Darren Thornbrugh | Michigan State University (original) (raw)
Papers by Darren Thornbrugh
U.S. Geological Survey National Gap Analysis Program and; Kansas Department of Wildlife and Parks
Environmental Monitoring and Assessment
Aquatic invertebrates are excellent indicators of ecosystem quality; however, choosing a sampling... more Aquatic invertebrates are excellent indicators of ecosystem quality; however, choosing a sampling method can be difficult. Each method and associated protocol has advantages and disadvantages, and finding the approach that minimizes biases yet fulfills management objectives is crucial. To test the effects of both sampling methods and sample handling – i.e., to composite samples or leave them as replicates – we collected aquatic invertebrates from the Niobrara River at Agate Fossil Beds National Monument, Nebraska using three methods and two sample handling protocols. We compared aquatic invertebrate assemblages collected with a Hester-Dendy multi-plate sampler, Hess sampler and a D-frame dipnet. We calculated six common bioassessment metrics from composite (combined) and replicate (separate) samples. Hess samples contained the highest taxonomic richness (capturing 77% of all taxa observed) and dipnet samples the least (47%). Hester-Dendy samples had the greatest proportion of Epheme...
Ecological Indicators
Watershed integrity is the capacity of a watershed to support and maintain the full range of ecol... more Watershed integrity is the capacity of a watershed to support and maintain the full range of ecological processes and functions essential to sustainability. Using information from EPA's StreamCat dataset, we calculated and mapped an Index of Watershed Integrity (IWI) for 2.6 million watersheds in the conterminous US with first-order approximations of relationships between stressors and six watershed functions: hydrologic regulation, regulation of water chemistry, sediment regulation, hydrologic connectivity, temperature regulation, and habitat provision. Results show high integrity in the western US, intermediate integrity in the southern and eastern US, and the lowest integrity in the temperate plains and lower Mississippi Valley. Correlation between the six functional components was high ( = 0.85-0.98). A related Index of Catchment Integrity (ICI) was developed using local drainages of individual stream segments (i.e., excluding upstream information). We evaluated the ability of the IWI and ICI to predict six continuous site-level indicators with regression analyses - three biological indicators and principal components derived from water quality, habitat, and combined water quality and habitat variables - using data from EPA's National Rivers and Streams Assessment. Relationships were highly significant, but the IWI only accounted for 1-12% of the variation in the four biological and habitat variables. The IWI accounted for over 25% of the variation in the water quality and combined principal components nationally, and 32-39% in the Northern and Southern Appalachians. We also used multinomial logistic regression to compare the IWI with the categorical forms of the three biological indicators. Results were consistent: we found positive associations but modest results. We compared how the IWI and ICI predicted the water quality PC relative to agricultural and urban land use. The IWI or ICI are the best predictors of the water quality PC for the CONUS and six of the nine ecoregions, but they only perform marginally better than agriculture in most instances. However, results suggest that agriculture would not be appropriate in all parts of the country, and the index is meant to be responsive to all stressors. The IWI in its present form (available through the StreamCat website; https://www.epa.gov/national-aquatic-resource-surveys/streamcat) could be useful for management efforts at multiple scales, especially when combined with information on site condition. The IWI could be improved by incorporating empirical or literature-derived relationships between functional components and stressors. However, limitations concerning the absence of data for certain stressors should be considered.
Ecological indicators, 2018
Watershed integrity is the capacity of a watershed to support and maintain the full range of ecol... more Watershed integrity is the capacity of a watershed to support and maintain the full range of ecological processes and functions essential to sustainability. Using information from EPA's StreamCat dataset, we calculated and mapped an Index of Watershed Integrity (IWI) for 2.6 million watersheds in the conterminous US with first-order approximations of relationships between stressors and six watershed functions: hydrologic regulation, regulation of water chemistry, sediment regulation, hydrologic connectivity, temperature regulation, and habitat provision. Results show high integrity in the western US, intermediate integrity in the southern and eastern US, and the lowest integrity in the temperate plains and lower Mississippi Valley. Correlation between the six functional components was high ( = 0.85-0.98). A related Index of Catchment Integrity (ICI) was developed using local drainages of individual stream segments (i.e., excluding upstream information). We evaluated the ability ...
Environmental monitoring and assessment, 2017
Random forest (RF) modeling has emerged as an important statistical learning method in ecology du... more Random forest (RF) modeling has emerged as an important statistical learning method in ecology due to its exceptional predictive performance. However, for large and complex ecological data sets, there is limited guidance on variable selection methods for RF modeling. Typically, either a preselected set of predictor variables are used or stepwise procedures are employed which iteratively remove variables according to their importance measures. This paper investigates the application of variable selection methods to RF models for predicting probable biological stream condition. Our motivating data set consists of the good/poor condition of n = 1365 stream survey sites from the 2008/2009 National Rivers and Stream Assessment, and a large set (p = 212) of landscape features from the StreamCat data set as potential predictors. We compare two types of RF models: a full variable set model with all 212 predictors and a reduced variable set model selected using a backward elimination approac...
Ecological Applications
Understanding and mapping the spatial variation in stream biological condition could provide an i... more Understanding and mapping the spatial variation in stream biological condition could provide an important tool for conservation, assessment, and restoration of stream ecosystems. The USEPA's 2008-2009 National Rivers and Streams Assessment (NRSA) summarizes the percent of stream lengths within the conterminous US that are in good, fair, or poor biological condition based on a multimetric index of benthic invertebrate assemblages. However, condition is usually summarized at regional or national scales, and these assessments do not provide substantial insight into the spatial distribution of conditions at unsampled locations. We used random forests to model and predict the probable condition of several million kilometers of streams across the conterminous US based on nearby and upstream landscape features, including human-related alterations to watersheds. To do so, we linked NRSA sample sites to the USEPA's StreamCat Dataset; a database of several hundred landscape metrics for all 1:100,000-scale streams and their associated watersheds within the conterminous US. The StreamCat data provided geospatial indicators of nearby and upstream land use, land cover, climate, and other landscape features for modeling. Nationally, the model correctly predicted the biological condition class of 75% of NRSA sites. Although model evaluations suggested good discrimination among condition classes, we present maps as predicted probabilities of good condition, given upstream and nearby landscape settings. Inversely, the maps can be interpreted as the probability of a stream being in poor condition, given human-related watershed alterations. These predictions are available for download from the USEPA's StreamCat website (https://w w w .epa. gov/national-aquatic-resource-surveys/streamcat). Finally, we illustrate how these predictions could be used to prioritize streams for conservation or restoration. This article is protected by copyright. All rights reserved.
Stream networks provide complex habitats for fish assemblages that can vary gradually along a gra... more Stream networks provide complex habitats for fish assemblages that can vary gradually along a gradient of stream size or abruptly at transition zones between large rivers and their tributaries. We evaluated the relative importance of these gradual and abrupt habitat transitions in regulating stream fish assemblages by quantifying roles of stream size and spatial position within a drainage network as a determinant of fish assemblage structure within the Kansas River basin, KS. We predicted fish assemblage structure to generally be dependent on stream size and that smaller streams would be influenced by their connectance to larger mainstem rivers. Fishes in the Kansas River basin varied along a gradient of stream size and longitude, and after controlling for these effects, there was evidence that connectivity to a larger river influenced species richness and assemblage structure. In 1 st order streams there was an increase in species richness with increasing distance from a mainstem confluence and species composition in larger tributaries (i.e., 4 th order streams) varied with proximity to the mainstem river. We also found an increase in species richness at sites located on smaller tributaries connected to a larger downstream mainstem. Species composition in 1 st and 4 th order streams also varied with connectance to the mainstem river. Within three intensively sampled tributaries, there was an abrupt change in fish fauna between the Kansas River and sample sites above the confluence, but only gradual change in assemblage structure within each tributary with a high degree of seasonal variation. In the first 20 stream km of these three mainstem tributaries adult fishes were more structured along a gradient away from the mainstem river than juveniles, potentially suggesting more generalized habitat needs of juvenile fishes. At the spatial and temporal scale of our analysis, it appeared the effects of large rivers on tributary streams were generally localized.
Canadian Journal of Fisheries and Aquatic Sciences, 2010
Http Dx Doi Org 10 1577 T07 169 1, Jan 9, 2011
... Carol A. Pacey a & Darren J. Thornbrugh a pages 1044-1049. ... [Taylor &a... more ... Carol A. Pacey a & Darren J. Thornbrugh a pages 1044-1049. ... [Taylor & Francis Online], [Web of Science ®], [CSA] View all references). Explanations for this paucity of evidence may include specimen collecting and preservation techniques (Crowder 19805. Crowder, LB 1980. ...
Canadian Journal of Fisheries and Aquatic Sciences, Feb 26, 2010
ABSTRACT
JAWRA Journal of the American Water Resources Association, 2015
Stream networks provide complex habitats for fish assemblages that can vary gradually along a gra... more Stream networks provide complex habitats for fish assemblages that can vary gradually along a gradient of stream size or abruptly at transition zones between large rivers and their tributaries. We evaluated the relative importance of these gradual and abrupt habitat transitions in regulating stream fish assemblages by quantifying roles of stream size and spatial position within a drainage network as a determinant of fish assemblage structure within the Kansas River basin, KS. We predicted fish assemblage structure to generally be dependent on stream size and that smaller streams would be influenced by their connectance to larger mainstem rivers. Fishes in the Kansas River basin varied along a gradient of stream size and longitude, and after controlling for these effects, there was evidence that connectivity to a larger river influenced species richness and assemblage structure. In 1 st order streams there was an increase in species richness with increasing distance from a mainstem confluence and species composition in larger tributaries (i.e., 4 th order streams) varied with proximity to the mainstem river. We also found an increase in species richness at sites located on smaller tributaries connected to a larger downstream mainstem. Species composition in 1 st and 4 th order streams also varied with connectance to the mainstem river. Within three intensively sampled tributaries, there was an abrupt change in fish fauna between the Kansas River and sample sites above the confluence, but only gradual change in assemblage structure within each tributary with a high degree of seasonal variation. In the first 20 stream km of these three mainstem tributaries adult fishes were more structured along a gradient away from the mainstem river than juveniles, potentially suggesting more generalized habitat needs of juvenile fishes. At the spatial and temporal scale of our analysis, it appeared the effects of large rivers on tributary streams were generally localized.
Biodiversity is declining precipitously in fluvial ecosystems due to factors like habitat alterat... more Biodiversity is declining precipitously in fluvial ecosystems due to factors like habitat alteration from landscape-level anthropogenic disturbances. Besides impacts experienced directly by organisms from such habitat changes, interactions among species, including competition and predation, will change with additions or loss of organisms responding to altered habitat. In Michigan streams, landscape-level disturbances like urbanization and agriculture affect various characteristics of habitat including stream thermal regimes which are important in controlling distributions and abundances of stream fishes, and thermal characteristics are considered one of the most important habitat factors structuring fish assemblages in this region. To allow for better management opportunities to current landscape-level disturbances and to plan for potential changes that may result with changes in climate, the goal of this study is to consider ways that stream thermal regimes structure fluvial fish a...
U.S. Geological Survey National Gap Analysis Program and; Kansas Department of Wildlife and Parks
Environmental Monitoring and Assessment
Aquatic invertebrates are excellent indicators of ecosystem quality; however, choosing a sampling... more Aquatic invertebrates are excellent indicators of ecosystem quality; however, choosing a sampling method can be difficult. Each method and associated protocol has advantages and disadvantages, and finding the approach that minimizes biases yet fulfills management objectives is crucial. To test the effects of both sampling methods and sample handling – i.e., to composite samples or leave them as replicates – we collected aquatic invertebrates from the Niobrara River at Agate Fossil Beds National Monument, Nebraska using three methods and two sample handling protocols. We compared aquatic invertebrate assemblages collected with a Hester-Dendy multi-plate sampler, Hess sampler and a D-frame dipnet. We calculated six common bioassessment metrics from composite (combined) and replicate (separate) samples. Hess samples contained the highest taxonomic richness (capturing 77% of all taxa observed) and dipnet samples the least (47%). Hester-Dendy samples had the greatest proportion of Epheme...
Ecological Indicators
Watershed integrity is the capacity of a watershed to support and maintain the full range of ecol... more Watershed integrity is the capacity of a watershed to support and maintain the full range of ecological processes and functions essential to sustainability. Using information from EPA's StreamCat dataset, we calculated and mapped an Index of Watershed Integrity (IWI) for 2.6 million watersheds in the conterminous US with first-order approximations of relationships between stressors and six watershed functions: hydrologic regulation, regulation of water chemistry, sediment regulation, hydrologic connectivity, temperature regulation, and habitat provision. Results show high integrity in the western US, intermediate integrity in the southern and eastern US, and the lowest integrity in the temperate plains and lower Mississippi Valley. Correlation between the six functional components was high ( = 0.85-0.98). A related Index of Catchment Integrity (ICI) was developed using local drainages of individual stream segments (i.e., excluding upstream information). We evaluated the ability of the IWI and ICI to predict six continuous site-level indicators with regression analyses - three biological indicators and principal components derived from water quality, habitat, and combined water quality and habitat variables - using data from EPA's National Rivers and Streams Assessment. Relationships were highly significant, but the IWI only accounted for 1-12% of the variation in the four biological and habitat variables. The IWI accounted for over 25% of the variation in the water quality and combined principal components nationally, and 32-39% in the Northern and Southern Appalachians. We also used multinomial logistic regression to compare the IWI with the categorical forms of the three biological indicators. Results were consistent: we found positive associations but modest results. We compared how the IWI and ICI predicted the water quality PC relative to agricultural and urban land use. The IWI or ICI are the best predictors of the water quality PC for the CONUS and six of the nine ecoregions, but they only perform marginally better than agriculture in most instances. However, results suggest that agriculture would not be appropriate in all parts of the country, and the index is meant to be responsive to all stressors. The IWI in its present form (available through the StreamCat website; https://www.epa.gov/national-aquatic-resource-surveys/streamcat) could be useful for management efforts at multiple scales, especially when combined with information on site condition. The IWI could be improved by incorporating empirical or literature-derived relationships between functional components and stressors. However, limitations concerning the absence of data for certain stressors should be considered.
Ecological indicators, 2018
Watershed integrity is the capacity of a watershed to support and maintain the full range of ecol... more Watershed integrity is the capacity of a watershed to support and maintain the full range of ecological processes and functions essential to sustainability. Using information from EPA's StreamCat dataset, we calculated and mapped an Index of Watershed Integrity (IWI) for 2.6 million watersheds in the conterminous US with first-order approximations of relationships between stressors and six watershed functions: hydrologic regulation, regulation of water chemistry, sediment regulation, hydrologic connectivity, temperature regulation, and habitat provision. Results show high integrity in the western US, intermediate integrity in the southern and eastern US, and the lowest integrity in the temperate plains and lower Mississippi Valley. Correlation between the six functional components was high ( = 0.85-0.98). A related Index of Catchment Integrity (ICI) was developed using local drainages of individual stream segments (i.e., excluding upstream information). We evaluated the ability ...
Environmental monitoring and assessment, 2017
Random forest (RF) modeling has emerged as an important statistical learning method in ecology du... more Random forest (RF) modeling has emerged as an important statistical learning method in ecology due to its exceptional predictive performance. However, for large and complex ecological data sets, there is limited guidance on variable selection methods for RF modeling. Typically, either a preselected set of predictor variables are used or stepwise procedures are employed which iteratively remove variables according to their importance measures. This paper investigates the application of variable selection methods to RF models for predicting probable biological stream condition. Our motivating data set consists of the good/poor condition of n = 1365 stream survey sites from the 2008/2009 National Rivers and Stream Assessment, and a large set (p = 212) of landscape features from the StreamCat data set as potential predictors. We compare two types of RF models: a full variable set model with all 212 predictors and a reduced variable set model selected using a backward elimination approac...
Ecological Applications
Understanding and mapping the spatial variation in stream biological condition could provide an i... more Understanding and mapping the spatial variation in stream biological condition could provide an important tool for conservation, assessment, and restoration of stream ecosystems. The USEPA's 2008-2009 National Rivers and Streams Assessment (NRSA) summarizes the percent of stream lengths within the conterminous US that are in good, fair, or poor biological condition based on a multimetric index of benthic invertebrate assemblages. However, condition is usually summarized at regional or national scales, and these assessments do not provide substantial insight into the spatial distribution of conditions at unsampled locations. We used random forests to model and predict the probable condition of several million kilometers of streams across the conterminous US based on nearby and upstream landscape features, including human-related alterations to watersheds. To do so, we linked NRSA sample sites to the USEPA's StreamCat Dataset; a database of several hundred landscape metrics for all 1:100,000-scale streams and their associated watersheds within the conterminous US. The StreamCat data provided geospatial indicators of nearby and upstream land use, land cover, climate, and other landscape features for modeling. Nationally, the model correctly predicted the biological condition class of 75% of NRSA sites. Although model evaluations suggested good discrimination among condition classes, we present maps as predicted probabilities of good condition, given upstream and nearby landscape settings. Inversely, the maps can be interpreted as the probability of a stream being in poor condition, given human-related watershed alterations. These predictions are available for download from the USEPA's StreamCat website (https://w w w .epa. gov/national-aquatic-resource-surveys/streamcat). Finally, we illustrate how these predictions could be used to prioritize streams for conservation or restoration. This article is protected by copyright. All rights reserved.
Stream networks provide complex habitats for fish assemblages that can vary gradually along a gra... more Stream networks provide complex habitats for fish assemblages that can vary gradually along a gradient of stream size or abruptly at transition zones between large rivers and their tributaries. We evaluated the relative importance of these gradual and abrupt habitat transitions in regulating stream fish assemblages by quantifying roles of stream size and spatial position within a drainage network as a determinant of fish assemblage structure within the Kansas River basin, KS. We predicted fish assemblage structure to generally be dependent on stream size and that smaller streams would be influenced by their connectance to larger mainstem rivers. Fishes in the Kansas River basin varied along a gradient of stream size and longitude, and after controlling for these effects, there was evidence that connectivity to a larger river influenced species richness and assemblage structure. In 1 st order streams there was an increase in species richness with increasing distance from a mainstem confluence and species composition in larger tributaries (i.e., 4 th order streams) varied with proximity to the mainstem river. We also found an increase in species richness at sites located on smaller tributaries connected to a larger downstream mainstem. Species composition in 1 st and 4 th order streams also varied with connectance to the mainstem river. Within three intensively sampled tributaries, there was an abrupt change in fish fauna between the Kansas River and sample sites above the confluence, but only gradual change in assemblage structure within each tributary with a high degree of seasonal variation. In the first 20 stream km of these three mainstem tributaries adult fishes were more structured along a gradient away from the mainstem river than juveniles, potentially suggesting more generalized habitat needs of juvenile fishes. At the spatial and temporal scale of our analysis, it appeared the effects of large rivers on tributary streams were generally localized.
Canadian Journal of Fisheries and Aquatic Sciences, 2010
Http Dx Doi Org 10 1577 T07 169 1, Jan 9, 2011
... Carol A. Pacey a & Darren J. Thornbrugh a pages 1044-1049. ... [Taylor &a... more ... Carol A. Pacey a & Darren J. Thornbrugh a pages 1044-1049. ... [Taylor & Francis Online], [Web of Science ®], [CSA] View all references). Explanations for this paucity of evidence may include specimen collecting and preservation techniques (Crowder 19805. Crowder, LB 1980. ...
Canadian Journal of Fisheries and Aquatic Sciences, Feb 26, 2010
ABSTRACT
JAWRA Journal of the American Water Resources Association, 2015
Stream networks provide complex habitats for fish assemblages that can vary gradually along a gra... more Stream networks provide complex habitats for fish assemblages that can vary gradually along a gradient of stream size or abruptly at transition zones between large rivers and their tributaries. We evaluated the relative importance of these gradual and abrupt habitat transitions in regulating stream fish assemblages by quantifying roles of stream size and spatial position within a drainage network as a determinant of fish assemblage structure within the Kansas River basin, KS. We predicted fish assemblage structure to generally be dependent on stream size and that smaller streams would be influenced by their connectance to larger mainstem rivers. Fishes in the Kansas River basin varied along a gradient of stream size and longitude, and after controlling for these effects, there was evidence that connectivity to a larger river influenced species richness and assemblage structure. In 1 st order streams there was an increase in species richness with increasing distance from a mainstem confluence and species composition in larger tributaries (i.e., 4 th order streams) varied with proximity to the mainstem river. We also found an increase in species richness at sites located on smaller tributaries connected to a larger downstream mainstem. Species composition in 1 st and 4 th order streams also varied with connectance to the mainstem river. Within three intensively sampled tributaries, there was an abrupt change in fish fauna between the Kansas River and sample sites above the confluence, but only gradual change in assemblage structure within each tributary with a high degree of seasonal variation. In the first 20 stream km of these three mainstem tributaries adult fishes were more structured along a gradient away from the mainstem river than juveniles, potentially suggesting more generalized habitat needs of juvenile fishes. At the spatial and temporal scale of our analysis, it appeared the effects of large rivers on tributary streams were generally localized.
Biodiversity is declining precipitously in fluvial ecosystems due to factors like habitat alterat... more Biodiversity is declining precipitously in fluvial ecosystems due to factors like habitat alteration from landscape-level anthropogenic disturbances. Besides impacts experienced directly by organisms from such habitat changes, interactions among species, including competition and predation, will change with additions or loss of organisms responding to altered habitat. In Michigan streams, landscape-level disturbances like urbanization and agriculture affect various characteristics of habitat including stream thermal regimes which are important in controlling distributions and abundances of stream fishes, and thermal characteristics are considered one of the most important habitat factors structuring fish assemblages in this region. To allow for better management opportunities to current landscape-level disturbances and to plan for potential changes that may result with changes in climate, the goal of this study is to consider ways that stream thermal regimes structure fluvial fish a...