Dataset DOI: 10.5061/dryad.p5hqbzm1b

Description of the data and file structure

The data was collected across a range of parcels within different sites using pitfall traps. Pitfall traps were used to sample ground invertebrate abundance and species richness. In year 1 (2022), just carabid species richness was analysed. In year 2 (2023) DNA metabarcoding was used to look at total ground invertebrate species richness. Invertebrate richness and abundance was analysed against England's statutory biodiversity metric scoring (distinctiveness*condition scoring). 

Files and variables

File: JAPPL-2025-00285-Data_v2.xlsx

Description: Datasheets used in the R code for analysis.

Sheets

Sheet 1: Y1 data:

Data on ground invertebrate abundance and richness for analysis from year 1 (2022). Includes distinctiveness*condition scoring values from the statutory biodiversity metric for each parcel.

Variables: Parcel_ID: unique identifier for each habitat parcel (this is consistent throughout all sheets), Site: identifies which landholding each habitat parcel belongs to, Habitat type: UK Habitat Classification type (UKHab) of the habitat parcel, Distinctiveness: habitat distinctiveness as determined by England Statutory Biodiversity Metric, Condition: habitat condition measured in the field as determined by England Statutory Biodiversity Metric, Distinctiveness.Condition: values for distinctiveness and condition multiplied together, All.Invert.Abundance: total invertebrate abundance values for each habitat parcel, Carabid.abundance: carabid beetle abundance values for each habitat parcel, Spider.abundance: spider abundance values for each habitat parcel, Rarefied.Richness: rarefied species richness values for each habitat parcel, All following columns denote the abundance of each carabid species listed in the column name, which were used to generate species richness values.

Sheet 2: Y2 Abundance and raw richness:

Data on ground invertebrate abundance and raw species richness values for analysis from year 2 (2023). Includes distinctiveness*condition scoring values from the statutory biodiversity metric for each parcel.

Variables: Parcel_ID: unique identifier for each habitat parcel (this is consistent throughout all sheets), Site: identifies which landholding each habitat parcel belongs to, Replicate: refers to which sampling period data was taken from (1= May, 2=June, 3= August, Total=summed 3 replicates), Habitat type: UK Habitat Classification type (UKHab) of the habitat parcel, Distinctiveness: habitat distinctiveness as determined by England Statutory Biodiversity Metric, Condition: habitat condition measured in the field as determined by England Statutory Biodiversity Metric,** Num.Pitfalls**: number of pitfall traps summed together for the total values, Distinctiveness.Condition: values for distinctiveness and condition multiplied together, All.Invert.Abundance_y2: total invertebrate abundance values for each habitat parcel, Carabid.abundance_y2: carabid beetle abundance values for each habitat parcel, Spider.abundance_y2: spider abundance values for each habitat parcel, Spider.Richness, Carabid.Richness, Rove.Richness, Collembola.Richness, Gastropod.Richness, and Hemiptera.Richness all refer to the raw species richness value for the summed replicates for each habitat parcel.

Sheet 3: Y2 Metabarcoding target OTUs:

Operational Taxonomic Unit (OTU) data for target taxa from year 2 (2023)

Variables: Sequence: genetic sequence used to make species ID, Kingdom, Phylum, Class, Order, Family, Genus, and Species columns refer to the taxonomy of the identified species. Further columns list the presence of this sequence in each sample. Column name denotes the habitat parcel name (e.g., 1_2) and the month in which the sample was collected (May June or August)

Sheet 4: Y2 species occurrence:

Species-level identifications derived from OTUs from year 2 (2023).

Variables: This spreadsheet is formatted so that it runs the code for species richness rarefaction in iNEXT. The first row is the samples, with each sample being a unique habitat parcel (same ID structure as above). The second row is the number of pitfall traps in each habitat parcel. Each row after that corresponds to a species and how many of the replicates it appeared in (1,2,3).

Sheet 5: Y2 rarefied species richness:

The outcome of the species richness rarefaction code. Variables: Parcel_ID: unique habitat parcel identifier, t: number of pitfall traps at which diversity estimate is calculated at, Method: rarefaction or extrapolation, Order.q: specifies the type of diversity being estimated, in this case, q=0 means that species richness is being calculated. SC: sampling coverage, Rarefied.richness: the rarefied species richness value, qD.LCL: lower confidence limit of the species richness value, qD:UCL: upper confidence limit. All other variables as defined in sheet 2.

Sheet 6: Y2 rarefied OTUs:

Rarefied OTU values from year 2 (2023). Variables: as above but using Operational Taxonomic Unit (OTU) richness rather than species richness. 

Sheet 7: Y2 family OTUs:

Family-level OTU data used for Non-metric multidimensional scaling (NMDS) analysis from year 2 (2023). 

Variables: Samples: denotes the unique parcel identifier, Replicate: 1,2,3 to denote whether sample was collected in May, June, or August. Each subsequent column represents a taxonomic family and how many OTUs from that family were present in that sample.

Within the sheets NA is used to denote missing data (e.g., due to interference with samples), or for values which aren't relevant to particular entries. "0" is used to denote zero.

Sheet 8: Variables NMDS:

Variables appended to the 3-dimensional NMDS plots. Variables are named as in sheet 2.

File: JAPPL-2025-00285_supplementary_data.csv

Description: Data used for the supplementary bayesian analysis

Variables: May.Parcel.ID, June.Parcel.ID, August.Parcel.ID: parcel IDs for each 2023 replicate, May.Invert.Abundance, June.Invert.Abundance, Aug.Invert.Abundance: invertebrate abundance totals for the 3 replicates in 2023, May.Distinctiveness.Condition, June.Distinctiveness.Condition, Aug.Distinctiveness.Condition: Distinctiveness multiplied by Condition scores as determined using England's Statutory Biodiversity Metric, May.Site, June.Site, Aug.Site: Landholding which each habitat parcel is contained within, SR.Parcel.ID: unique parcel ID for rarefied species richness analysis, Site.SR: landholding each SR.Parcel is contained within, Rarefied.richness.y2: rarefied species richness values from 2023 iNEXT analysis, SR.distinctiveness.condtion: Distinctiveness multiplied by Condition scores as determined using England's Statutory Biodiversity Metric.

Parcel.ID.y1: habitat parcel IDs for 2022 data, Site.y1: landholdings with 2022 habitat parcels are contained within, Invert.abundance.y1: invertebrate abundance values from 2022, Rarefied.richness.y1: Rarefied species richness value from year 1, Distinctiveness.condtion.y1: Distinctiveness multiplied by Condition scores as determined using England's Statutory Biodiversity Metric.

Code/software

Data is stored in a .xlsx file. Data analysis was conducted in R, using the following packages: 

library(dplyr)

library(ggplot2)

library(iNEXT)

library(MASS)

library(vegan)

library(tidyverse)

library(lme4)

library(scatterplot3d)

library(DHARMa)

library(simr)

library(brms)