Free-flowing river segments provide refuges for many imperiled aquatic biota that have been extirpated elsewhere in their native ranges. These biodiversity refuges are also foci of conservation concerns because species persisting within isolated habitat fragments may be particularly vulnerable to local environmental change. We have analyzed long-term (14- and 20-year) survey data to assess evidence of fish species declines in two southeastern U.S. rivers where managers and stakeholders have identified potentially detrimental impacts of current and future land uses. The Conasauga River (Georgia and Tennessee) and the Etowah River (Georgia) form free-flowing headwaters of the extensively dammed Coosa River system. These rivers are valued in part because they harbor multiple species of conservation concern, including three federally endangered and two federally threatened fishes. We have used data sets comprising annual surveys for fish species at multiple, fixed sites located at river shoals to analyze occupancy dynamics and temporal changes in species richness. Our analyses incorporate repeated site-specific surveys in some years to estimate and account for incomplete species detection, and test for species-specific (rarity, mainstem-restriction) and year-specific (elevated frequencies of low- or high-flow days) covariates on occupancy dynamics. In the Conasauga River, analysis of 26 species at 13 sites shows evidence of temporal declines in colonization rates for nearly all taxa, accompanied by declining species richness. Four taxa (including one federally endangered species) have reduced occupancy across the Conasauga study sites, with three of these taxa apparently absent for at least the last 5 years of the study. In contrast, a similar fauna of 28 taxa at 10 sites in the Etowah River shows no trends in species persistence, colonization or occupancy. None of the tested covariates show strong effects on persistence or colonization rates in either river. Previous studies and observations identify contaminants, nutrient loading, or changes in benthic habitat as possible causes for fish species declines in the Conasauga River. Our analysis provides baseline information that could be used to assess effectiveness of future management actions in the Conasauga or Etowah rivers, and illustrates the use of dynamic occupancy models to evaluate evidence of faunal decline from time-series data.
Fish species occupancy File A1
Species detections by survey for 13 Conasauga River sites (1995 – 2014) and 10 Etowah River sites (2001-2014). Data fields are: species (Taxon); site name (Site.no); survey year and replicate number written as xxxx.y, where xxxx is year and y is replicate number (1-3). A value of “1” is shown where a species was detected in a survey; “0” indicates the species was not detected in the survey. Blanks indicate no survey data are available for a given site, year, and replicate combination.
File A1.csv
Fish species occupancy File A2
Just Another Gibbs Sampler (JAGS) code as implemented in R using the package r-jags to fit multi-taxa dynamic occupancy models to detection/non-detection data for the Conasauga and Etowah river study sites. The terms “ntaxa”, “nsite”, and “nyear” refer to the number of taxa, sites, and years, respectively, included in the data set; nrep is the maximum number of replicate, within-year surveys across all sites and years. Code is shown for the basic (no covariates) model, with lines added and marked with “#” to show how random-slopes models were fit for streamflow covariates.
File A2.docx
Fish species occupancy Table A1
Detection probabilities for 26 fish taxa at 13 sites in the Conasauga River mainstem sampled multiple years, 1995-2014, and for 28 fish taxa at 10 sites in the Etowah River mainstem sampled multiple years, 2001-2014. Values are posterior means (and 95% credible intervals) estimated using a multi-taxa, dynamic occupancy model applied to detection data for each river.
Table A1.docx
Fish species occupancy Table A2
Species-specific rarity values used as covariates in dynamic occupancy models for 26 fish taxa in the Conasauga River (1995-2014) and 28 taxa in the Etowah River, GA (2001-2014). Values are the proportion of all surveys having counts of individuals in which a species was represented by 1-4 individuals.
Table A2.docx
Fish species occupancy Table A3
Species-specific slope estimates in logit-regression models of persistence and colonization probabilities as functions of a variable representing low-flow frequency in dynamic occupancy models for 26 fish taxa at 13 sites in the Conasauga River (1995-2014). The low-flow variable was an annual count of days in March through September with daily average discharge less than the 10th percentile of the mean monthly flow based on the period-of-record for U.S. Geological Survey streamgage 02384500, Conasauga River near Eton GA. Prior to analysis, the flow variable was transformed by subtracting the mean and dividing by the standard deviation of the untransformed data. Species-specific slopes are on the logit scale and were calculated as the sum of the fixed-effect and the species-specific random effect for the slope relating low-flow days to persistence or colonization. The 2.5% and 97.5% values bracket the 95% credible interval for the slope estimate.
Table A3.docx
Fish species occupancy Table A4
Species-specific slope estimates in logit-regression models of persistence and colonization probabilities as functions of a variable representing high-flow frequency in dynamic occupancy models for 26 fish taxa at 13 sites in the Conasauga River (1995-2014). The high-flow variable was an annual count of days in March through September with daily average discharge greater than the 90th percentile of the mean monthly flow based on the period-of-record for U.S. Geological Survey streamgage 02384500, Conasauga River near Eton GA. Prior to analysis, the flow variable was transformed by subtracting the mean and dividing by the standard deviation of the untransformed data. Species-specific slopes are on the logit scale and were calculated as the sum of the fixed-effect and the species-specific random effect for the slope relating high-flow days to persistence or colonization. The 2.5% and 97.5% values bracket the 95% credible interval for the slope estimate.
Table A4.docx
Fish species occupancy Table A5
Species-specific slope estimates in logit-regression models of persistence and colonization probabilities as functions of a variable representing low-flow frequency in dynamic occupancy models for 28 taxa at 10 sites in the Etowah River, GA (2001-2014). The low-flow variable was an annual count of days in March through September with daily average discharge less than the 10th percentile of the mean monthly flow based on the period-of-record for U.S. Geological Survey streamgage 02392000, Etowah River at Canton GA. Prior to analysis, the flow variable was transformed by subtracting the mean and dividing by the standard deviation of the untransformed data. Species-specific slopes are on the logit scale and were calculated as the sum of the fixed-effect and the species-specific random effect for the slope relating low-flow days to persistence or colonization. The 2.5% and 97.5% values bracket the 95% credible interval for the slope estimate.
Table A5.docx
Fish species occupancy Table A6
Species-specific slope estimates in logit-regression models of persistence and colonization probabilities as functions of a variable representing high-flow frequency in dynamic occupancy models for 28 taxa at 10 sites in the Etowah River, GA (2001-2014). The high-flow variable was an annual count of days in March through September with daily average discharge greater than the 90th percentile of the mean monthly flow based on the period-of-record for U.S. Geological Survey streamgage 02392000, Etowah River at Canton GA. Prior to analysis, the flow variable was transformed by subtracting the mean and dividing by the standard deviation of the untransformed data. Species-specific slopes are on the logit scale and were calculated as the sum of the fixed-effect and the species-specific random effect for the slope relating high-flow days to persistence or colonization. The 2.5% and 97.5% values bracket the 95% credible interval for the slope estimate.
Table A6.docx
Fish species occupancy Figure A1
March-September hydrograph, 1982-2014, U.S. Geological Survey streamgage 02384500 Conasauga River near Eton, highlighting low-flow years during the study period (red).
Figure A1.jpeg
Fish species occupancy Figure A2
March-September hydrograph, 1982-2014, U.S. Geological Survey streamgage 02392000 Etowah River at Canton, highlighting low-flow years during the study period (red).
Figure A2.jpeg