Kelly Maloney is a Research Ecologist at Eastern Ecological Science Center located at Kearneysville, WV.
Dr. Kelly O. Maloney is an ecologist whose research focuses on the effects of anthropogenic activities on the quantity and quality of freshwater resources with a goal to synthesize scientific findings into tools to aid in the monitoring, assessment and management of these precious resources. Dr. Maloney conducts and coordinates a highly diverse range of research to address the informational needs of the DOI, its partners, state agencies and NGOs. Dr. Maloney has centered his research program on two areas: 1) ecological flow requirements of aquatic systems, and 2) effects of anthropogenic activities on aquatic ecosystem structure and function. Within each focal area he conducts research to answer questions at multiple scales, employing a combination of field surveys, statistical analyses, computer simulations and meta-analyses.
He held post-doctoral positions at the Illinois Natural History Survey and the Smithsonian Environmental Research Center prior to joining the U.S. Geological Survey Leetown Science Center in June of 2010.
Education and Certifications
B.S. Environmental Resource Management, 1994,The Pennsylvania State University
M.S. Earth and Environmental Science, 2000, Lehigh University
M.P.S. Discrete and Statistical Science, 2004, Auburn University
Ph.D. Biological Sciences, 2004, Auburn University
Science and Products
Tracking Status and Trends in Seven Key Indicators of River and Stream Condition in the Chesapeake Bay Watershed
Time marches on, but do factors driving instream habitat and biology remain consistent?
Altered flow affects the biological health of streams in the Chesapeake Bay watershed
Projecting stream conditions under future land-use and climate scenarios
Mapping riverine habitats of the Delaware River using bathymetric LiDAR
Assessing stream health and fish habitat in streams of the Chesapeake Bay Watershed
Exploring the potential effects of shale oil and gas development on freshwaters
Warm Freshwater Ecosystems
Model predictions of biological condition for small streams in the Chesapeake Bay Watershed, USA
Attribution of Chessie BIBI and fish sampling data to NHDPlusV2 Catchments within the Chesapeake Bay Watershed
Fish community and species distribution predictions for streams and rivers of the Chesapeake Bay Watershed
North American Bird Banding Program Dataset 1960-2021 retrieved 2021-07-25
Community metrics from inter-agency compilation of inland fish sampling data within the Chesapeake Bay Watershed
North American Bird Banding Program Dataset 1960-2020 retrieved 2020-06-26
Land Cover, Climate, and Geological conditions summarized within Maryland DNR Biological Stream Survery (MBSS) Catchments
Chesapeake Bay Watershed historical and future projected land use and climate data summarized for NHDPlusV2 catchments
Shale gas data used in development of the Disturbance Intensity Index for the Pennsylvania portion of the Upper Susquehanna River basin in Maloney et al. 2018.
Multispecies approaches to status assessments in support of endangered species classifications
Explainable machine learning improves interpretability in the predictive modeling of biological stream conditions in the Chesapeake Bay Watershed, USA
Using fish community and population indicators to assess the biological condition of streams and rivers of the Chesapeake Bay watershed, USA
Techniques to improve ecological interpretability of black box machine learning models
Time marches on, but do the causal pathways driving instream habitat and biology remain consistent?
Linking altered flow regimes to biological condition: An example using benthic macroinvertebrates in small streams of the Chesapeake Bay watershed
Using expert knowledge to support Endangered Species Act decision‐making for data‐deficient species
A Bayesian framework for assessing extinction risk based on ordinal categories of population condition and projected landscape change
Sediment dynamics and implications for management: State of the science from long‐term research in the Chesapeake Bay watershed, USA
A random forest approach for bounded outcome variables
Shale gas development has limited effects on stream biology and geochemistry in a gradient-based, multiparameter study in Pennsylvania
Disentangling the potential effects of land-use and climate change on stream conditions
Non-USGS Publications**
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Science and Products
- Science
Tracking Status and Trends in Seven Key Indicators of River and Stream Condition in the Chesapeake Bay Watershed
Identifying and tracking the status of, and trends in, stream health within the Chesapeake Bay watershed is essential to understanding the past, present, and future trajectory of the watershed’s resources and ecological condition. A team of USGS ecosystem scientists is meeting this need with an initiative to track the status of, and trends in, key indicators of the health of non-tidal freshwater...Time marches on, but do factors driving instream habitat and biology remain consistent?
Issue: Stream ecosystems are affected by a complex set of interacting terrestrial and aquatic stressors. With many streams experiencing degraded conditions that often correspond with increased anthropogenic activities, an important outcome of the Chesapeake Bay Program is to improve stream health. The USGS is conducting research to better understand the complex factors affecting stream health...Altered flow affects the biological health of streams in the Chesapeake Bay watershed
Issue: The natural cycle of water flow, known as the flow regime, is one of the primary habitat conditions needed for healthy biological communities in streams. However, human activities have drastically altered the natural flow regime of most of the world’s rivers and streams, including those in the Chesapeake watershed, which has resulted in changes not only to the natural habitat but also...Projecting stream conditions under future land-use and climate scenarios
Issue: Global change, particularly changes in land use and climate, is dramatically altering stream conditions throughout the world. Healthy streams are important for freshwater fisheries, wildlife, and public recreation. The Chesapeake Bay Program (CBP) has a goal of improving the health of streams throughout the Chesapeake Bay watershed, which includes an outcome of improving the condition of 10...Mapping riverine habitats of the Delaware River using bathymetric LiDAR
Ecosystem management and assessment of rivers requires detailed data on bathymetry before estimates of aquatic habitats can be determined. However, mapping bathymetry in shallow rivers is challenging due to river depth limitations for watercraft.Assessing stream health and fish habitat in streams of the Chesapeake Bay Watershed
Streams and rivers provide habitat for a diverse array of aquatic and semi-aquatic species. However, human alteration to landscapes and riverscapes has affected this habitat resulting in its degradation and thus loss of habitat and associated sensitive aquatic species. While this relationship has been known for many years, only recently has the availability of data and analytical capabilities...Exploring the potential effects of shale oil and gas development on freshwaters
Widespread shale oil and gas (unconventional oil and gas, UOG) has only recently begun and many gaps in our knowledge of its potential effects to freshwaters exist.Warm Freshwater Ecosystems
These systems are characterized as 4th order and larger nontidal riverine systems, which includes many of the intermediate and larger size rivers, such as the Penobscot, Connecticut, Hudson, Delaware, and Susquehanna Rivers and their larger tributaries of the northeastern U.S. Fish passage, thermal stress, and ecological flows are likely important issues in these systems. Fish health issues and... - Data
Model predictions of biological condition for small streams in the Chesapeake Bay Watershed, USA
This data release contains predictions of stream biological condition as defined by the Chesapeake basin-wide index of biotic integrity for stream macroinvertebrates (Chessie BIBI) using Random Forest models with landscape data for small streams (≤ 200 km2 in upstream drainage) across the Chesapeake Bay Watershed (CBW). Predictions were made at eight time periods (2001, 2004, 2006, 2008, 2011, 201Attribution of Chessie BIBI and fish sampling data to NHDPlusV2 Catchments within the Chesapeake Bay Watershed
This data release links fish survey data from a suite of programs in the Chesapeake Bay watershed as well the benthic macroinvertebrate sites included in the Chesapeake Bay Basin-wide Index of Biotic Integrity (Chessie BIBI) developed by the Interstate Commission on the Potomac River Basin (ICPRB) and available from the Chesapeake Bay Program. The data set contains site name, survey program, coordFish community and species distribution predictions for streams and rivers of the Chesapeake Bay Watershed
This data release contains predictions of selected fish community metrics and fish species occurrence using Random Forest models with landscape data for inland reaches across the Chesapeake Bay Watershed (CBW). Predictions were made at four time intervals (2001, 2006, 2011, and 2016) according to changes in landcover using the National Land Cover Database (NLCD). The fish sampling data used to comNorth American Bird Banding Program Dataset 1960-2021 retrieved 2021-07-25
The North American Bird Banding Program is directed in the United States by the U.S. Geological Survey (USGS) Bird Banding Laboratory (BBL), Eastern Ecological Science Center at the Patuxent Research Refuge (EESC) and in Canada by the Bird Banding Office (BBO), Environment and Climate Change Canada (ECCC). The respective banding offices have similar functions and policies and use the same bands, rCommunity metrics from inter-agency compilation of inland fish sampling data within the Chesapeake Bay Watershed
This data release contains calculated metrics which summarize various biodiversity and functional/life history trait information about fish communities sampled across the Chesapeake Bay Watershed as well as ancillary data related to time/place of sampling and sampling methodology. The fish sampling data used to compute these metrics were compiled from various fish sampling programs conducted by stNorth American Bird Banding Program Dataset 1960-2020 retrieved 2020-06-26
The North American Bird Banding Program is directed in the United States by the U.S. Geological Survey (USGS) Bird Banding Laboratory (BBL), Eastern Ecological Science Center at the Patuxent Research Refuge (EESC) and in Canada by the Bird Banding Office (BBO), Environment and Climate Change Canada (ECCC). The respective banding offices have similar functions and policies and use the same bands, rLand Cover, Climate, and Geological conditions summarized within Maryland DNR Biological Stream Survery (MBSS) Catchments
This dataset consists of several measures of landscape characteristics, each of which is summarized from raster data within spatial polygons. These spatial polygons represent the land area upstream of sampled stream reaches. These stream reaches were sampled by the Maryland Department of Natural Resources for the Maryland Biological Stream Survey program during survey rounds one, two, and four. LaChesapeake Bay Watershed historical and future projected land use and climate data summarized for NHDPlusV2 catchments
This dataset consists of historical estimates and future projections of land use and climate data summarized within the 1:100,000 National Hydrography Dataset Version 2 (NHDPlusV2) framework for catchments and upstream accumulated watersheds. Historical land use data are for the year 2005 and future land use projections are for the years 2030, 2060, and 2090. The projections offer a unique combinaShale gas data used in development of the Disturbance Intensity Index for the Pennsylvania portion of the Upper Susquehanna River basin in Maloney et al. 2018.
Data on 17 metrics of shale gas development in the Pennsylvania portion of the Upper Susquehanna River basin that was collated from a variety of sources and summarized at the upstream catchment scale. Data were also standardized by upstream area and transformed into rank scores based on metric distribution and then summarized into a Disturbance Intensity Index (DII). See Maloney et al. 2018 for de - Publications
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Multispecies approaches to status assessments in support of endangered species classifications
Multispecies risk assessments have developed within many international conservation programs, reflecting a widespread need for efficiency. Under the United States Endangered Species Act (ESA), multispecies assessments ultimately lead to species-level listing decisions. Although this approach provides opportunities for improved efficiency, it also risks overwhelming or biasing the assessment procesExplainable machine learning improves interpretability in the predictive modeling of biological stream conditions in the Chesapeake Bay Watershed, USA
Anthropogenic alterations have resulted in widespread degradation of stream conditions. To aid in stream restoration and management, baseline estimates of conditions and improved explanation of factors driving their degradation are needed. We used random forests to model biological conditions using a benthic macroinvertebrate index of biotic integrity for small, non-tidal streams (upstream area ≤2Using fish community and population indicators to assess the biological condition of streams and rivers of the Chesapeake Bay watershed, USA
The development of indicators to assess relative freshwater condition is critical for management and conservation. Predictive modeling can enhance the utility of indicators by providing estimates of condition for unsurveyed locations. Such approaches grant understanding of where “good” and “poor” conditions occur and provide insight into landscape contexts supporting such conditions. However, as aTechniques to improve ecological interpretability of black box machine learning models
Statistical modeling of ecological data is often faced with a large number of variables as well as possible nonlinear relationships and higher-order interaction effects. Gradient boosted trees (GBT) have been successful in addressing these issues and have shown a good predictive performance in modeling nonlinear relationships, in particular in classification settings with a categorical response vaTime marches on, but do the causal pathways driving instream habitat and biology remain consistent?
Stream ecosystems are complex networks of interacting terrestrial and aquatic drivers. To untangle these ecological networks, efforts evaluating the direct and indirect effects of landscape, climate, and instream predictors on biological condition through time are needed. We used structural equation modeling and leveraged a stream survey program to identify and compare important predictors drivingLinking altered flow regimes to biological condition: An example using benthic macroinvertebrates in small streams of the Chesapeake Bay watershed
Regionally scaled assessments of hydrologic alteration for small streams and its effects on freshwater taxa are often inhibited by a low number of stream gages. To overcome this limitation, we paired modeled estimates of hydrologic alteration to a benthic macroinvertebrate index of biotic integrity data for 4522 stream reaches across the Chesapeake Bay watershed. Using separate random-forest modelUsing expert knowledge to support Endangered Species Act decision‐making for data‐deficient species
Many questions relevant to conservation decision making are characterized by extreme uncertainty due to lack of empirical data and complexity of the underlying ecological processes, leading to a rapid increase in the use of structured protocols to elicit expert knowledge. Published ecological applications often employ a modified Delphi method, where experts provide judgments anonymously and mathemA Bayesian framework for assessing extinction risk based on ordinal categories of population condition and projected landscape change
Many at-risk species lack standardized surveys across their range or quantitative data capable of detecting demographic trends. As a result, extinction risk assessments often rely on ordinal categories of risk based on explicit criteria or expert elicitation. This study demonstrates a Bayesian approach to assessing extinction risk based on this common data structure, using three freshwater musselSediment dynamics and implications for management: State of the science from long‐term research in the Chesapeake Bay watershed, USA
This review aims to synthesize the current knowledge of sediment dynamics using insights from long‐term research conducted in the watershed draining to the Chesapeake Bay, the largest estuary in the U.S., to inform management actions to restore the estuary and its watershed. The sediment dynamics of the Chesapeake are typical of many impaired watersheds and estuaries around the world, and this synA random forest approach for bounded outcome variables
Random forests have become an established tool for classication and regres- sion, in particular in high-dimensional settings and in the presence of non-additive predictor-response relationships. For bounded outcome variables restricted to the unit interval, however, classical modeling approaches based on mean squared error loss may severely suer as they do not account for heteroscedasticity in theShale gas development has limited effects on stream biology and geochemistry in a gradient-based, multiparameter study in Pennsylvania
The number of horizontally drilled shale oil and gas wells in the United States has increased from nearly 28,000 in 2007 to nearly 127,000 in 2017, and research has suggested the potential for the development of shale resources to affect nearby stream ecosystems. However, the ability to generalize current studies is limited by the small geographic scope as well as limited breadth and integration oDisentangling the potential effects of land-use and climate change on stream conditions
Land‐use and climate change are significantly affecting stream ecosystems, yet understanding of their long‐term impacts is hindered by the few studies that have simultaneously investigated their interaction and high variability among future projections. We modeled possible effects of a suite of 2030, 2060, and 2090 land‐use and climate scenarios on the condition of 70,772 small streams in the ChesNon-USGS Publications**
Dale, V. H., P. J. Mulholland, L. M. Olsen, J. W. Feminella, K. O. Maloney, D. C. White, A. Peacock, and T. Foster. 2004. Selecting a suite of ecological indicators for resource management. L. A. Kapustka, H. Gilbraith, M. Luxon, and G. R. Biddinger (editors). Landscape ecology and wildlife habitat evaluation: critical information for ecological risk assessment, land-use, management activities and biodiversity enhancement practices. American Society for Testing and Materials STP 1458. ASTM International, West Conshohocken, PA.Maloney, K.O. and D.E. Weller. 2011. Anthropogenic disturbance and streams: land use and land-use change affect stream ecosystems via multiple pathways. Freshwater Biology 56: 611-626. https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2427.2010.02522.x**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
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