DOI: 10.5061/dryad.0645r
title: Data from: Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation

description: 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.
description: Fish species occupancy
 File A1Species 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.csvFish species occupancy
 File A2Just 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.docxFish species occupancy
 Table A1Detection 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.docxFish species occupancy
 Table A2Species-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.docxFish species occupancy
 Table A3Species-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.docxFish species occupancy
 Table A4Species-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.docxFish species occupancy
 Table A5Species-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.docxFish species occupancy
 Table A6Species-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.docxFish species occupancy
 Figure A1March-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.jpegFish species occupancy
 Figure A2March-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