Dr. Clay L. Pierce

Dr. Clay L Pierce

  • Emeritus Collaborating Faculty Member
  • Iowa Cooperative Fish and Wildlife Research Unit Assistant Leader – Retired


Area of Expertise

  • Aquatic Ecology
  • Aquatic Conservation
  • Fisheries Ecology

Biographical Sketch

Clay Pierce retired in 2020 after serving 27 years as the Assistant Leader for Fisheries of the U.S. Geological Survey’s Iowa Cooperative Fish and Wildlife Research Unit at Iowa State University, and as a Collaborating NREM Faculty Member. He taught graduate courses (Fisheries Science, Stream Ecology), supervised graduate students, and did research in the disciplines of aquatic ecology, aquatic conservation, and fisheries ecology in wetlands, lakes, rivers, and streams of Iowa and the Midwest. Clay advised or co-advised 31 graduate students, received 54 research grants totaling over $3.4 million, and authored or co-authored over 80 peer-reviewed publications. At the time of his retirement, Clay’s publications had received nearly 2,800 citations and his career h-index was 29. Clay is a native of Minnesota and received his B.S. (1980) at Mankato State University, his M.S. (1982) at the University of Kentucky, and his Ph.D. (1987) at the University of Maryland. Prior to coming to Iowa, Clay was an assistant professor at Eastern Illinois University (1989-1993) and a postdoctoral researcher at McGill University (1987-1989).


Fisheries Science - This graduate-level course explored concepts, approaches, and techniques for assessment of recreational and commercial fisheries. Topics ranged from basic principles to applications, and from individual fish to entire ecosystems. Weekly in-class quantitative exercises, quantitative homework assignments, computer simulation modeling, group projects addressing real fisheries issues identified by Iowa Department of Natural Resources Fisheries Bureau staff, and discussion of primary literature were emphasized.

Stream Ecology - Offered at the graduate- and advanced undergraduate levels, this course explored the biological, chemical, physical, and geomorphological processes shaping the structure and function of flowing water ecosystems. Topics from basic principles to synthetic theories of stream ecosystems were covered, as well as applications for management of water quality, biological integrity, and fisheries in streams and rivers. Laboratory sessions and field exercises provided hands-on experiences. Students worked on reports of their field and laboratory studies in small groups. Team-taught with Dr. Thomas Isenhart.


Publications Link

Google Scholar Link

Conservation of the Endangered Topeka Shiner - Topeka shiners are native to the Upper Midwest but currently occupy only roughly 20% of their original range. Their declining distribution and low abundance resulted in their federal listing as an endangered species in 1998. Disappearance of their slow-water and oxbow wetland habitat is primarily responsible for the plight of the Topeka shiner, and thus they are a symbol of how altered landscapes resulting from intensive agriculture can harm native species. Clay led a team of faculty members, biologists from several agencies and non-governmental organizations, industry stakeholders, and several graduate students to comprehensively study the status, habitat relationships, and recovery strategies for this endangered species. The team identified several habitat and fish assemblage characteristics associated with presence and abundance of Topeka shiners, and managing for these characteristics is now part of the U.S. Fish and Wildlife Service’s Recovery Plan. Collaboration with the Iowa Geological Survey resulted in restored oxbows being termed “multi-purpose oxbows”, which are now highly valued for their provision of multiple ecosystem services such as hydrological retention, nutrient sequestration, water quality improvement, habitat enhancement, as well as conservation of the endangered Topeka shiner. Publications 1, 2, 3, 4, 5, 6, 7.

Effects of Habitat Alteration, Artificial Wetland Construction, and Pesticides on Amphibians in Iowa Wetlands - Amphibians are declining throughout the world due to habitat loss, diseases, contaminants and other factors. Iowa’s landscape is heavily modified and 90% of the historic wetland area has been converted to row crop agriculture. Not only is amphibian habitat severely reduced in Iowa, but pesticide use in agricultural areas also threatens amphibian populations. In collaboration with U.S. Geological Survey scientists and two graduate students, Clay helped study amphibian populations in several wetlands. Conservation Reserve Enhancement Program wetlands are constructed in agricultural areas to sequester sediment and nutrients, and although they present quite different habitat and water quality than naturally occurring wetlands, these differences did not have significant impacts on amphibians. Amphibians in both wetland types had significant tissue concentrations of several pesticides. A subsequent study with leopard frogs used a novel approach combining radio telemetry, pesticide analysis of tissues, and passive pesticide samplers moved among habitat types in the landscape to mimic frog movements. Tissue concentrations were highest in early spring following overwintering in wetlands. Body concentrations declined in summer as frogs occupied terrestrial habitats but avoided crop fields where pesticide concentrations were highest. Results are now being used for decision-making regarding wetland creation, wetland restoration, and pesticide regulation. Publications 1, 2, 3, 4, 5, 6.

Dynamics of the Asian Carp Invasion of Iowa Rivers - Asian carp are expanding throughout the Upper Mississippi River Basin and are of great concern due to their numerous impacts. Asian carp reproduce and grow quickly, and populations can become dense in a short time. Asian carp compete with early life stages of native species and reduce abundances of native and economically important species where they have become established. In collaboration with a faculty member and several graduate students, Clay helped quantify Asian carp distribution, abundance, growth, and reproduction and a suite of environmental variables in several interior Iowa rivers to predict future expansion of Asian carp in Iowa’s interior rivers. The studies were coordinated with several state and federal research efforts, and results will contribute to basin-wide monitoring. Results of the Iowa study will be used by the Iowa Department of Natural Resources to control the abundance and spread of Asian carp as well as to evaluate candidate dams for removal. Publications 1, 2, 3, 4, 5.

Factors Influencing Mercury Concentrations in Iowa Fishes - Mercury contamination in aquatic ecosystems has become a global concern. Mercury bioaccumulates in fish and can reach high levels that are harmful to humans when eaten. Mercury concentrations in fish tissue tend to increase with fish age and size, although concentrations can be variable due to a variety of other factors. In collaboration with a faculty member, an agency biologist, and a graduate student, Clay helped quantify seasonal variation in mercury concentrations in largemouth bass, and mercury concentrations in several species of fish in Iowa lakes and rivers, along with a suite of environmental characteristics to develop models predicting concentrations. All studies revealed that mercury concentrations are generally low in Iowa fishes regardless of location. Seasonal differences between species and related to fish size were demonstrated, and differences due to locations were also revealed, such as higher mercury concentrations in shallow lakes than in other lake types, and in rivers of the Paleozoic Plateau ecoregion compared with other rivers. Results will be used by the Iowa Department of Natural Resources to revise consumption advisories and thus will benefit human health. Publications 1, 2.

Fish Assemblages in Iowa’s Interior, Non-Wadable Rivers - Non-wadable rivers are prominent aquatic resources across Iowa’s landscape, yet their fish assemblages are less well studied than their wadable counterparts due to sampling difficulty and safety concerns. The goal of this project was to better understand these important habitats and their fish assemblages. In collaboration with a faculty member, an agency biologist, and two graduate students, Clay helped determine that fish assemblages were strongly related to the number of dams between sampling sites and large downstream rivers, and many species were limited to occurring below the dam furthest downstream. Habitat specialists, especially fluvial and backwater specialists have declined compared with historical collections. Pressing issues such as habitat degradation, effects of dams on fish passage, range fragmentation, and occurrence and spread of invasive species could not be effectively addressed in Iowa’s non-wadable rivers without results of this project. In addition, the Iowa Department of Natural Resource’s dam mitigation program is using these findings and associated thalweg depth maps to promote and justify their dam removal/mitigation projects. Recently the potential spread of invasive fish such as Asian carp has introduced another consideration into discussions of dam removal, and results of this project have and will continue to play a role in decision-making. Publications 1, 2, 3.

Effects of Introduced Common Carp and Invading Zebra Mussels on Water Quality and the Native Biological Community of Clear Lake - This study was built on Clay’s earlier Clear Lake carp study and attempted to understand the interactions and effects of introduced common carp, invading zebra mussels, and the native biological community on water quality in Clear Lake. The ultimate goal was to organize this knowledge into a simulation model for predicting future changes and the outcomes of management actions. In collaboration with agency biologists and two graduate students, Clay helped deliver numerous results, ranging from improved quantitative modeling approaches to construction of a whole-lake food web to construction of a carp population model and whole-ecosystem simulation model that can be parameterized and run by novices. The population simulation model is being used by the Iowa Department of Natural Resources for managing their nuisance common carp populations. The ecosystem simulation model provides a tool for scientists, managers and other decision makers to evaluate effects of potential ecosystem changes and alternative management actions in Clear Lake and other similar systems. Publications 1, 2, 3, 4.

Iowa Stream Fish Species of Greatest Conservation Need - Stream fishes are among Iowa’s most imperiled animals. Habitat and water quality degradation associated with Iowa’s extensive agricultural land use is pervasive and are not only important causes of past degradation, are also primary impediments to future restoration of Iowa’s stream fish faunas. In collaboration with a faculty member and a graduate student, Clay helped improve understanding, management, and protection of Iowa’s rarest stream fishes. Most of the rare species examined were declining in occurrence. IAGAP models produced by an earlier project were poor occurrence predictors for most of these species, likely due to their reliance on coarse, GIS-derived predictor variables. New models developed using a combination of site-measured, fine-scale variables and landscape-level variables were superior to the IAGAP models. Every state in the U.S. has a mandate to monitor the status of species of conservation need, and this study accomplished that goal for several fish species in Iowa. In addition, it demonstrated what will be necessary for Iowa to fully comply with its responsibility. Publications 1, 2, 3.

Fish Assemblage Relationships with Physical Habitat and Land Cover in Wadable Iowa Streams - This study is the most comprehensive, definitive analysis of stream fish assemblage relationships with habitat and landscape characteristics in Iowa. In collaboration with an agency biologist and a graduate student, Clay helped determine that fish assemblage characteristics were strongly associated with habitat. Sites dominated by fine substrates, deeply incised channels, and with row-cropped riparian zones supported fewer species and assemblages with lower biotic integrity. Sites with coarse substrates and abundant cover supported assemblages with greater biotic integrity. Habitat was strongly associated with land cover. Sites with natural land cover had more complex habitat with wider and more variable channel form, greater residual pool volumes, more large woody debris and more riparian vegetation canopy, while sites dominated by row crop land cover tended to have less complex habitat, highly sloped banks, and more fine substrates. The emerging bioeconomy, with its current emphasis on agricultural production of corn for ethanol, threatens to intensify agricultural alteration of the Iowa landscape in the future and further degrade habitat and fish assemblages in Iowa streams. Results of this study clearly demonstrate that increasing percentages of row crop agriculture in catchments and riparian areas, as will be necessary for increased corn production, will lead to further habitat degradation in Iowa streams, which in turn will be deleterious to fish assemblages. Results of this study have become central arguments for the need for land use reform and stream restoration in Iowa and other agriculturally dominated areas. Publications 1, 2, 3.

Seasonal Distribution, Aggregation, and Habitat Selection of Common Carp in Clear Lake, Iowa - Clear Lake is Iowa’s third largest natural lake and has an annual recreation-related value of over $43 million to the local economy, but has severely declining water quality, degraded habitat, and a reduced and less diverse fishery than in earlier decades. Common carp were introduced in the early 1900s and have become highly abundant. Common carp have well documented deleterious effects on lakes world-wide, and in Clear Lake they are both symptomatic of the decline in overall environmental health as well as a roadblock to future recovery. The primary goal of this study was to locate times and places where common carp are aggregated in Clear Lake using radio telemetry, and thus vulnerable to efficient removal by seining. A secondary goal was to determine seasonal patterns of association with habitat characteristics such as depth and substrate that might generalize to other lakes. In collaboration with a graduate student, Clay helped document strong patterns of aggregation and habitat utilization tendencies. Common carp were found in a tight aggregation in late fall and early winter, and then again in a different location in spring during spawning. Results of this study are now being used by the Iowa Department of Natural Resources in cooperation with a commercial fishing company to guide annual common carp removal by seining. The approach of identifying locations and timing of aggregation to guide removal has been incorporated into common carp management by other states. Publications 1, 2.

Fish Passage and Fish Assemblages in a Western Iowa Stream Modified by Grade Control Structures - Over 400 rip-rap grade control structures have been built in streams in western Iowa to halt upstream progression of head-cutting, stabilize streambanks, and ultimately to protect bridges, roads, and cropland from damage or loss. Many more grade control structures are proposed or under construction. This study was aimed at determining the effects of grade control structures on fish passage and fish assemblages in western Iowa streams, and identifying an appropriate slope for modification of existing structures and construction of new structures. In collaboration with a faculty member and a graduate student, Clay helped determine that the first generation of grade control structures had steep 4:1 slopes, and these structures were shown to impede fish passage. Modification of grade control structures to lessen the slope to approximately 15:1 resulted in significant passage by several species and improvement in fish assemblage health in portions of the stream previously blocked from fish passage. Results of this study are now being used by the Iowa Department of Natural Resources and the Hungry Canyons Alliance in their advice to and oversight of western Iowa county engineers as they modify existing grade control structures and design and build new structures. Publications 1, 2, 3, 4.

Simulating the Long-Term Viability of the Shoepack Lake Muskellunge Population: Potential Threats from Fishing and Naturally Occurring Lake Draw-Down - This study was aimed at evaluating threats to the long-term viability of the genetically unique strain of muskellunge in Shoepack Lake in Voyageurs National Park. Shoepack Lake is subject to periodic draw-down and surface area reduction due to wash-out of a beaver dam that maintains the lake’s normal size. Fishing pressure was relatively low but increasing at the time of the study primarily due to a contract with a private fly-in guide service. In collaboration with a U.S. Geological Survey biologist and a graduate student, Clay helped assess population size, genetically effective population size, fishing pressure, and fishing harvest over a two-year period, and results were used in a model simulating effects of lake draw-down and fishing on long-term viability. Simulations assuming increased fishing resulted in increased risk of loss of long-term viability, especially if combined with periods of lake draw-down. Results of this study were used by the National Park Service in cooperation with the Minnesota Department of Natural Resources as justification for two key regulation changes in Voyageurs National Park. First, the minimum length limit for muskellunge in Shoepack Lake was raised, essentially making it a catch-and-release fishery. Second, the National Park Service no longer allows private fly-in guides to bring clients to Shoepack Lake, which has reduced fishing pressure. Publications 1, 2.

An Aquatic Gap Analysis of Iowa - The Iowa Aquatic Gap Analysis Project (IAGAP) was an ambitious effort to:

(1) construct a statewide database and a GIS framework for analysis of stream channel and watershed characteristics down to the level of individual stream reaches, (2) assemble a comprehensive, historical, statewide database of fish community samples documenting the presence of species in stream reaches, (3)  model species presence to establish the potential fish communities that every stream reach throughout the state could be expected to support, and (4) characterize land stewardship along stream reaches to enable comparison of potential fish communities to the degree of stream protection. In collaboration with a research associate and university research professionals, Clay helped conduct an analysis of land stewardship that identified an alarmingly low level of protection. Roughly 99% of stream reaches in Iowa lack irrevocable easements or other mandates to prevent conversion of natural habitat types to anthropogenic habitat types. The study identified major impediments to conservation of aquatic biodiversity in Iowa, and suggested solutions that a variety of stakeholder agecies will use. In addition to the broad impact of guiding conservation of aquatic biodiversity, the IAGAP project provided several useful intermediate products, including the Iowa Stream Reach Database, the Iowa Species Occurrence Database, and the Iowa Stream Fish Atlas. The Iowa Species Occurrence Database is noteworthy because prior to this project, there was no central depository for stream fish survey information in Iowa. Report 1.

An Empirical Model for Estimating Annual Consumption by Freshwater Fish Populations - Effective management of freshwater fisheries requires knowledge of the fish populations to be managed and an understanding of the processes that define their relationships with the environment and control their dynamics. Fisheries managers routinely survey population characteristics such as abundance and size, but quantifying the important processes and relationships, such as prey consumption, is attempted far less frequently. A major reason prey consumption information is seldom obtained is the complexity of available approaches and the lack of accessible and versatile tools for estimating consumption. In collaboration with an agency biologist and a graduate student, Clay helped assemble 74 paired estimates of annual population consumption and mean annual population abundance from the Spirit Lake study and from the literature. The data set included 14 freshwater fish species from ten different bodies of water. From this data set a simple linear regression model was developed predicting annual population consumption. The model provides a simple tool enabling managers to generate consumption estimates from data they routinely obtain, and because the model was developed with data from many species and a wide range of systems, it can be applied to an equally wide range of species and systems. Another important application of this model will be in generating input for ecosystem modeling, which requires population consumption estimates for all species. Because this contribution to the toolbox of fisheries managers allows them to make much more insightful decisions about current and proposed management alternatives, the impact of this study will be significant.  Publication 1.

Fish Population and Community Characteristics in the Missouri and lower Yellowstone Rivers: Relationships with Hydrological Characteristics and Human Alterations - This project was part of one of the largest coordinated studies ever attempted by a group of Cooperative Research Units. Along with the main collaborative study, scientists at each Coop Unit directed a unique study carried out by a Ph.D. student. The Iowa Unit Ph.D. study, directed by Clay, combined state-of-the-art multivariate and time-series hydrological analyses with an original approach to growth estimation which, together, allowed examination of potential effects of flow alterations on fish. One of Clay’s more noteworthy contributions to this effort was in conceiving a novel approach for estimating instantaneous growth rate from samples obtained at varying time intervals within a river segment. This technique resulted in comparable instantaneous growth estimates among segments throughout the river, despite differences in sampling schedules among segments. The initial request by the funding agency for a study of population characteristics of a single species was modified by Clay and other peer scientists to encompass the entire benthic fish community. This community approach resulted in the portion of the study under Clay’s direction revealing that the benthic fish community composition in the lower, channelized portion of the Missouri River differs significantly from portions upstream. Results of this study are now an integral part of our understanding of the Missouri and lower Yellowstone rivers, and have been used by many state and federal agencies as well as legislative bodies in management and policy decision-making. Publications 1, 2, 3, 4, 5.

Piscivore Consumption and Prey Fish Production in Spirit Lake: Trophic Supply and Demand in an Important Iowa Fishery - This study was the first attempt to quantify the entire annual consumption demand of both juvenile and adult piscivores from six species (walleye, northern pike, smallmouth bass, largemouth bass, yellow perch, black crappie) over a three-year period. Two important insights resulted from this comprehensive approach, conceived by Clay and carried out in collaboration with an agency biologist and three graduate students. First, the predator-prey relationship between age-0 walleye and yellow perch is fundamentally different in Spirit Lake than in virtually all previously studied systems, which implies that the mechanisms assumed to regulate their population dynamics are also different. Second, the majority of prey fish consumption in Spirit Lake is directly attributable to walleye stocking. Although unrelated to the primary focus of this project, another significant finding was a 25% decline in native fish species over the last 70 years. Results of this study provided Iowa Department of Natural Resources fishery managers with a tool and a blueprint to evaluate existing conditions and potential management scenarios in Spirit Lake and similar systems. The first application of this tool provided information needed to help justify the then-controversial muskellunge stocking program in Spirit Lake. The walleye stocking program in Spirit Lake and other Iowa lakes is now informed by results of this study, which highlighted the importance of understanding the consumptive impacts of gamefish populations and the need to balance expectations for attaining gamefish abundance levels with the availability of food fish required. Publications 1, 2, 3, 4, 5, 6, 7.