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Research Activities

Detailed descriptions of the pre-treatment conditions for each of the communities being studied can be found in The Hardwood Ecosystem Experiment: A Framework for Studying Responses to Forest Management.

Vegetation: Forest Dynamics and Acorn Production

Birds: Breeding birds, Cerulean warbler, Owls

Mammals: Bats, Small mammals, White-tailed deer

Reptiles & Amphibians: Salamanders

Insects: Wood-boring beetles and Moths (Lepidoptera)

Fire: Prescribed fire 

Fungi: Ectomycorrhizal fungi

Hardwood Ecosystem Experiment Species List, 2006-2015 (PDF: 204 KB)
This list includes all species documented since the initiation of the HEE in 2006.


Forest Dynamics


Project Investigators
Mike Saunders, Purdue University, msaunder@purdue.edu
Mike Jenkins, Purdue University, jenkinma@purdue.edu

Wildlife managers face a conundrum when asked to manage a species that requires a specific type of sub-climax habitat. If you remove the habitat, you lose the animal. Conversely, if you leave the habitat alone, it will become over-mature and eventually cause a decline of the species. This is the issue facing wildlife biologists and timber managers in Indiana where many of our species are dependent on Oak/Hickory forests. For many years, these forests have been allowed to grow without harvest or fire, and the result is that the understory of these woods is now filled with species such as maples and beeches that are the true local climax habitat.

Inventory plots are being installed to characterize the long-term, landscape-level changes in forest canopy structure and overstory recruitment by oak and other highly valued tree species in response to forest management. These plots will also allow spatial modeling of oak regeneration in response to overstory canopy and other environmental valuables, thereby linking local, seed dispersal mechanisms to the landscape pattern. Data concerning herbaceous plants and seedlings is also recorded at these same plots. Plots are installed across all treatment types on a 75 meter by 150 meter grid, linking them to avian inventories and, eventually, an associated dead wood inventory.

Acorn Production

Acorn x-raysProject Investigator
Robert K. Swihart, Purdue University, (765) 494-3575, rswihart@purdue.edu

Dr. Swihart is studying the removal of fallen acorns to determine which consumers in the forest community are benefiting from this important food supply, how use varies with food availability and consumer density, and whether differences occur due to tree harvesting. A series of semi-permeable enclosures is used to restrict access to acorns by vertebrates of different size, from deer to mice. Future work may study the dispersal of acorns into harvest openings to improve our understanding of forest regeneration processes.


Breeding Birds

Breeding Bird

Project Investigator
John B. Dunning, Purdue University, (765) 494-3565, jdunning@purdue.edu


Many species of songbirds that nest in mature forests of the eastern United States are declining, and it is thought that forest management activities may be part of the cause for the declines, but also may be part of the solution. Since the beginning of the HEE project, field technicians under the direction of Dr. John Dunning of the Department of Forestry and Natural Resources have conducted surveys of breeding birds at the HEE study areas to establish the distribution and abundances of species across the sites and to monitor how the bird communities change in response to forest management.

Since the first timber harvests, we have looked at how birds respond, not only at the specific sites where timber management is conducted but also across the larger spatial scales of the HEE project. Birds are surveyed with 10-minute point counts, during which field technicians record all birds seen and heard within 100 meters of permanently marked locations. Melissa Malloy, who received her Master’s degree from the FNR department, focused initially on predicted changes in the distribution of common breeders across the study regions in the first years after the harvests, but current studies by Patrick Ruhl (a Ph.D. student) and Ken Kellner (a post-doctoral researcher) are looking at longer term impacts on both species distribution and breeding success. While all birds are surveyed, some species are of management or conservation concern, and therefore are of special interest. These include migratory songbirds such as the Wood Thrush and Acadian Flycatcher, resident species such as Blue Jays that play important ecological roles as nest predators and acorn dispersers, and unusual birds such as the Golden Eagles, which winter locally in the region and the Worm-eating Warbler, a habitat specialist that breeds in the steep forested slopes of southern Indiana. Surprisingly, Worm-eating Warblers have proven to be one of the most common species caught during the breeding season in the clearcuts in later years, when those patches are densely vegetated with early succession shrub and tree species. The role of the young forest habitat in the clearcut patches is the focus of Patrick Ruhl’s ongoing research.

Cerulean Warbler

Cerulean Warbler

Project Investigator
Kamal Islam, Ball State University, (765) 285-8847, kislam@bsu.edu

Dr. Kamal Islam and his students at Ball State University have been studying the Cerulean Warbler in southern Indiana since 2000. This tiny migratory songbird of conservation concern has experienced long-term population declines on its breeding grounds during the past 40 years. We are trying to understand factors responsible for the decline of this species in Indiana, where it is listed as ‘endangered’. Although Cerulean Warblers are generally associated with mature forests, their territories are often characterized by canopy gaps, and these birds are attracted to small openings in the forest created by various forest practices. The presence of Cerulean Warblers in selectively-cut stands suggests that canopy gaps are likely an important habitat variable. Our primary objective in the context of the HEE is to determine how Cerulean Warbler populations respond to different forest treatments by 1) measuring estimates of relative abundance and 2) quantifying reproductive output. An additional research question links the importance of arthropod abundance in oaks and hickories (compared to other tree species), and Cerulean Warbler nestling diet. Recently, we have expanded our research to include fledgling dispersal using radio-transmitters. Evidence from studies of other migratory songbirds suggests that fledglings of mature forest species move into early successional habitats, such as those created by forest harvest. Results from our studies have potential management implications for the conservation of this declining species.


Barred Owl

Project Investigators
John B. Dunning, Purdue University, (765) 494-3565, jdunning@purdue.edu
Robert K. Swihart, Purdue University, (765) 494-3575, rswihart@purdue.edu

An exciting project was initiated during the winter of 2009-2010 that will continue for the next few years. In order to get a better study on how different parts of the overall forest community interact in response to timber management, we were interested in examining owl populations in and around the HEE study region. To implement this project, we have engaged the local birding community, making this a good example of “citizen science.”

Owls are top predators in the regional food webs, feeding on species groups that are already under study in the HEE project, namely small mammals (the prey of Great Horned Owls and Barred Owls) and forest insects (Eastern Screech-Owls). All three of these species are permanent residents (e.g., they are non-migratory). In addition to different prey, the three species have different territory sizes. Thus we were interested in conducting focused studies on population sizes and territory placement in the region surrounding the HEE study areas. Surveys are conducted in each of the nine HEE research areas, elsewhere throughout Morgan-Monroe and Yellowwood State Forests, in Brown County State Park, and in parts of the Hoosier National Forest including the Deam Wilderness area.

Due to the wide-ranging area we wanted to survey, we recruited volunteer birders from the region to conduct surveys of forest night birds (primarily owls, but also Eastern Whip-poor-wills and the related Chuck-Will’s-Widows in the summer). Surveys are done in mid-winter because most of the owls breed from January – March and are most responsive to recordings of their calls at this time. The surveys targeting Barred Owls are repeated in May-July to attempt to detect family groups and therefore get an impression of reproductive success.

Initial analyses have shown that Barred Owls and Eastern Screech-Owls were not affected strongly by the timber harvests in the state forests. Barred Owls were almost absent from Brown County State Park, but the screech-owls were common there (perhaps because Barred Owls are known to be screech-owl predators). We expect to continue the winter and summer surveys for at least two more years. If funding becomes available, we would also like to conduct a radio-telemetry study to examine how the owls use harvest and edge areas for foraging habitat. If you are interested in volunteering with this project, please contact the HEE Project Coordinator.




Project Investigators
Joy O’Keefe, University of Illinois, (217) 300-6933, jmokeefe@illinois.edu

For many species of wildlife, particularly game animals such as deer and turkey, we have enough scientific knowledge to predict the results of timber harvest on local populations. Such is not the case for the endangered Indiana bat (Myotis sodalis). Part of the problem is that these bats spend their summers in old dead or dying trees with loose bark. In these snags the females form large colonies (often with 100+ individuals) and raise their young. So biologists are very concerned that timber harvest will either remove the roost trees or the next generation of roost trees.

Although Indiana bats will use almost any large tree with sloughing bark and substantial solar exposure, oaks and hickories seem to be some of the better roosts because one dead tree will hold onto its bark for many years. Maples are rarely used and seem not to form high quality roosts, while no one has ever recorded an Indiana bat using a beech. Thus, we also face a situation that as oak-hickory forests become beech maple forests, they may become less valuable to bats. One way of turning back the clock on succession is by using timber harvest—the overall goal of Hardwoods Ecosystem Experiment is to determine the impact of harvest on a wide variety of wildlife.

To determine the impact of timber harvest on bats we are “trapping” bats in 2 ways. First, we are using mist-nets to capture them as they fly through an opening in the forest. This allows us to directly handle the bats and determine their age, sex, reproductive state, even if they have been captured before. Unfortunately, mist-nets are only effective when placed in an area, such as a roadway or stream, where bats are funneled into the net. Thus, they are not very good for detecting bats that are simply flying through, or over a forest. To “trap” these bats we are using a device called an Anabat® Detector that converts the echolocation calls of bats into an electronic file. Once these data are stored, we can go back and identify many of the calls to species. This technique allows us to “capture” many more bats, but we do not have the detailed information about the individuals such as we get from netting.

Small Mammals


Project Investigator
Robert K. Swihart, Purdue University, (765) 494-3575, rswihart@purdue.edu

Small mammals are important but seldom-seen components of forest ecosystems. They play important roles as seed dispersers, seed predators, and food for larger animals. The Hardwood Ecosystem Experiment is studying the effect of forest management on small mammal populations and communities. Dr. Robert Swihart designed a study in which livetrapping grids were established at 32 sites during summer of 2007, and trapping has been conducted regularly since then to determine short-term responses of small mammals to harvesting. Attributes of habitat also were measured around each trap, in the area scheduled for harvest, and in each of the 900-acre management units, to assess whether certain attributes are consistently associated with use by small mammals. Eastern chipmunk numbers increased with harvest opening size – abundance was 38% to 84% greater than in unharvested sites. White-footed mice were unaffected by small to medium-sized openings but declined by 32% in the largest 10-acre openings. Short-tailed shrews tended to increase slightly in association with 1-acre openings but declined slightly in larger openings. Other factors also influenced abundance: numbers were lower for shrews and mice on sites with southwestern aspects and following years of poor acorn production. Chipmunks and mice benefited from increased woody debris created by harvests, but shrews avoided harvest areas without a well-developed layer of leaf litter.

We currently are evaluating effects of timber harvest and prescribed fire on the survival of small mammals and on their behavior as seed dispersers.

White-tailed Deer

Project Investigators
Scott Haulton, DNR Division of Forestry, (317) 234-5725, shaulton@dnr.IN.gov
Mike Saunders, Purdue University, (765) 430-1440, msaunder@purdue.edu
Robert K. Swihart, Purdue University, (765) 494-3575, rswihart@purdue.edu

When examining oak regeneration in Indiana, one must not underestimate the power of the white-tailed deer. Although the deer in the study forests do not appear to be having as much of a devastating impact as they did in nearby Brown County State Park in the 1980s and 1990s, excluding deer from regeneration sites may have a positive impact on growing oak seedlings.

Thirty-two deer exclosures were erected in and around many of the harvest areas during 2009. These exclosures are 72 ft by 72 ft and 8 ft tall. The exclosure placement is relative to the edge of the harvest opening. In four 3-acre group selections, an exclosure is placed near the center of the opening, one is along the edge, and one is outside the 3-acre opening in the single-tree harvested matrix. In four of the six 10-acre clearcuts, a center, edge, and matrix exclosure is supplemented by an additional exclosure within the opening between the center exclosure and the edge. The four 10-acre shelterwood areas will only have a single center exclosure until the second shelterwood entry removes some of the overstory trees.

Each fenced exclosure has an unfenced reference plot associated with it to compare vegetation response to deer browsing. Researchers will be looking at the effects of deer (and other herbivores like rabbits) on hardwood growth and survival and how these effects vary among the different harvest types (clearcut, shelterwood, group selection) and in relation to the distance from the harvest boundary.

Reptiles & Amphibians


Zigzag salamander

Project Investigator
Robert K. Swihart, Purdue University, (765) 494-3575, rswihart@purdue.edu

Terrestrial plethodontid salamanders are an ideal group of species to monitor forest ecosystem integrity and biodiversity across the eastern United States. They play a significant role in nutrient recycling by consuming vast quantities of invertebrates and in turn serve as prey items for other forest species. They are sensitive to environmental stresses, and they are often the most abundant vertebrates in deciduous forests.

However, our current knowledge of the effects of timber harvesting on salamander populations is incomplete. Most studies suffer from a lack of replication among various silvicultural treatments and focus solely on immediate post-treatment responses. The terrestrial salamander portion of the Hardwood Ecosystem Project is designed to evaluate the effects of timber harvesting on the diversity, abundance, and demographics of woodland salamanders. Beginning in May 2007, a total of 66 coverboard grids (30 boards per grid) were placed within the 9 study areas. The coverboard grids were checked every other week from September through November. In the spring of 2008, nearly 2000 quadrat surveys (1x1m plots) were added to the coverboard sampling and the sampling period was extended to include Spring sampling in addition to the Fall sampling. We have used the first years of data to evaluate the immediate response of plethodontid salamander populations in regenerating forests < 5 years old and are currently evaluating long-term harvest effects (7-10 years post-harvest) on terrestrial salamander populations among the various harvest treatments.


Wood-boring beetles


Project Investigator
Jeff Holland, Purdue University, (765) 494-7739, jdhollan@purdue.edu

Dr. Jeffrey Holland of Purdue’s Department of Entomology and his graduate students are studying the influence of different types of forestry management on assemblages of longhorned beetles. Some of these beetles are devastating pests of forest trees, while many others play important ecological roles by decomposing rotting wood, acting as natural thinning agents, and reducing fire fuel load.

Understanding how the assemblages of species changes over time under different management techniques will allow us to both promote the biodiversity of those native species providing ecosystem services and limit economic losses from the few pest species. The beetles are sampled using arrays of four different types of traps that each has characteristics to attract certain types of beetle. Thirty-six of these arrays were used to sample the longhorned beetles for about one and a half months in 2006 and three months in 2007. The sampling arrays will continue to sample after the harvests to detect changes in the assemblages of beetles. This is a diverse beetle family and they have found 70 longhorned beetle species during this project so far.

Moths (Lepidoptera)
Luna moth

Project Investigator
Keith Summerville, Drake University, (515) 271-2265, keith.summerville@drake.edu

Dr. Keith Summerville’s goal for his contributions to the Hardwood Ecosystem Experiment is to develop a deeper understanding of how both anthropogenic and stochastic disturbances create structure in moth species assemblages. In particular, Keith is testing hypotheses related to the relative contributions of timber harvest, prescribed fire, variation in weather, and impact of timber pests on forest Lepidoptera. Based on the last eight years research, Keith has determined that moth species assemblages are relatively resilient to low volume timber harvests. Summer droughts and high volume timber harvests appear to interact to create novel species assemblages dominated by generalist species. In 2015, Keith collected pre-burn data on moth communities in stands slated for fall 2015 or spring 2016 burns. Keith’s sampling methodology utilizes battery-powered light traps that draw the moths in and traps them in a funnel capped bucket. Twenty of these traps were set for five different nights in the summer of 2007-2015.


Prescribed Fire

Project Investigator

Mike Saunders, Purdue University, msaunder@purdue.edu   Prescribed fire
Oak forests in eastern North America were borne of fire.  Fire shaped the species, the size and the spatial distribution of trees within these cherished forests.  Over the past century, fire suppression and fragmentation has reduced the resistance and resilience of these forests to pests, pathogens, weather and changing climate.  This is leading to a slow conversion of these oak forests to maple forests, which has important implications to the ecology and economy of eastern North America.  For example, oak forests host more wildlife species, both old and young forest specialists, than most other forest types in the East. Due to the critical role that fire plays in regenerating oak, prescribed burning began in several areas in 2015. Over time, researchers are examining the effects of fire on vegetation, small mammal, bird, moth, beetle, and spider populations as well as the effects of fire on tree quality.



Ectomycorrhizal fungi

Fungi on a decaying tree

Project Investigator
M. Catherine Aime, Purdue University, (765) 496-7853, maime@purdue.edu

Fungi are one of the primary drivers of ecosystem function; it is generally acknowledged that strong interactions and feedbacks occur between soil microbial communities and most plant species. Fungi play primary roles in decomposition, nutrient cycling, and carbon cycling – yet they remain vastly understudied across most biomes. One reason is due to difficulties in sampling. Traditional research of fungi in the environment primarily relies on specimen-based or culturing methodologies to assess the communities that are present. These methods have a number of inherent limitations. The main body of the organisms are microscopic, present as threadlike filaments that are located underground or in wood, and out of direct sight most of the time. When they decide to fruit, the reproductive structures are ephemeral, with the fruitbodies only persisting for a short time in the environment. Finally, many types of fungi cannot be readily cultured from the soil or from wood.

New technologies such as next-generation sequencing allow us to take an environmental sample of soil or wood and to look at the DNA of all of the fungi that are present, but “hidden” in the ecosystem. From a single small soil sample, it is possible to capture the presence of dozens, or even hundreds of fungal species. As a part of this research, we are examining the fungal communities that exist in the soil around five tree species – white oak, chestnut oak, tulip tree, beech, and sugar maple. We are also examining how these communities change across geographic and temporal gradients, as well as through a result of different forest management strategies. The primary group we will be targeting are ectomycorrhizal (ECM) fungi, but we will report all species that were encountered throughout the sampling in the spring, summer, and fall of 2018 and 2019. ​

Past Research Activities