Data for: Functional redundancy of weed seed predation is reduced by intensified agriculture
Data files
Mar 05, 2024 version files 86.63 KB
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agricultural_intensity.csv
2.29 KB
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pred.cards.csv
58.25 KB
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README.md
9.04 KB
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weed_genus_redundancy_all.csv
17.04 KB
Mar 04, 2024 version files 86.75 KB
Abstract
Intensive agriculture, a driver of biodiversity loss, can diminish ecosystem functions and their stability. Biodiversity can increase functional redundancy and is expected to stabilize ecosystem functions. Few studies however have explored how agricultural intensity affects functional redundancy and its link with ecosystem function stability. Here, within a continent-wide study, we assess how the functional redundancy of seed predation is affected by agricultural intensity and landscape simplification. By combining carabid abundances with molecular gut content data, functional redundancy of seed predation was quantified for 65 weed genera across 60 fields in four European countries. Across weed genera, functional redundancy was reduced with high field management intensity and simplified crop rotations. Moreover, functional redundancy increased the spatial stability of weed seed predation within fields. We found that ecosystem functions are vulnerable to disturbance in intensively managed agroecosystems, providing empirical evidence of the importance of biodiversity for stable ecosystem functions across space.
README: Data for: Functional redundancy of weed seed predation is reduced by intensified agriculture
This dataset was created as part of the research project BioAWARE “Could Biodiversity Assure Weed regulation for Resilient Ecosystem service provision?” Field data were collected from 60 cereal fields in four European countries (France, Austria, Czech Republic, and Sweden) between May and July 2018.
The following .csv and .R files included in this file, contain data and code used for:
- Estimating, analysing, and visualising the relative proportion of variance in predation redundancy across 65 weed genera attributed to two aspects of agricultural intensity (field management intensity, and crop rotation diversity), two aspects of landscape simplification ( the proportion of semi-natural habitat and the length in meters of the interface between crop and semi-natural habitat), and the country-level random effect.
- Analyzing and visualising heatmaps of the effects of all aspects of agricultural intensity and landscape simplification on the functional redundancy in predation of 65 weed genera.
- Analysis and visualisation of the variation in the sum of redundancy of predation to each aspect of agricultural intensity and landscape simplification.
- Estimation, analysis, and visualisation of the relationship between spatial variability of Poa annua predation estimates on seed cards and redundancy of Poa predation.
Data collection methods
Functional redundancy in predation pressure is the exponential Shannon diversity of each carabid species-specific predation pressure on each weed genus. Data on each carabid species' weed-specific pressure were collected using pitfall traps and molecular gut content analysis. Data on weed seed predation were collected by using seed cards with 50 seeds of the weed Poa annua.
Through landscape analysis and the software CHLOE 4.0, we extracted the landscape data. The landscape data were based on the Corine Land Cover (CLC) classification, available national databases, and additional field surveys. Field management intensity data were estimated after communicating with farmers. For details on the data collection methods, we refer to the manuscript.
Data set link: https://doi.org/10.5061/dryad.dfn2z357r
Description of the data and file structure
Data and File Overview
- File count: 5
- File formats: .csv, .R
List of contents
- weed_genus_redundancy_all.csv
- agricultural_intensity.csv
- pred.cards.csv
- HMSC_model.R
- Poa_model.R
Set up
- The HMSC_model.R, weed_genus_redundancy_all.csv, and agricultural_intensity.csv should be used with one another to produce statistical analysis to investigate the impact of the agricultural intensity and landscape simplification on the functional redundancy in seed predation. Specifically, produce statistical analysis and visualisation of the relative proportion of variance in predation redundancy across 65 weed genera attributed to the aspects of agricultural intensity and landscape simplification, the heatmaps of the effects of agricultural intensity and landscape simplification on the functional redundancy in predation of 65 weed genera, and visualisation of the variation in the sum of redundancy of predation for each aspect of agricultural intensity and landscape simplification.
- The pred.cards.csv, the weed_genus_redundancy_all.csv, and the Poa_model.R should be used together to produce statistical analysis and visualisation of the relationship between spatial variability of Poa annua predation estimates on seed cards and functional redundancy of Poa genus predation.
Recommended set software tools: Rstudio version 4.1.3
File details
Details for weed_genus_redundancy_all.csv
Description: a comma-separated (CSV) file containing estimates of functional redundancy in predation for 65 weed genera across 60 cereal fields. The file is currently formatted for use with R.
Format: .csv
Dimensions: 60 rows, 67 columns
Size: 17.04 KB
Variables:* Column A (field_number): Number of the sampled field; 1-60
* Column B - BO: Functional Redundancy in seed predation of the weed genera: Achillea (column B), Aethusa (column C), Agrostis (column D), Alopecurus (column E), Amaranthus (column F), Anthriscus (column G), Apera (column H), Arabidopsis (column I), Arenaria (column J), Artemisia (column K), Avena (column L), Bellis (column M), Brassica (column N), Bromus (column O), Capsella (column P), Cerastium (column Q), Chenopodium (column R), Cirsium (column S), Convolvulus (column T), Crepis (column U), Dactylis (column V), Daucus (column W), Deschampsia (column X), Descurainia (column Y), Echinochloa (column Z), Elymus (column AA), Epilobium (column AB), Erigeron (column AC ), Euphorbia (column AD), Fallopia (column AE), Galinsoga (column AF), Galium (column AG), Geranium (column AH), Geum (column AI), Glechoma (column AJ), Lolium (column AK), Matricaria (column AL), Mentha (column AM), Myosotis (column AN), other (column AO), Papaver (column AP), Persicaria (column AQ), Phleum (column AR), Pimpinella (column AS), Plantago (column AT), Poa (column AU), Polygonum (column AV), Ranunculus (column AW), Raphanus (column AX), Rumex (column AY), Setaria (column AZ), Silene (column BA), Sinapis (column BB), Solanum (column BC), Sonchus (column BD), Stellaria (column BE), Taraxacum (column BF), Thlaspi (column BG), Trifolium (column BH), Tripleurospermum (column BI), Trisetum (column BJ), Tussilago (column BK), Urtica (column BL), Veronica (column BM), Vicia (column BN), Viola (column BO). The functional redundancy is the exponential Shannon diversity of each carabid species-specific predation pressure on each weed genus. Method developed by Feit et al.2019. Ecology Letters, 22, 1568–1577. It was estimated per field and weed genus by combining carabid abundance, feeding probability of each weed genus, and body-mass-related feeding rate.
Details for agricultural_intensity.csv
Description: a comma-separated (CSV) file containing estimates of two aspects of agricultural intensity and two of landscape simplification across 58 cereal fields. The file is currently formatted for use with R.
Format: .csv
Dimensions: 58 rows, 6 columns
Size: 2.29 KB
Variables:* Column A (Country): Country in which the sampled field was located; France (FR), AU (Austria), Czech Republic (CZ), Sweden (SW).
* Column B (Field): Number of the sampled field; 1-60.
* Column C (pSNH): Proportion of seminatural habitat surrounding each field.
* Column D (iSNH): Length in meters of the interface between crops and semi-natural habitat.
* Column E (ManagementIntensity): Number of field visits by the farmer to conduct operations, from the crop sown (including soil preparation) until harvest. The field operations performed during the field visits were pre-sowing soil preparations, pesticide applications (including insecticides, herbicides, and fungicides), fertilizer applications, inversion or non-inversion tillage, and harvest.
* Column F (SCDI): Crop rotation diversity, calculated as the Shannon diversity index of the crops sown in the same field during the previous five years.
Details for pred.cards.csv
Description: a comma-separated (CSV) file containing estimates of Poa annua weed seed predation as measured on seed cards per sampling point and sampling session. The file is currently formatted for use with R.
Format: .csv
Dimensions: 1921 rows, 9 columns
Size: 58.25 KB
Variables:* Column A (Plot_ID): Code of each sampling point
* Column B (Caged): Code that the seed card was enclosed in a mesh cage (1 cm² wire mesh) to exclude vertebrate predators; "C" denotes "cage"
* Column C (Seed_card_count): Number of Poa annua seeds counted on the seed cards after 7 days of exposure to predation.
* Column D (Country): Country in which the sampled field was located; France (FR), AU (Austria), Czech Republic (CZ), Sweden (SW)
* Column E (Session): Number of the sampling session; 1 for mid-May for FR, AU and CZ and mid-June for SW. 2 for mid-June for FR, AU and CZ and mid-July for SW
* Column F (Field): Number of the sampled field; 1-60
* Column G (Transect): Sampling transect of the field; a-d
* Column H (Distance): Distance of the sampling point from the field edge in meters; 4/8/16/32
* Column I (predation): Proportion of Poa annua seeds removed from each seed card to the number of offered seeds; 0-100
HMSC_model.R\
Description: R file to produce statistical analysis and visualisation of the impact of the agricultural intensity and landscape simplification on the functional redundancy in seed predation.\
Format: R\
Size: 10.47 KBPoa_model.R\
Description: Produce statistical analysis and visualise of the relationship between spatial variability of Poa annua predation estimates on seed cards and functional redundancy of Poa genus predation.\
Format: R\
Size: 1.96 KB
Methods
This dataset contains information on the functional redundancy of seed predation for 65 weed genera and field estimates of weed seed predation. It also contains data on two aspects of agricultural intensity (field management intensity, measured as the number of field visits by the farmer to conduct operations, and crop rotation diversity) and two aspects of landscape simplification (the proportion of semi-natural habitat surrounding each field, and the length of the interface between crops and semi-natural habitat). The data were collected in 2018 from 60 cereal fields located in four European countries. Data organisation and analysis were conducted in Microsoft Excel and R. The primary objective of the data was to investigate the impact of agricultural intensity and landscape simplification on the functional redundancy of seed predation and to explore the link between functional redundancy and spatial stability (degree of within-field spatial variability) of field estimates of seed predation. Functional redundancy is the exponential Shannon diversity of carabid species-specific predation pressure on each weed genus. Data on each carabid species' weed-specific pressure were collected using pitfall traps and molecular gut content analysis. Data on weed seed predation were collected by using seed cards with 50 seeds of the weed Poa annua. Landscape data were extracted through landscape analysis, using the software CHLOE 4.0. These landscape data were based on the Corine Land Cover (CLC) classification, available national databases, and additional field surveys. Field management intensity data were estimated after communicating with farmers.