DOI: 10.5061/dryad.b2rbnzsnk
title: Networks in aquatic communities collapse upon neonicotinoid-induced stress

description: Freshwater ecosystems worldwide are under pressure from neonicotinoid
 insecticides. While recognized that communities of species are responsible
 for ecosystem functioning, it remains unknown if neonicotinoid-induced
 community transformations negatively affect ecosystem functioning.
 Therefore, we employed an experimental approach with 36 naturally
 established freshwater ecosystems exposed to increasing field realistic
 concentrations of the neonicotinoid thiacloprid. Upon exposure, we found
 severe degradation of ecosystem functioning in the form of loss of organic
 matter consumption and dramatic shifts in primary productivity. This
 functional decline coincides with strongly eroded species co-occurrence
 networks to the point that these are indistinguishable from randomized
 assemblages of species. Together, these findings show how current
 environmental concentrations of a neonicotinoid can strongly disrupt
 freshwater ecosystem functioning via degradation of the invertebrate food
 web. Since this dramatic ecosystem degradation occurs below nearly all
 identified ecotoxicological risks, we call here for the reconsideration of
 the use of these insecticides.
description: # Networks in aquatic communities collapse upon neonicotinoid-induced
 stress
 [https://doi.org/10.5061/dryad.b2rbnzsnk](https://doi.org/10.5061/dryad.b2rbnzsnk) The full datasets for water chemistry, biodiversity assessment, ecosystem functioning and accompanying codes for co-occurence network development are provided. ### Description of the data and file structure Please see the Readme per excel file. The .csv files: * 6.Rawdata.csv * 7.Taxa_ClassFamiliesDisplayName.csv * 8.Taxa_OrderingChordDiagram.csv * 3.Random_Interactions_Option1_ZIPoverdisp_TotalAbundancePerTreatment_cor000-100_run6.csv * 4.Random_Interactions_Option1_ZIPoverdisp_TotalAbundancePerTreatment_cor000-100_run6_Null.csv are used to perform the modeling behind and making of Figure 3, 4, S5 and S6. Please note that the files  6.Rawdata.csv, 7.Taxa_ClassFamiliesDisplayName.csv, and 8.Taxa_OrderingChordDiagram.csv are simply reorded datafiles to assist with coding of the file 'Co-occurrence_Figure3_and_S5.R'. The actual raw data of these files are given in a more logical format '2.Rawbiodiversityassay.xlsx'. **File** * **6.Rawdata.csv** A reordered file containing all abundance data per taxon (Column F to CK). Column A to C give the dates when the sample was taken. Column D the respective test ditch. Column E the nominal test concentration of Thiacloprid in μg/L. **File** * **7.Taxa_ClassFamiliesDisplayName.csv** This file contains all taxonomic information (columns A-F). Cells where no data is filled in means that this taxonomic level was not identified. For ease of use, leave these cells empty. Column G 'Name' is an unique identifier based on the lowest level of taxonomic identification available. **File** * **8.Taxa_OrderingChordDiagram.csv** This file helps to keep a consistent order in taxon-taxon correlation within co-occurrence figures. Column A and B indicate the two correlating taxa and their respective classes are given in column E and F. Column C is simply to indicate correlations between the taxa and column D is used for coloring of the correlation, please see the code in Co-occurrence_Figure3_and_S5. **File** * **3.Random_Interactions_Option1_ZIPoverdisp_TotalAbundancePerTreatment_cor000-100_run6.csv** is an *optional* step to test networks versus null models produced per test concentration of Thiacloprid. Readme:  The code for these null models is given in the R file 'Networks_Figure4_and_S6.R'. The null models run from Spearman's correlation strength 0 - 100. In case NA is given, this means that no correlations were produced at this correlation strength. If 'Inf' is given, this means infinite, these are removed later on in figure production with the mentioned R script. column A: step of the model (with steps of 0.01 | rho |). Leave A1 empty for coding. column B: 'conc' = Nominal concentration Thiacloprid in water in (µg/L) column C: 'rho' = Absolute Spearman's correlation strength column D: 'randcors_null_median' = median number of correlations of 1000 generated random communities column E to F contain confidence intervals around the 1000 generated random communities to plot the associated uncertainties around the null model. **File**  * **4.Random_Interactions_Option1_ZIPoverdisp_TotalAbundancePerTreatment_cor000-100_run6_Null.csv** is the null model as used in the paper. But note that new null models can also be produced following file 'Networks_Figure4_and_S6.R'. Readme:  This datafile contains the used randomized null model in the paper. The code for this null model is given in the R file 'Networks_Figure4_and_S6.R'. The null model runs from Spearman's correlation strength 0 - 100. In case NA is given, this means that no correlations were produced at this correlation strength. Do not remove NA as this information is needed for figure production. If 'Inf' is given, this means infinite, these are removed later on in figure production with the mentioned R script. This null model data is used to reproduce figures as given. However, one can opt to create a new null model with the codes provided in the R file mentioned in row 5. This null model is based on the control of the experiment (see paper section 'Statistics on community network and structure'). column A: step of the model (with steps of 0.01 | rho |). Leave A1 empty for coding. column B: 'conc' = Nominal concentration Thiacloprid in water in (µg/L) column C: 'rho' = Absolute Spearman's correlation strength column D: 'randcors_null_median' = median number of correlations of 1000 generated random communities column E to F contain confidence intervals around the 1000 generated random communities to plot the associated uncertainties around the null model. ### Code/Software All codes are provided in R scripts format. These codes can be used to reproduce co-occurrence and network results and figures. The codes provided are the R files: * Co-occurrence_Figure3_and_S5. Which is used to reproduce co-occurrence matrices and associated statistics and Figures 3 and S5. * Networks_Figure4_and_S6.R Which is used to built null models and test networks per test concentration of Thiacloprid statistically against the produced null models. And to construct figures 4 and S6. Accompanying packages are: tidyr dplyr Hmisc pscl VGAM fitdistrplus circlize