Environmental Data: Biodiversity and Abundance in beaver systems

Description

This dataset contains processed species richness, abundance, richness of unique species and evenness data collected to evaluate the ecological impacts of b...

Citation

Moser, V., Minnig, S., Capitani, L., Boch, S., Cramer, N., Edman, O., Hofmann, P., Hürbin, A., Obrist, M. K., Robinson, C., Tinner, D., Zehnder, L., Angst, C., Pomati, F., Risch, A. C. (2025). Biodiversity and Abundance in beaver systems. EnviDat. https://www.doi.org/10.16904/envidat.693.

Resources

• biodiversity_updownstream.R

  biodiversity_updownstream to test if control location up- or Downstream had an effect on our results (Table S9)

  biodiversity_updownstream.R

• biodiversity_spiders_plots_with_boxplots.R

  biodiversity_spiders_plots_with_boxplots to test the influence of beavers on richness, abundance, unique species richness and evenness, spiderplot and boxplots

  biodiversity_spiders_plots_with_boxplots.R

• aquatic_invertebrates_Pool_Control.R

  aquatic_invertebrates_Pool_Control to clean and calculate the aquatic invertebrates biodiversity data

  aquatic_invertebrates_Pool_Control.R

• biodiversity_cleaning_Pool_Control.R

  biodiversity_cleaning_Pool_Control to clean and calculate the biodiversity data and combine it with landuse

  biodiversity_cleaning_Pool_Control.R

• biodiversity_landuse_plot.R

  biodiversity_landuse_plot to test the influence of beavers on richness, abundance, unique species richness and evenness under different land use intensities

  biodiversity_landuse_plot.R

• biodiversity_nestedness.R

  biodiversity_nestedness to test the influence of different land use regimes on beta and gamma diversity

  biodiversity_nestedness.R

• biodiversity_spiders_plots.R

  biodiversity_spiders_plots to test the influence of beavers on richness, abundance, unique species richness and evenness

  biodiversity_spiders_plots.R

• community_data_presence_absence_Pool_Control.csv

  community_data_presence_absence_Pool_Control containing data on abundance of taxa recorded for all communities except aquatic invertebrates (see script). It includes zeros when a taxon was not recorded, with columns "site" (sampling site), "sample" (sampling location within site), "community" (species group), "taxon_lowest" (lowest common identification ranks used per community, e.g., order/suborder or species) "abundance" (number of the taxa in taxon_lowest), "laufnummer" (unique identifier per sampling point)

  community_data_presence_absence_Pool_Control.csv

• landuse.csv

  landuse containing land-use covariates, with columns "laufnummer" (unique identifier per sampling point), "site" (sampling site), "sample" (sampling location within site), "extensive_agriculture" (area of extensive agriculture in m2 within a radius of 250 m around the sample), "intensive_agriculture" (area of intensive agriculture in m2 within a radius of 250 m around the sample), "natural" (area of natural land in m2 within a radius of 250 m around the sample), "urban.raw" (area of urban land in m2 within a radius of 250 m around the sample), "missing" (area missing in m2 from GIS data within a radius of 250 m around the sample), "urban" (combined urban.raw and missing in m2 within a radius of 250 m around the sample), "agriculture" (combined extensive and intensive agricultural area in m2 within a radius of 250 m around the sample).

  landuse.csv

• aquatic_invertebrates_biodiv_Pool_Control.csv

  aquatic_invertebrates_biodiv_Pool_Control containing the cleaned aquatic-invertebrate biodiversity for Pool/Control after rank-aware reconciliation, with columns "laufnummer" (unique identifier per sampling point), "site" (sampling site), "sample" (sampling location within site), "community" (species group), "abundance" (total individuals after reallocation, rounded), "richness" (number of pruned taxa at the analysis rank), "shannon" (Shannon–Wiener index for the sample), "simpson" (Simpson diversity for the sample), "evenness" (Pielou’s evenness for the sample), "unique_species" (taxa unique to this sample vs the paired sample within the same site).

  aquatic_invertebrates_biodiv_Pool_Control.csv

• mzb_species_community_Pool_Control.csv

  mzb_species_community_Pool_Control containing the raw aquatic-invertebrate records used to calculate biodiversity, with columns "laufnummer" (unique identifier per sampling point), "site" (sampling site), "sample" (sampling location within site), "location" (sampling location row within site), "community" (species group), "taxon" (higher taxon, e.g., order/class), "family" (family), "genus" (genus), "species" (species), "genus_species" (genus and species combined), "taxon_ibch" (level of identification with IBCH method), "taxon_low" (lowest identification as provided in the raw import), "abundance" (individual counts).

  mzb_species_community_Pool_Control.csv

• overall_biodiv_Pool_Control.csv

  overall_biodiv_Pool_Control containing biodiversity metrics for Pool/Control, with columns "laufnummer" (unique identifier per sampling point), "site" (sampling site), "sample" (sampling location within site), "community" (species group), "richness" (number of taxa at the community’s "taxon_lowest" rank), "abundance" (total individuals).

  overall_biodiv_Pool_Control.csv

• sampling_dates.xlsx

  sampling_dates contains when the data was collected, with columns "site" (sampling site), "bats_1" (first period of bat survey in June), "bats_2" (second period of bat survey in June), "bats_3" (first period of bat survey in July), "bats_4" (second period of bat survey in July), "flying_arthropods_1" (period of flying arthropod sampling in June), "flying_arthropods_2" (period of flying arthropod sampling in July), "terrestrial arthropods" (date of terrestrial arthropod survey), "vegetation survey" (date of vegetation survey), "plankton" (date of plankton survey), "fish" (date of fish survey), "amphibians" (period of amphibians survey), "dragonflies and damselflies" (period of dragonflies and damselflies survey), "macrophytes" (period of macrophytes survey), "aquatic invertebrates" (date of aquatic invertebrates survey).

  sampling_dates.xlsx

• site_info.csv

  site_info containing information on the sites and samples, with columns "laufnummer" (unique identifier per sampling point), "site" (sampling site), "sample" (sampling location within site), "location" (sampling location row within site), "sample_nr" (sampling number within location)

  site_info.csv

• biodiversity_unique_species.R

  biodiversity_unique_species to test he abundance and occurance of unique species(Table S7)

  biodiversity_unique_species.R

• README_v3.txt

  README text file providing context for the data. Please do not hesitate to contact us if you have any questions, updated 20260114

  README_v3.txt