Some recent projects include:

  • Inventorying ravine plant communities. INHS botanists worked with the Lake County Forest Preserve District to inventory the vegetation in ravines along the Lake Michigan North Shore in Lake County and northern Cook County—delicate ecosystems that help manage water runoff and provide habitat for many rare plant and animal species. These baseline vegetation data will help scientists and land managers understand how development impacts the ravines’ plant communities, prioritize management in high-quality communities, and inform restoration efforts in degraded areas.
  • Assessing the effectiveness of wetland mitigation banks. Wetland mitigation banks are large-scale restoration projects that agencies and companies buy credits toward to compensate for damage their developmental projects caused to wetlands. A research team including INHS botanists Greg Spyreas and Andy Olnas recently compared plant community composition, richness, and quality for wetland mitigation banks to that of natural wetlands to determine whether mitigation banks are actually achieving “no net loss” of wetland habitat. Their study revealed that mitigation banks do not come close to reaching the floristic quality standards set by high-quality, reference wetlands. Further, the mitigation banks’ plant community composition is distinct from that of reference wetlands, mostly due to the prevalence of invasive species in these large restorations. 
  • Examining restoration strategies for a floodplain forest. INHS botanist Susan McIntyre and her colleagues assessed the effectiveness of restoring former agricultural land in Rock River, Illinois to a floodplain forest. They found that lower-cost treatments like passive restoration and acorn planting resulted in areas with few trees and dense stands of the invasive reed canarygrass (Phalaris arundinacea). Alternatively, areas restored with bareroot and balled-and-burlapped tree plantings—a more expensive approach—fared much better, sporting greater plant species richness, closed tree canopies, and decreased densities of reed canarygrass. These data can be used by practitioners to help weigh initial costs against potential restoration outcomes.

Transportation infrastructure support

INHS botanists work with the Illinois Department of Transportation (IDOT) to survey and assess plant communities within current transportation infrastructure corridors and future project areas. These efforts help IDOT comply with federal regulations regarding environmental impact, clean water, wetlands, and endangered species. It also helps the agencies grow and maintain Illinois’ transportation infrastructure in a way that helps ensure natural plant communities are preserved for future generations.

INHS Biological Survey and Assessment Program (BSAP) scientists visit sites within and around the IDOT transportation networks, searching for threatened and endangered species and identifying high-quality natural areas whose plant communities’ composition and structure resemble pre-European settlement conditions. When a high-quality plant community is found, INHS botanists map the site, survey its vegetation, compile a thorough species list, and collect plant specimens for documentation. This work has led to the discovery of many new imperiled plant species populations and high-quality natural communities across Illinois.

INHS Wetland Science Program botanists, soil scientists, and GIS specialists work closely with IDOT to identify, protect, maintain, and restore wetlands in Illinois. They conduct botanical surveys and wetland delineations within the transportation infrastructure corridors and assist IDOT in locating sites that are appropriate for wetland restoration. When impacts to wetlands are unavoidable, IDOT attempts to offset these impacts using created or restored wetlands near the impacted site. INHS wetland scientists work with Illinois State Geological Survey scientists to monitor these restored sites and report on progress toward restoration objectives. They also conduct applied research on the ecology and conservation of wetland ecosystems.

University of Illinois natural areas

Natural areas coordinator Jamie Ellis and research specialist Nathan Hudson manage, maintain, protect, and coordinate access to about 1,000 acres of lands and waters at 12 sites that are part of the University of Illinois’ natural areas. These mostly forested properties (e.g., Trelease Woods and Brownfield Woods) in parts of Champaign, Vermilion, and McLean counties are available to the University community for research and teaching purposes.

Rare species

INHS botanists assess the conservation status and vulnerabilities of rare and imperiled plant species in Illinois and across the United States. They also conduct large-scale surveys and species-specific studies, collecting the distribution, demographic, life history, and threat information needed to develop effective conservation and management strategies for rare plants.

Conservation status and vulnerability

More than 300 plant species are listed as threatened and endangered in Illinois and many others are increasingly vulnerable due to habitat degradation, loss, and fragmentation, invasive species, poaching/overexploitation, pollution, and climate change.

An INHS research team recently evaluated the climate change vulnerability for 331 of Illinois’ threatened and endangered plant species. Findings showed that 88 percent of threatened and endangered plants are vulnerable to climate change, and 6 percent are extremely vulnerable. Habitat loss, barriers from land use change, seed dispersal ability, and sensitivity to changing temperatures and precipitation are the leading factors.

Currently, INHS botanists are using NatureServe methodology to update the state conservation statuses (S-Ranks) of Illinois’ threatened and endangered plants and a selected number of non-listed plant species of highest conservation concern. They plan to compile a matrix of threats for these species and generate an ArcGIS map with accompanying geodatabase that shows imperiled plant hotspots to assist in prioritization of land acquisition, protection, and stewardship. These data and tools will assist the Illinois Department of Natural Resources in their efforts to conserve and protect Illinois flora.

Large-scale surveys

INHS botanists work with federal, state, and local agencies to document the location of imperiled plant species through large-scale surveys.

For instance, INHS Biological Survey and Assessment Program scientists conduct botanical surveys within Illinois Department of Transportation (IDOT) roadway corridors to confirm the presence or absence of threatened and endangered plant species. These data enable IDOT to avoid and/or mitigate impacts to rare plant populations and inform rare plant conservation efforts by partnering agencies.

​​Recently, INHS botanists worked with the Lake County Forest Preserve District to document listed plant species and other plants of concern in ravines along the Lake Michigan North Shore in Lake County and northern Cook County. These baseline data will help guide land managers and Plants of Concern program researchers and volunteers with future monitoring and management efforts in these delicate ravine ecosystems.

Species-specific studies

INHS botanists collect detailed data on focal plant species to aid in conservation efforts.

For example, the INHS Plant Ecology Lab led by Brenda Molano-Flores works on a range of rare plant projects, from demographic studies and habitat-suitability modeling, to examining plant reproductive ecology, pollinator communities, and population genetic structure.


Endemic to the Midwest, kittentails (Synthris bullii) is a rare prairie species that is listed as state threatened in Illinois. INHS Plant Ecology Lab scientists have collected extensive data for this imperiled plant at populations across its range. These data include plant abundance and density, reproductive output, pre-dispersal seed predators, and seed germination. They have also examined the species’ pollination biology and the impact of habitat degradation like woody encroachment on kittentails’ reproductive ecology. Recently, lab members assessed the species’ seed viability after prolonged seed storage and found that they were still viable, suggesting that seed harvesting and storage could aid in the recovery of this species.

Sangamon phlox

The Illinois state endangered plant Sangamon phlox (Phlox pilosa subsp. sangamonensis) is only found in two Illinois counties (Champaign and Piatt counties) where it is endemic to the Sangamon River basin. INHS botanist David Zaya and his colleagues are examining how population size impacts the species’ reproduction success and are conducting genetic studies to look for evidence of inbreeding within populations and/or hybridization with a related species, woodland phlox (Phlox divaricata).

Pima pineapple cactus

The federally endangered Pima pineapple cactus (Coryphantha scheeri var. robustispina) grows in the semi-desert grassland and Sonoran desert-scrub of southern Arizona and northern Mexico. To help inform conservation measures for this rare cactus, INHS botanists Brenda Molano-Flores and David Zaya re-surveyed populations at six sites in Altar Valley, Arizona where long-term monitoring had previously occurred and used population viability analyses (PVA) to estimate extinction probabilities for those populations. They found the cactus persisting at five of six sites, but overall population sizes were decreasing. Further, their PVA predicts that five sites will lose more than half their individuals within 50 years.

Kaibab bladderpod

Endemic to the Kaibab Plateau of Arizona, the Kaibab bladderpod (Physaria kaibabensis) is being evaluated for federal listing due to its limited range; however, information on the species’ ecology is very limited. INHS Plant Ecology Lab scientists have studied six Kaibab bladderpod sites, collecting much-needed data on plant density, habitat characteristics and disturbances, flower visitors, pollination biology, pollen grain morphology, reproductive output, pre-dispersal seed predators, and seed germination. They are also conducting genetic analyses to compare the Kaibab bladderpod’s diversity to closely related species in the same region, and to check for signs of reduced genetic diversity and hybridization. These data will inform conservation and management efforts as well as any future federal listing decisions for this rare plant.

Tobusch fishhook cactus

The federally threatened Tobusch fishhook cactus (Sclerocactus brevihamatus ssp. tobuschii) is endemic to limestone outcrops of the Edwards Plateau in Texas. INHS botanists David Zaya and Brenda Molano-Flores are analyzing a decades-long demographic data set on this rare species to examine population trends over time and assess how its populations have been impacted by fire and climate change. They will also provide recommendations on how future monitoring could be conducted to support successful conservation and management actions for the species.

White birds-in-a-nest

Restricted to the longleaf pine ecosystem of the Florida panhandle, white birds-in-a-nest (Macbridea alba) is listed as federally threatened and Florida state endangered. INHS botanists with the Plant Ecology Lab conducted habitat suitability and projection modeling for this rare mint. They also documented the species’ habitat associations and used population surveys and germination studies to understand its reproductive ecology.

Butterwort species

INHS Plant Ecology Lab scientists traveled to the Florida Panhandle multiple years to study the federally threatened and Florida state endangered Panhandle butterwort(P. ionantha) and the Florida state-threatened yellow-flowered butterwort (P. lutea) and swamp butterwort (P. planifolia). They aim to inform conservation strategies for these three imperiled predatory plants with data they collected on:

  • population size and genetic diversity/structure;
  • pollinator visitation and community structure; 
  • the effect of habitat structure on plant reproduction and prey capture;
  • breeding system dynamics; and
  • seed germination, seedling survivorship, and seed banks.

Invasive species

Because new botanical invasive species are introduced almost every year, and we are seldom able to completely eradicate them, the total number of plant invasive species in Illinois is increasing. Approximately one-third of the plants in most woodlands, wetlands, and grasslands in Illinois are non-native species. These invasions can cause economic damage, displace native species, alter ecosystem functions, and interfere with ecological restoration goals.

INHS botanists with the Critical Trends Assessment Program (CTAP) and Wetland Science Program survey plant communities in habitats across Illinois. Through the course of their work, the botanists gather invasive species distribution data that can inform invasive plant control strategies.

  • A recent INHS study using over 20 years of CTAP wetland data found that dominant, exotic plants reduce biodiversity and abundance more than dominant native plants do.
  • Wetland Science Program scientists survey the plants found within wetlands along the Illinois Department of Transportation roadway network. An analysis of their data from over 2,000 Chicagoland wetlands revealed the presence of exotic plants in over 99 percent of these wetlands, and that, on average, exotics made up over a third of individual wetlands’ plant species.

Plant-insect interactions


Insect pollinators are vital to the reproduction and thus long-term survival of many plant species, yet many pollinators face a multitude of threats.

The INHS Plant Ecology Lab led by Brenda Molano-Flores documents insect pollinator communities for rare and imperiled plants and examines how pollinators affect the plants’ reproductive success. Recent work has included conducting pollinator observations for three carnivorous butterwort (Pinguicula) species in the Florida Panhandle and the Kaibab bladderpod (Physaria kaibabensis) in the Kaibab Plateau of Arizona.

Molano-Flores is also working with scientists from the INHS Collaborative Ecological Genetics Lab to examine how environmental DNA (eDNA) left behind on flowers could be leveraged to document pollinator communities, as performing traditional pollinator observation studies can be time consuming and expensive.

Monarch butterflies

Conservation efforts for monarch butterflies have encouraged the widespread planting of milkweeds—monarch caterpillars’ sole food source—but it’s unclear how the landscape influences the success of such plantings. INHS scientist David Zaya is leading a community science project examining how monarch butterfly egg laying and caterpillar growth respond to different garden and landscape variables through the University of Illinois’ I-Pollinate program. Data from the project will help us better understand and use gardens to contribute to the conservation and resurgence of monarchs and other pollinators.

Zaya is also examining how site management and plant abundance, diversity, and density influence monarch oviposition on milkweeds in Illinois Department of Natural Resources and Conservation Reserve Program properties. His work will provide practitioners with information on which sites contribute the most to monarch conservation and which of their management and milkweed planting strategies are the most effective.


Bumble bees are important pollinators, but their numbers are declining due to habitat loss, diseases, pesticides, and other factors. INHS scientists travel to sites around Illinois surveying native bumble bees, with a focus on species in greatest conservation need. By studying the insects’ habitat and plant preferences, the scientists hope to determine ways to stop population declines and inform management efforts.

Urban Biotic Assessment Program (UBAP) scientists have been surveying for the federally endangered rusty patched bumble bee at sites near and within the Illinois Tollway corridor. Once active in Illinois, this rare bumble bee is now on the brink of extinction. The team’s work helps to ensure that the Tollway can make decisions about the location and timing of construction and maintenance projects to avoid negatively impacting it.

Native plant herbivores

INHS researchers are assessing populations and examining the genetic diversity and structure of the rattlesnake-master stem borer moth, a state endangered species threatened by habitat loss, pesticide use, and habitat fragmentation. This species’ larvae bore exclusively into the stems and roots of the native prairie plant rattlesnake master (Eryngium yuccafolium), where they pupate.

Crop pests

Agricultural insect pests have always caused problems for Illinois growers. Some pest species have affected crop production for the past century, but newly arrived pests, new pest behaviors, and changes in management tactics demand continued vigilance, research, and action to maintain sustainable and profitable crop production in Illinois.

The Illinois Cooperative Agricultural Pest Survey (CAPS) focuses on the early detection of invasive pests through surveys of both the pathways of potential introduction and the commodities they can impact. The CAPS program works with the U.S. Department of Agriculture Animal and Plant Health Inspection Service Plant Protection and Quarantine and the Illinois Department of Agriculture. If pests are detected, surveys are then conducted to determine the extent of the area occupied by the pest. Depending on the pest, eradication plans are put in place.

Corn rootworm

Corn rootworm beetles are the most devastating pests of America’s most valuable crop, corn. Annual yield losses and management costs of western corn rootworms (WCR) and the closely-related northern corn rootworm (NCR) may exceed $2 billion across the U.S. Corn Belt. These agricultural pests have evolved resistance to insecticides, annual crop rotation, and every rootworm-specific bacterial toxin engineered into transgenic “Bt” corn hybrids.

INHS insect behaviorist Joseph Spencer has studied the ecology, behavior, biology, and resistance of WCR for over 25 years, making progress in understanding the role of WCR behavior in pest adaptations to annual crop rotation and Bt corn hybrids. From changes in female egg-laying affinity for cornfields to patterns of intra- and interfield movement in Bt corn and startling adaptations of the WCR microbiota and gene expression in feeding individuals, “paying attention” to what WCR are doing is a foundation for understanding. Current work studying the status of WCR and NCR resistance to the toxins expressed in Bt corn hybrids as well as efforts to improve adoption of integrated pest management-based controls are aimed at providing sustainable tactics that work for farmers.


INHS houses three plant collections at the Robert Evers Laboratory:

  • The Illinois Natural History Survey (ILLS) Herbarium contains approximately 275,000 vascular plant specimens. About 80 percent of these specimens were collected in Illinois, including a significant number of state threatened and endangered species. ILLS also has sizable holdings from Great Smokey Mountains National Park, Kyrgyzstan, and China. Data for all ILLS vascular plant specimens are available to the public through the Consortium of Midwest Herbaria.
  • The University of Illinois Plant Biology (ILL) Herbarium holds approximately 520,000 vascular plant specimens, including roughly 4,000 type specimens. One-third of its specimens are from early Illinois; one-third come from other states, largely from the west; and the remaining third are from outside the United States.
  • The University of Illinois Crop Evolution Laboratory (CEL) Herbarium contains approximately 55,000 specimens. Specializing in Poaceae, this important crop plant collection contains many artificial hybrids of our cultivated plants and collections of their wild ancestors.

Together, these collections contain over 1 million specimens, making INHS the caretaker of the second largest herbarium in Illinois and the 10th largest in the United States.

Algal and bryophyte collections

Together the ILLS and ILL herbariums contain over 5,600 algal specimens and over 55,000 bryophyte specimens. Among the algae specimens are over 2,600 exsiccati, most notably a complete set of the Phycotheca Boreali-Americana, which contains about 90 percent of all marine algae found on the coasts of the United States. The bryophyte holdings include over 986 exsiccati, 286 of which are Musci Americani exsiccati specimens gathered during the Second Land Arctic Expedition of 1825.


With the support of funding from the National Science Foundation, Mellon Foundation, and other organizations, INHS is working to digitize all of its herbarium specimens—particularly type specimens—so that the valuable data they contain are accessible worldwide. Data from the plant, algal, and bryophyte collections can be searched using the INHS collections portal, the Bryophyte Portal, and the Consortium of Midwest Herbaria Portal.


Illinois Plants Database

The Illinois Plants Database summarizes each Illinois plant species’ scientific name and taxonomic classification, distribution and occurrence records (presented as county-level maps), trait and habitat information, flowering phenology, and coefficient of conservatism (C-value, a value assigned based on the species sensitivity to anthropogenic disturbance and its likelihood of being found in high-quality native habitat remnants). The database also includes a photo gallery for each species.

Pest degree calculators

INHS scientist Kelly Estes and Illinois State Water Survey researchers recently updated two pest degree day calculators for commodity and specialty crop growers in Illinois, featuring seven-day weather forecasts, graphs, and insect emergence maps to track accumulated degree days and light for the most notorious pests, including corn flea beetle and the prediction of potential Stewart’s Wilt severity, Japanese beetle emergence, and brown marmorated stinkbug activity. These tools help farmers plan pest management efforts and use pest control more efficiently. Because temperature controls the rate that insects develop, the new degree day calculators use data from the Water Survey’s network of weather monitoring stations so growers can calculate degree days accumulated in their region of the state for specific pests, such as the codling moth, spotted wing drosophila, corn rootworm, or emerald ash borer.