Data from: Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation

Freeman MC, Hagler MM, Bumpers PM, Wheeler K, Wenger S, Freeman B

Date Published: August 8, 2017

DOI: https://doi.org/10.5061/dryad.0645r

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Title Fish species occupancy File A1
Downloaded 6 times
Description 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.
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Title Fish species occupancy File A2
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Description 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.
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Title Fish species occupancy Table A1
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Description 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.
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Title Fish species occupancy Table A2
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Description 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.
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Title Fish species occupancy Table A3
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Description 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.
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Title Fish species occupancy Table A4
Downloaded 3 times
Description 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.
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Title Fish species occupancy Table A5
Downloaded 2 times
Description 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.
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Title Fish species occupancy Table A6
Downloaded 3 times
Description 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.
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Title Fish species occupancy Figure A1
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Description March-September hydrograph, 1982-2014, U.S. Geological Survey streamgage 02384500 Conasauga River near Eton, highlighting low-flow years during the study period (red).
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Title Fish species occupancy Figure A2
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Description March-September hydrograph, 1982-2014, U.S. Geological Survey streamgage 02392000 Etowah River at Canton, highlighting low-flow years during the study period (red).
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When using this data, please cite the original publication:

Freeman MC, Hagler MM, Bumpers PM, Wheeler K, Wenger S, Freeman B (2017) Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation. Journal of Fish and Wildlife Management, online in advance of print. https://doi.org/10.3996/122016-jfwm-090

Additionally, please cite the Dryad data package:

Freeman MC, Hagler MM, Bumpers PM, Wheeler K, Wenger S, Freeman B (2017) Data from: Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation. Dryad Digital Repository. https://doi.org/10.5061/dryad.0645r
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