DOI: 10.5061/dryad.n2z34tms5
title: Data from: Natural disturbances can produce misleading bioassessment results: identifying metrics to detect anthropogenic impacts in intermittent rivers

description: Ecosystems experience natural disturbances and anthropogenic impacts that
 affect biological communities and ecological processes. When natural
 disturbance modifies anthropogenic impacts, current widely used
 bioassessment metrics can prevent accurate assessment of biological
 quality. Our aim was to assess the ability of biomonitoring metrics to
 detect anthropogenic impacts at both perennial and intermittent
 sites, and in the latter including both flowing and disconnected
 pool aquatic phases. Specifically, aquatic macroinvertebrates
 from 20 rivers were sampled along gradients of natural
 flow intermittence (natural disturbance) and anthropogenic
 impacts to investigate their combined effects on widely used
 river biomonitoring metrics (i.e. taxonomic richness and standard
 biological indices) and novel functional metrics, including
 functional redundancy (i.e. the number of taxa contributing
 similarly to an ecosystem function, here a trophic function) and response
 diversity (i.e. how functionally similar taxa respond to natural
 disturbance and anthropogenic impacts). Our results showed that natural
 flow intermittence can confound river bioassessment, and that a set of new
 functional metrics could be used as effective alternatives to standard
 metrics in naturally disturbed intermittent rivers.
description: <strong>RSTUDIO (usage notes):</strong>
 0_FD_functions.R <br> # R functions to estimate functional
 metrics and perform null models.
 0_model_functions<br> # R functions required to run the
 models and perform null models.
 0_quality_funct_space_fromdist.R <br> # R function for
 computing the quality of functional multidimensional functional spaces.It
 is required to estimate functional metrics and perform null
 models. 1_metric_preparation.R <br> # R script to
 estimate widely used river biomonitoring metrics (i.e. taxonomic richness
 and standard biological indices) and novel functional metrics, including
 functional redundancy (i.e. the number of taxa contributing similarly to
 an ecosystem function, here a trophic function) and response diversity
 (i.e. how functionally similar taxa respond to natural disturbance and
 anthropogenic impacts).  2_models.R <br> # R
 script to run the models assessing the ability of biomonitoring metrics to
 detect anthropogenic impacts at both perennial and intermittent sites. It
 was used in both all aquatic-phases dataset and flowing-phases
 dataset.  3_null_models<br> # R script to run the
 null models. It was used in both all aquatic-phases dataset and
 flowing-phases dataset. 
 ############################################################################<br> Input files: bloc_e<br> # Number of categories of each effect trait. bloc_r<br> # Number of categories of each response trait. effect_traits<br> "# Trophic characteristics of each genus were gathered from the Freshwater Information Platform (http://www.freshwaterecology.info) (Moog, 2002; Schmidt-Kloiber & Hering, 2015): grazers, miners, xylophagous, shredders, gatherers, active and passive filter feeders, predators, parasites and others. Same as with response traits, for genera without traits or for taxa not identified to genus, averaged data from other genera within the same family or from family-level traits were used. This was the case for 24 taxa identified to genus: Atrichopogon, Berdeniella, Chelifera, Chironomus, Dolichopeza, Eristalis, Hexatoma, Hydrellia, Limnephilus, Limnophora, Lispe, Niphargus, Orimarga, Oxycera, Ptychoptera, Satcheliella, Scatella, Selysiothemis, Sepedon, Simulium, Stratiomys, Tipula, Tonnoriella and Wiedemannia, as well as for the Chironomidae and Ceratopogonidae identified to subfamily or tribe. " family_vs_genera<br> # Family names of each used genus. final_set<br> "# Final set of widely used and functional metrics, and a set of the descriptors of flow intermittence and anthropogenic impacts. It is used in both all aquatic-phases dataset and flowing-phases dataset. Hydrological variables were: the hydrological regime of each site (HR; where 0 refers to perennial rivers and 1 to intermittent ones; calculated by using the TREHS software), the number of days in the disconnected pool phase since last sample was taken (DPi; calculated from temperature data loggers), and the total number of zero-flow days (i.e. disconnected pool or dry riverbed) during the 30-week study period (ZFt; calculated from temperature data loggers). Besides, to calculate the ZFt, we used the total number of days in the disconnected pool phase (total_DP) and the total number with dry riverbed (total_dry). The extent of anthropogenic impacts at each site was measured using the number of impacts in the Mediterranean reference criteria (MRC) (Sánchez-Montoya et al., 2009). " response_traits<br> "# Traits related to resilience and resistance strategies to estimate functional richness (FRic, Villéger, Mason, & Mouillot 2008) and functional dispersion (FDis, Laliberté & Legendre, 2010; hereafter, RD) for the whole community and each trophic group. Categories of response traits: asexual reproduction, with resistance forms (i.e. diapause or dormancy, cocoons), aerial respiration (i.e. spiracle, hydrostatic vesicle), flier and burrower (i.e. epibenthic) or interstitial (i.e. endobenthic) locomotion and substrate relation, less than a year life cycle duration, more than one reproduction cycles per year, aerial active and aquatic passive (i.e. drift) dissemination (see Table S1 in Supplementary Information). Response traits were compiled from Tachet, Richoux, Bournaud, and Usseglio-Polatera (2010). Same as with effect traits, for genera without traits or for taxa not identified to genus, averaged data from other genera within the same family or from family-level traits were used. This was the case for 24 taxa identified to genus: Atrichopogon, Berdeniella, Chelifera, Chironomus, Dolichopeza, Eristalis, Hexatoma, Hydrellia, Limnephilus, Limnophora, Lispe, Niphargus, Orimarga, Oxycera, Ptychoptera, Satcheliella, Scatella, Selysiothemis, Sepedon, Simulium, Stratiomys, Tipula, Tonnoriella and Wiedemannia, as well as for the Chironomidae and Ceratopogonidae identified to subfamily or tribe. "