DOI: 10.5061/dryad.zs7h44jjx
title: Data from: Connectivity and nutrient enrichment affect the productivity and stability of aquatic meta-ecosystems

description: Despite major human impacts on aquatic connectivity (e.g. channelization,
 damming) and on nutrient inputs (e.g. agriculture, sewage), empirical
 studies on the combined impacts of these effects are rare. To better
 understand the interactive role of connectivity and nutrient enrichment in
 shaping meta-ecosystem stability, we set up a mesocosm experiment
 mimicking a minimal meta-ecosystem composed of two ponds (upstream and
 downstream). The upstream pond received varying water volumes from a
 mesotrophic lake (ranging from 0 to 40 % mesocosm volume per week), and
 five levels of nutrient enrichment (phosphorus and nitrogen). The
 experiment featured a fractional factorial design, with 13 unique
 treatment combinations monitored over 14.5 weeks. We found that
 connectivity increased phytoplankton biomass in highly nutrient-enriched
 meta-ecosystems, that connectivity and nutrient enrichment independently
 promoted synchrony and spatial homogeneity of phytoplankton biomass within
 metaecoystsems, and that our treatments did not influence temporal
 stability beyond the initial nutrient-induced biomass increase.
 Furthermore, while intermediate levels of connectivity stimulated
 zooplankton biomass and diversity, the increase was counteracted with
 nutrient enrichment. We conclude that increased ecosystem connectivity is
 likely to exacerbate the negative effects of nutrient enrichment on
 primary production and consumer diversity across watersheds while
 homogenizing temporal population dynamics.
description: # Data from: Connectivity and nutrient enrichment affect the productivity
 and stability of aquatic meta-ecosystems DOI: 10.5061/dryad.zs7h44jjx Data
 from an experiment where 1000 L plastic mesocosms (ponds) were filled with
 water from a mesotrophic lake. The lake water was piped into a ~100,000 L
 reservoir near the experimental site, and was sampled at the same time as
 the ponds. The ponds were grouped into meta-ecosystems, each containing
 one or two ponds. Most meta-ecosystems were composed of two ponds, with
 different levels of connectivity (also referred to as Movement in the code
 and data) between the upstream and downstream. Every week, a
 pre-determined percentage of the pond volume (10, 20, 30, or 40 %) was
 emptied from the downstream pond, moved from the upstream to downstream
 pond, and used to refill the upstream pond with lake water. In the code
 and data, the upstream and downstream is often coded as Node 1 and 2,
 respectively. A control connectivity (0 %) was also included in the
 experiment and did not involve any water transfer. The control
 connectivity ponds were alone in their respective metaecosytems, and are
 coded as Node 1. The experiment also featured a nutrient enrichment
 treatment, ranging from 0 to 200 μg P L^-1^ per week. Nitrogen was also
 supplemented at the same molar ratio as present in the lake of 31:1 N:P.
 Nutrients were added after the connectivity treatment had been applied
 (same day). For more details on the experimental design, see the
 associated paper, published in Royal Society B. ## Description of the data
 and file structure Unless otherwise specified, all `.csv` files use commas
 (`,`) to separate columns and periods as decimal points (`.`).
 `Data/Treatments.csv` and `Data/Treatments (alphabetical).csv` contain a
 mapping between the ID assigned to each pond, the connectivity and
 nutrient enrichment treatments, and the position of the pond in the
 meta-ecosystem. * **Mesocosm**: ID attributed to a pond. * **Movement**:
 Connectivity treatment (% pond volume displaced per week). *
 **NutrientP**: Nutrient enrichment treatment (μg P added per L per week).
 * **Node**: Upstream (1) or downstream (2) pond. `Data/Metaecosystems.csv`
 as above, but contains an additional column: * **Metaecosystem**: ID
 attributed to a metaecosystem. `Data/Metaecosystems-Replicate.csv` as
 above, but contains an additional column: * **Replicate**: provides a
 (non-unique) ID ("A" or "B") to each replicate
 metaecosytem. ### Chlorophyll *a* data `Data/FP-final/ExportMain/Data.bdb`
 contains the data collected from the Fluoroprobe instrument in the native
 proprietary format. `Data/FP-final/ExportMain/FP.txt` is a tab-separated
 file which contains the experimental chlorophyll *a* data, as exported
 from the Fluoroprobe instrument software. See Fluoroprobe manual for
 details. * **Comment** contains [the pond ID (column named Mesocosm
 elsewhere)]-[filtered or unfiltered]. All samples were measured as
 filtered and unfiltered through a 22 μm sieve, but ultimately, only the
 unfiltered data was used for the analysis. `Data/Pilot/FP-dilution series
 SEPT292022.txt` is a tab-separated file which contains the chlorophyll *a*
 data for the self-shading correction, as exported from the Fluoroprobe
 instrument software. See Fluoroprobe manual for details. * **Comment**
 contains [the pond ID (here, a single sample was used, from the highly
 concentrated F4 pond)]-[% dilution](filtered). The [% dilution] indicates
 the percentage to which the sample was diluted. As above, we also measured
 samples that were filtered through a 22 μm sieve, but ultimately did not
 use this data. `Data/FP-final/FP_clean.csv` contains the tidy data used
 for the data analysis: * **Mesocosm**: ID attributed to a pond. *
 **Date**: Sampling date in YYYY-MM-DD format. * **Green.Algae**,
 **Bluegreen**, **Diatoms**, **Cryptophyta**, **Yellow.substances**:
 different classes of phytoplankton (and yellow substances) as detected by
 the Fluoroprobe using the factory-calibrated parameters (μg L^-1^). These
 values were not used in our analysis. * **Chla**: total chlorophyll *a*
 (μg L^-1^) corrected for self-shading at high concentrations (see paper,
 Supplemental Figure 3). ### Nutrient data `Data/Nutrients/N-TN DN Gonzalez
 (McGill) - LEAP 2022.xlsx` has the raw total and dissolved nitrogen data
 (analysed by technicians at the GRIL analytical laboratory at UQAM
 (Université de Quebéc à Montéral)). The different sheet names correspond
 to dates on which the samples were analysed, not collected. * **Sample
 ID**: ID given to various controls and samples. The samples are named as
 follows: [Pond ID] [DN or TN, for dissolved or total nitrogen] ((X10)).
 Dissolved samples were filtered through 0.22 μm syringe filters and
 represent the dissolved fraction of the total nitrogen. Some samples,
 identified with (10X) were diluted by a factor of 10 to provide more
 accurate measurements. * **Concentration (ppm)**: The measured total
 nitrogen concentration in the sample (ppm; equal to mg/L). * **Corrected
 conc. (ppm)**: The measured concentration corrected for the negative
 control (Sample ID: EAU NANO + PERSULFAT) and, if necessary for the sample
 dilution. * **NOTES**: Comments from the analyst. * The smaller table on
 the right, with column names "Standard ID", "Concentration
 (ppm)", "Peak height", and "CV (%)" contains data
 that were used to calculate a calibration curve (see Supplemental Text 1
 in the paper's electronic supplemental materials for a brief method
 summary and references). `Data/Nutrients/P Gonzalez (McGill) - LEAP
 2022.xlsx` has the raw total and dissolved phosphorus data (analysed by
 technicians at the GRIL analytical laboratory at UQAM (Université de
 Quebéc à Montéral)). The different sheet names correspond to dates on
 which the samples were analysed, not collected. * **Sample ID**: ID given
 to various controls and samples. The samples are named as follows: [Pond
 ID] [DP or TP, for dissolved or total phosphorus]. Dissolved samples were
 filtered through 0.22 μm syringe filters and represent the dissolved
 fraction of the total phosphorus. * **Absorbance (@890nm)**: Measured
 absorbance at 890 nm wavelength. * **Absorbance Fe (@890nm)**: unused *
 **Concentration (ug/L)**: Total phosphorus concentration in the sample
 (corrected for dilution, if present). * **NOTES**: Comments from the
 technician. Some samples, identified here, were diluted by a factor of
 four to provide more accurate measurements. * The smaller table on the
 right, with column names "Standard ID", "Concentration
 (ppm)", "Absorbance (@890nm)", and "CV (%)"
 contains data that were used to calculate a calibration curve (see
 Supplemental Text 1 in the paper's electronic supplemental materials
 for a brief method summary and references). `Data/Nutrients/Nutrients.csv`
 contains the tidy nutrient analysis data used for the analysis: *
 **Date**: Sampling date in YYYY-MM-DD format. * **Mesocosm**: ID
 attributed to a pond. * **Nutrient**: nutrient analysed (nitrogen (N) or
 phosphorus (P)). * **Fraction**: Dissolved (filtered through 0.45 μm
 syringe filter). * **conc**: the concentration measured (units specified
 in **unit** column - μg/L for P and mg/L for N) * **unit**: specifies the
 units used for **conc** column. ### Environmental data (YSI)
 `Data/YSI_raw/` folder contains files `YSI1.csv` through `YSI6.csv` along
 with `YSI Aug 15.csv`. WARNING: these files contain incorrect dates (see
 `Data/YSI_date_correction.csv` for the correction key). The columns are as
 in `Data/YSI_clean.csv`, except **Site**, which was renamed to
 **Mesocosm** in the clean version (see below).
 `Data/YSI_date_correction.csv` contains the correction key for the files
 in the `Data/YSI_raw` folder: * **MeasuredDate**: incorrect date in the
 `Data/YSI_raw` files. * **ActualDate**: the true date on which the
 measurements were taken `Data/YSI_clean.csv` contains the data with the
 corrected dates: * **Timestamp**: Date and time at which measurements were
 taken. Note: time may be unreliable in some cases. * **Mesocosm**: ID
 attributed to a pond. * **Specific Conductance (uS/cm)**, **Dissolved
 Oxygen (mg/L)**, **pH_1 (Units)**, **Temperature (C)** are
 self-explanatory. * The remaining columns are not useful. ### Zooplankton
 data `Data/Zooplankton/ZoopCounts.csv` contains the raw zooplankton counts
 along with some comments: * **Sample Date** Sampling date, in Month
 (abbreviated)-Day format (all in 2022). * **Pond ID**: ID attributed to a
 pond. * **Date Counted**: Date the sample was counted, in Month
 (abbreviated)-Day format (all in 2022). * **Transfer (%)**: Connectivity
 treatment (% pond volume transferred per week). * **Nutrients**: Nutrient
 treatment (μg P added per L per week). * **Node**: Upstream (1) or
 downstream (2) pond. * **Counter**: One of two people that performed the
 task of counting (Michelle or April). * **Daphnia** to **Copepoda**:
 Crustacean zooplankton counts, per taxonomic group (number per 4 L water
 volume). * **TOTAL**: Total numbers of crustacean zooplankton (number per
 4 L water volume). * **Nauplii** to **Rotifers**: Other forms of
 zooplankton, and other organisms. Note that Rotifers were only counted by
 Michelle and not included in the final analysis (number per 4 L water
 sample volume). * **Notes**: Notes about the sample, along with a
 qualitative assessment of the rotifer species present reported by
 Michelle. `Data/Zooplankton/ZoopCountsClean.csv` is as above, but without
 the **TOTAL** and **Rotifers**, which were excluded from the analysis
 along with a new column: * **Date**: The sampling date in YYYY-MM-DD
 format. `Data/Zooplankton/ZoopCountsCleanLong.csv` is as above, but in
 long form: * **Taxa**: The different taxa. * **Abundance**: The number of
 individuals per 4 L of sample volume. * Note that columns **Daphnia** and
 **Other** were excluded from the **Taxa** column due to a lack of
 individuals and irrelevance to the study, respectively. * Additionally,
 the columns described for the file `Data/Treatments.csv` are included.
 `Data/Zooplankton/ZoopBiomass.csv` is as above, but with a species-based
 estimate for the per-individual dry mass: * **Dry mass**: Species-based
 estimate for the per-individual dry mass (mg/individual) * **Ref**: Source
 for the dry mass estimate. * **Biomass**: The total biomass per individual
 per sample (mg per 4 L of sample volume)
 `Data/Zooplankton/ZoopBiomass.csv` is as above, but with a species-based
 estimate for the per-individual dry mass: * **Dry mass**: Species-based
 estimate for the per-individual dry mass (mg/individual) * **Ref**: Source
 for the dry mass estimate. * **Biomass**: The total per-species biomass
 per sample (mg per 4 L of sample volume)
 `Data/Zooplankton/ZoopBiomassSummary.csv`: * **Date**: The sampling date
 in YYYY-MM-DD format. * **Mesocosm**: ID attributed to a pond. *
 **Biomass**: The total zooplankton biomass per sample (mg per 4 L of
 sample volume) `Data/ZooplanktonTraits/Hebert2016-short.csv` is a `csv2`
 file (comma for the decimal point and a semicolon for the separator) and
 contains data used for the species-specific individual-based dry mass
 estimates. This file contains a subset of the relevant columns published
 as a data paper by Hébert et al. (2016; see "Zooplankton Dry Mass
 Estimation" section below). * **Species**: Scientific name of
 species. Note that "-(M)" indicates male individuals. *
 **Genus**: Scientific name of genus. * **Group**: Scientific name of a
 more general taxonomic group (*Copepoda* or *Cladocera*). * **Habitat**:
 Type of habitat (Freshwater or Marine). * **Dry.mass**: Dry body mass of a
 single individual (mg per individual). * **Ref.dm**: Reference code for
 dry mass. See Hébert et al. (2016) for reference key.
 `Doc/MesocosmLayour.pdf` is a diagram which shows the spatial layout of
 the experimental ponds. `R/` contains the code necessary to fit the models
 and produce the figures in the paper (see section "Code" below).
 `Rmd/ModelFits/` contains the fitted models, helpful for generating the
 figures (see section "Code" below). `DESCRIPTION` contains a
 list of R packages used for this project (see section "Code"
 below). `LEAP 2022.Rproj` is a RStudio project file helpful for executing
 code included in the project (see section "Code" below). ##
 Zooplankton Dry Mass Estimation Three references were used for estimating
 dry weight of various zooplankton (see R code in
 `R/DataGetters/getZoopData`, in the function `getZoopBiomass()`): \[1]
 Hébert, M.-P., Beisner, B.E. and Maranger, R. (2016), A compilation of
 quantitative functional traits for marine and freshwater crustacean
 zooplankton. Ecology, 97: 1081-1081.
 [https://doi.org/10.1890/15-1275.1](https://doi.org/10.1890/15-1275.1)
 \[2] Rosen, R. A. (1981). Length-Dry Weight Relationships of Some
 Freshwater Zooplanktona. Journal of Freshwater Ecology, 1(2), 225–229.
 [https://doi.org/10.1080/02705060.1981.9664034](https://doi.org/10.1080/02705060.1981.9664034) \[3] Anderson, D. H., & Benke, A. C. (1994). Growth and reproduction of the cladoceran Ceriodaphnia dubia from a forested floodplain swamp. Limnology and Oceanography, 39(7), 1517-1527. [https://doi.org/10.4319/lo.1994.39.7.1517open_in_new](https://doi.org/10.4319/lo.1994.39.7.1517open_in_new) ## Code To re-run the analyses for this paper, use scripts found in `R/Figures/`. Here, `ChlaMeta.R` is used for meta-ecosystem level plotting, whereas `ContourChla.R` contains the code for plotting the upstream and downstream ponds separately. These scripts automatically load the appropriate scripts from `R/DataGetters` which are used to load the appropriate and necessary data. Additionally, some model fitting operations take some time, and are included in either `R/Objects` or `Rmd/ModelFits`. In these cases, the model fitting operation is commented out in the code. If you would like to re-fit some data, simply un-comment the model fitting section. All file paths used are relative to the project directory ("LEAP2022"). If using RStudio, open "LEAP 2022.Rproj" to automatically set the correct working directory. The DESCRIPTION file contains all required R packages. Note: Unicode text in figures may not render properly on Mac computers.