DOI: 10.5061/dryad.n5tb2rc5b
title: Spatial variation in abundance parameters of a federally threatened groundwater salamander within and among central Texas headwater creeks

description: Semi-arid conditions in central Texas relegate Eurycea salamanders to
 aquatic habitats influenced by groundwater (i.e., springs, spring-fed
 creeks, and subterranean water in alluvium and aquifers). Many studies
 have noted that epigean (surface) populations of central Texas Eurycea
 occur near spring outlets. Consequently, the U.S. Fish and Wildlife
 Service designated surface critical habitat units for three species as a
 uniform distance up and downstream of occupied spring outlets. Here, we
 used data from visual encounter and quadrat surveys to model relative
 abundance and relative density, respectively, of federally threatened
 Jollyville Plateau Salamanders (E. tonkawae) in relation to downstream
 distance from a spring outlet in headwater creeks. We additionally use
 recapture data to investigate movement within these systems and in
 relation to the critical habitat units. Consistent with other studies, E.
 tonkawae relative abundance and relative density decreased with increasing
 distance from a spring outlet, and E. tonkawae occurred outside of its
 federally designated surface critical habitat unit at some sites.
 Importantly, the downstream extent of E. tonkawae and the rate of change
 in relative abundance and relative density varied among sites which is
 incongruent with the uniform federal surface critical habitat distance. We
 observed limited movement within the headwater creeks with most
 salamanders recaptured within 5 m of their previous capture location.
description: # Spatial variation in abundance parameters of a federally threatened
 groundwater salamander within and among central Texas headwater creeks
 [https://doi.org/10.5061/dryad.n5tb2rc5b](https://doi.org/10.5061/dryad.n5tb2rc5b) ## Description of the data and file structure **Spatial variation in abundance parameters of a federally threatened groundwater salamander within and among central Texas headwater creeks** Zachary C. Adcock, Andrew R. MacLaren, Michelle E. Adcock, and Michael R.J. Forstner This document contains a description of the metadata, data, and notes for all analyses and results included in the associated manuscript. These items are organized by topic, and for each set of results, the associated data file and R code file are provided. Metadata notes We conducted the study between May 2013 and August 2016. Survey and salamander capture dates are included in the accompanying data files. All salamanders included in the study are Jollyville Plateau Salamanders (*Eurycea tonkawae*) according to genetic analyses and distributions presented in Devitt et al. (2019). Coordinates are rounded to the nearest degree following Dryad's data guidance for threatened and endangered species. | Spring Complex | Site (Headwater Creek) | Latitude | Longitude | County | State | Country | | :----------------------- | :--------------------- | :------- | :-------- | :--------- | :---- | :------ | | Avery Deer Spring | Avery Deer 1 | 31 | -98 | Williamson | Texas | USA | | Avery Deer Spring | Avery Deer 2 | 31 | -98 | Williamson | Texas | USA | | Avery Springhouse Spring | Avery Springhouse | 31 | -98 | Williamson | Texas | USA | | Hill Marsh Spring | Hill Marsh | 31 | -98 | Williamson | Texas | USA | | MacDonald Well | MacDonald Well | 31 | -98 | Travis | Texas | USA | | PC Spring | PC 1 | 31 | -98 | Williamson | Texas | USA | | PC Spring | PC 2 | 31 | -98 | Williamson | Texas | USA | Task 1: Data exploration and summary statistics for captured salamanders Purpose 1: Explore potential patterns in salamander distribution (distance from a spring outlet) among reproduction condition (gravid and non-gravid) and size classes. Purpose 2: Summary statistics for salamander detection distances (distance from a spring outlet) among reproduction condition and size classes. Data file = Adcock_etal_data_exploration_captures.csv R code file = Adcock_etal_data_exploration_captures.R Task 2: Data exploration and summary statistics for recaptured salamanders Purpose 1: Explore potential patterns in salamander recapture locations (distance from a spring outlet). Purpose 2: Summary statistics for salamander movement between capture and recapture occasions. Data file = Adcock_etal_data_exploration_recaptures.csv R code file = NA (All calculations are completed within the excel file and available on the “recapture calculations” tab.) Task 3: Relative abundance modeling Purpose 1: Evaluate salamander counts from visual encounter surveys at each site (headwater creek) in comparison to the distance from the primary spring outlet. Purpose 2: Perform model selection, assess model fit, and assess model adequacy. Purpose 3: Use the top model to make predictions that are depicted in the associated figure (Figure 2). Data file = Adcock_etal_relative_abundance_analyses.csv R code file = Adcock_etal_relative_abundance_analyses.R Task 4: Relative density modeling Purpose 1: Evaluate salamander counts from quadrat surveys at each site (headwater creek) in comparison to the distance from the primary spring outlet. Purpose 2: Perform model selection, assess model fit, and assess model adequacy. Purpose 3: Use the top model to make predictions that are depicted in the associated figure (Figure 3). Data file = Adcock_etal_relative_density_analyses.csv R code file = Adcock_etal_relative_density_analyses.R ### Files and variables #### File: Adcock\_etal\_data\_exploration\_captures.csv **Description:**  ##### Variables * complex: spring complex * site: individual headwater creek per spring complex * year: capture year * day: capture day of year * survey.type: quadrat (quad), visual encounter survey (ves), or incidental capture * female: Is the captured salamander a gravid female: 0 (no) or 1 (yes)? * svl: snout-vent-length (mm) of captured salamander * size: size class of captured salamander: juvenile (juv), subadult (sub), adult * size2: Is the captured salamander an adult: no (non) or yes (adult)? * dist: location (distance from a spring outlet) of each captured salamander #### File: Adcock\_etal\_data\_exploration\_recaptures.xlsx **Description:**  ##### Variables * spring complex: spring complex * site: individual headwater creek per spring complex * date: day-month-year of salamander capture * day of year: capture day of year * survey type: quadrat (quad), visual encounter survey (ves), or incidental capture * zca collector #: unique identification number for each salamander capture * individual id #: unique identification number for each individual salamander as identified through pattern recognition * gravid female: Is the captured salamander a gravid female: 0 (no) or 1 (yes)? * total length (mm): snout to tip of tail length (mm) of captured salamander * snout-vent-length (mm): snout-vent-length (mm) of captured salamander * distance from spring outlet (m): linear distance of each salamander capture from the nearest spring outlet * distance moved (m): linear distance that an individual salamander moved between captures; positive numbers indicate downstream movement and negative numbers indicate upstream movement * absolute distance moved (m): linear distance that an individual salamander moved between captures ignoring movement direction * days between captures: number of days between capture and recapture of an individual salamander * movement rate (m/day): absolute distance moved divided by days between captures #### File: Adcock\_etal\_relative\_abundance\_analyses.csv **Description:**  ##### Variables * complex: spring complex * site: individual headwater creek per spring complex: Avery Deer 1 (AD1), Avery Deer 2 (AD2), Avery Springhouse (AS), Hill Marsh (HM), MacDonald Well (MW), PC Spring 1 (PC1), PC Spring 2 (PC2) * year: year of visual encounter survey * day: day of visual encounter survey * avg.dist: the average downstream distance (as measured from a spring outlet) of the visual encounter survey * objects: number of cover objects searched during each visual encounter survey * obs: number of observed salamanders in each visual encounter survey * caps: number of captured salamanders in each visual encounter survey * samp: sampling method, visual encounter survey locations were either opputunistic or spatially stratified #### File: Adcock\_etal\_relative\_density\_analyses.csv **Description:**  ##### Variables * complex: spring complex * site: individual headwater creek per spring complex: Avery Deer 1 (AD1), Avery Deer 2 (AD2), Avery Springhouse (AS), Hill Marsh (HM), MacDonald Well (MW), PC Spring 1 (PC1), PC Spring 2 (PC2) * quad: unique label for each quadrat survey * year: year of quadrat survey * day: day of quadrat survey * dist: the downstream distance (as measured from a spring outlet) of the quadrat survey * objects: number of cover objects searched during each quadrat survey * obs: number of observed salamanders in each quadrat survey * caps: number of captured salamanders in each quadrat survey * samp: sampling method, quadrats were either randomly located using a systematic or stratified random sampling technique ## Code/software Program R R Core Team. 2024. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. [https://www.R-project.org/](https://www.R-project.org/).