DOI: 10.5061/dryad.hx3ffbgkn
title: An analysis of the effects of prior drying and vertebrate colonization on ecological functioning and vertebrate fitness

description: We investigated the legacy effects of drying and refilling of wetlands via
 mesocosms on growth and survival of recolonizing aquatic vertebrates and
 their subsequent effects on ecological function. Specifically, we tested
 the effects of prior drying on anuran and fish growth and survival (using
 Gompertz growth curves), and joint effects of vertebrates and drying on
 periphyton biomass, and whole-system gross primary productivity. Using 64
 1,000-L hard plastic cattle tanks to create replicate aquatic mesocosms,
 four trophic treatments (no vertebrate control, larval anurans, fish,
 larval anurans and fish) were crossed with two drying treatments (undried
 and dried-refilled) to simulate different outcomes of colonization by two
 common vertebrate guilds and drying/refilling cycles. Mesocosms with
 anuran treatments received 50 Lithobates blairi tadpoles (1,600
 total) and mesocosms with fish treatments received one Lepomis cyanellus
 juvenile (32 total). We recorded anuran growth rates, survival, and
 time/size at metamorphosis, fish growth, gross primary productivity, and
 periphyton biomass over 12 weeks from 9 May 2021 to 1 August 2021. This
 dataset contains 4 R script files (one for each of the 4 components of
 this study: Amphibians, fish, gross primary productivity, and periphyton)
 along with their corresponding Excel files. Survival for each tank was
 calculated as the total number of emerged frogs from weeks 1–12 divided by
 50 (initial number of larvae per tank). Size at metamorphosis was
 determined by dry mass (g) measured after 72 hours in a drying oven at 60°
 C. Metamorph dry mass and wet mass were strongly correlated (grams dry
 mass = 0.1957*grams wet mass – 0.0398; R2 = 0.9733) and we chose dry mass
 for size at metamorphosis to reduce variability caused by water weight. We
 measured the dry mass of metamorphosed frogs to the nearest 0.01g. Time to
 metamorphosis was measured as the days past the first day of the
 experiment (9 May 2021) to the day the frog reached Gosner stage 46
 (Gosner, 1960). We calculated relative fish growth as the change in
 standard length (SL) over the duration of the experiment divided by the
 initial SL for each fish. Individual fish growth calculations used each of
 the single fish per tank as independent replicates. Relative fish growth
 measurements for fish within the same treatments (n = 8) were combined and
 analyzed together. Gross primary productivity values were collected by
 measuring dissolved oxygen (DO) values after sunset for maximum DO and
 before sunrise for minimum DO. DO measurements were collected using a YSI
 meter (ProQuatro XA00088 – 02; YSI Inc., Yellow Springs, OH, USA) as a
 percentage out of 500.   Gompertz growth curves provided
 estimates of asymptotic larval body mass (Wmax), maximum growth rate (K),
 and the time at which growth rates reach K (xm). However, only Wmax and K
 were included in statistical analyses as they were the primary parameters
 of interest for our study. All statistical analyses were performed in
 RStudio version 4.1.1 (R Core Team, 2021). We constructed generalized
 linear models (GLMs; ‘stats’ package in R; R Core Team, 2021) for each of
 Wmax, K, number of emerged frogs (survival), size at metamorphosis, time
 to metamorphosis, range of metamorph sizes, and range of metamorphosis
 days as response variables with drying treatment as the predictor
 variable. We also constructed GLMs with fish growth as the response
 variable and a combination of drying treatment and anuran presence as
 predictor variables with interaction terms. We then used type II ANOVAs
 for models without significant interaction terms and type III ANOVAs for
 models with interaction terms via the ‘car’ package in R (Fox &
 Weisberg, 2019) to determine the treatment effects on above response
 variables. GLM model fit and assumptions were checked by a visual
 assessment of the plotted residuals of each GLM model. Since GPP varied
 nonlinearly over the duration of the experiment (Fig. 4), we investigated
 the effects of drying and refilling and trophic treatment on GPP using
 generalized additive mixed models (GAMMs) with the ‘gam’ function (‘mgcv’
 package; Wood, 2015). The GAMM model included trophic treatment and drying
 treatment as parametric effects, trophic treatment over time, drying
 treatment over time, and time as cubic regression smoother terms, and
 individual mesocosm and individual mesocosm over time as random effects.
 The number of knots was set to -1 to utilize the generalized
 cross-validation method to automatically choose the number of knots for
 the model. GAMMs allow us to test hypotheses related to main effects
 (e.g., trophic treatment, drying treatment) within non-linear time series
 while accounting for random effects related to individual mesocosms and
 changes over time due to seasonality. We then used a subsequent ANOVA via
 the ‘anova.gam’ function within the ‘gam’ package to determine treatments
 effects.  We investigated the effects of drying and refilling and
 trophic treatment on periphyton biomass using GAMMs constructed and
 analyzed identically to GPP except that they are only for experimental
 days 19–80. This is because periphyton sampling techniques were not
 standardized until after the second week of data collection. Because data
 for periphyton biomass was right-skewed and included some 0’s that were
 not true zeros (periphyton was present but below measurement limits), we
 added 0.5 to each measurement (untransformed mean was 1.838 g) and then
 log-transformed them. Models run with the transformed data met the
 assumptions of GAMMs and subsequent ANOVAs.
description: All data were collected in the field at the location of the
 experimental study. All field data were entered into Excel sheet format
 and subsequently analyzed via the R Studio software program. The only
 modification to the collected data is the following: data from tank #1
 were omitted from periphyton and gross primary productivity analyses due
 to a separate amphibian species ovipositing within that tank. 
description: All statistical analyses were performed in RStudio version 4.1.1
 (R Core Team, 2021). All packages required for the statistical analyses
 within the R program are listed at the top of each R script file. All
 files submitted are either .xslx or .Rmd file types and both Microsoft
 Excel and R Studio will be required to open the data files.