Modeling Occupancy of Rare Stream Fish Species in the Upper Cumberland and Kentucky River Basins

Open-File Report 2020-1100
Prepared in cooperation with U.S. Fish and Wildlife Service
By: , and 



Biological conservation often requires an understanding of how environmental conditions affect species occurrence and detection probabilities. We used a hierarchical framework to evaluate these effects for several Appalachian stream fish species of conservation concern: Chrosomus cumberlandensis (BSD; blackside dace), Etheostoma sagitta (CAD; Cumberland arrow darter), and Etheostoma spilotum (KAD; Kentucky arrow darter). Etheostoma susanae (Cumberland darter) also is present in the study area but was too rare to model in this analysis. In this study, conducted by the U.S. Geological Survey in cooperation with the U.S. Fish and Wildlife Service, fish and habitat data were collected from 205 randomly selected stream sites in the upper Cumberland and Kentucky River Basins (120 and 85 sites, respectively) of Kentucky and Tennessee. Sites were sampled with 10 spatial replicates (2 meter x 5 meter electrofishing zones) to enable estimation of detection probabilities and environmental effects. The best models (that is, lowest Akaike information criterion scores) showed the effects of agriculture (negative) on occurrence of BSD and stream conductivity (negative) on occurrence of CAD and KAD. These effects were statistically more important than measures of basin area, elevation, and substrate size. Conductivity and agriculture showed nonlinear effects on species occurrence, and effects of conductivity were more precise above 400 microsiemens per centimeter than below this threshold. Models incorporated detection-level effects of electrofishing time (positive), flow velocity (negative), sand substrate (positive), and gravel/cobble substrate (negative). Models accounting for detection of BSD estimated occupancy rates similar to the observed proportion of occupied sites (0.10), but the best-supported models for CAD and KAD increased expected occupancy by about 4 percent for each species (from 0.17 to 0.21 for CAD and from 0.07 to 0.11 for KAD). Results of this study provide new inferences for modeling stream fish occurrence and detection processes and highlight the importance of continued monitoring and assessment of rare fish species in Appalachian headwater streams.

Suggested Citation

Hitt, N.P., Rogers, K.M., Kessler, K., and Macmillan, H., 2020, Modeling occupancy of rare stream fish species in the upper Cumberland and Kentucky River Basins: U.S. Geological Survey Open-File Report 2020–1100, 22 p.,

ISSN: 2331-1258 (online)

Study Area

Table of Contents

  • Acknowledgments
  • Abstract
  • Introduction
  • Methods
  • Results
  • Discussion
  • References Cited
Publication type Report
Publication Subtype USGS Numbered Series
Title Modeling occupancy of rare stream fish species in the upper Cumberland and Kentucky River Basins
Series title Open-File Report
Series number 2020-1100
DOI 10.3133/ofr20201100
Year Published 2020
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Leetown Science Center
Description vi, 22 p.
Country United States
State Kentucky, Tennessee, Virginia
Other Geospatial Cumberland River basin, Kentucky River basin
Online Only (Y/N) Y
Additional Online Files (Y/N) N
Google Analytic Metrics Metrics page
Additional publication details