/EMODnet-Biology-benthos-trends

Temporal trends in the composition of benthic communities based on presence-absence data

Primary LanguageR

Temporal Turnover in European Macrobenthos Communities

Introduction

This product builds on the EMODnet Biology data product Presence/absence data of macrozoobenthos in the European Seas to derive estimates of temporal turnover in benthic communities on a spatial grid across European seas. This product only uses species-level records, and only uses sampling events where the full macrobenthic community was surveyed (i.e. where there are no 'NA' values in the presence/absence dataset for any species). Six time periods are considered, based on data availability: before 1990, 1990-1999, 2000-2004, 2005-2009, 2010-2014, and 2015 and after. A 1 degree grid is used to obtain reasonable numbers of repeat samples per grid cell. The code below could be adapted to set different time periods and/or a different grid resolution. This readme describes the product structure, including the workflow to generate the required derived datasets and the process for turning them into gridded maps of community turnover.

Directory structure

EMODnet_benthos_trends/
├── analysis
├── data/
│   ├── derived_data/
│   └── raw_data/
├── docs/
├── product/
└── scripts/
  • analysis - Markdown or Jupyter notebooks
  • data - Raw and derived data
  • docs - Rendered reports
  • product - Output product files
  • scripts - Reusable code

Data series

This product uses the EMODnet Biology data product Presence/absence data of macrozoobenthos in the European Seas. This is available as a single NetCDF file - because that file is large (~3.2GB) it is not included here. Rather, this product uses two datasets that are derived from the NetCDF file, and which are available in data/derived_data: sample_events.csv is a table of unique sampling events, including latitude, longitude, and sampling date; and pres_df.csv is a table of species presences, referenced by sample id (linked to sample_events) and species identity given as WoRMS AphiaID. The full workflow for deriving these datasets from the raw NetCDF file is described in docs/benthos-trends-dataprep.

Data product

The product (available in the product directory in this repository) includes a series of gridded estimates of macrobenthic community turnover in European seas. The six time periods are as defined above (before 1990, 1990-1999, 2000-2004, 2005-2009, 2010-2014, and 2015 and after), and turnover metrics are calcuated at the cell level for all possible pairwise time comparisions - from a minimum of 1 (where a cell contains observations from only two time periods) to a maxmimum of 15 (where a cell contains observations in all six time periods).

The diversity measures used are:

Beta diversity - these metrics are derived using the beta function in the BAT package (Cardoso et al. 2022). There are three measures: Btotal (total beta diversity), which is then decomposed into Brepl (turnover due to species replacement) and Brich (turnover due to changes in species richness), such that Btotal = Brepl + Brich. Filenames for these three measures begin with "beta_tot", "beta_repl", and "beta_rich" for Btotal, Brepl and Brich respectively. Each of these measures can vary between 0 and 1.

We also calculate three measures of species turnover using the betadiver function in the vegan package (Oksanen et al. 2022) with method = NULL, to give species in common (a) in a grid cell between two time periods, as well as species lost (b) and species gained (c). Filenames for these measures begin with "sp_shared", "sp_lost", and "sp_gained" for a, b and c respectively. Values are in numbers of species, with a minimum of 0 and a maximum of the total number of species within a grid cell across both time periods under comparison.

Finally we also provide b and c as proportions of all species observed in the grid cell across both time periods (i.e. proportion of species lost, b / (a + b + c) and proportion of species gained, c / (a + b + c)) as measures of relative species turnover. Filnames for these measures begin with "p_sp_lost" and "p_sp_gained" for the proportion of species lost and gained respectively. Values of both can vary between 0 and 1.

Gridded estimates of each diversity measure are produced in R (R Core Team 2022) as SpatRaster objects using the terra package (Hijmans 2023). They are provided here as A NetCDF file (a single file with each diversity measure x time comparison combination included as a separate variable, giving 120 variables in total) and as GeoTiff files (one file per diversity measure, with one layer per time comparision within each file, as well as a single file of all combinations matching the structure of the NetCDF file).

More information:

The full workflow for deriving the products from the datasets derived from the European presence/absence data product is set out in https://emodnet.github.io/EMODnet-Biology-benthos-trends/ (source markdown documents are also available in the analysis folder of this repository).

References

Cardoso P, Mammola S, Rigal F, Carvalho J (2022). BAT: Biodiversity Assessment Tools. R package version 2.9.2, https://CRAN.R-project.org/package=BAT

Herman, P M J (2022) Summary presence/absence maps of macro-endobenthos in European Seas, based on the EMODNET Biology database. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project Phase IV (EMFF/2019/1.3.1.9/Lot 6/SI2.837974), funded by the by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund. https://www.vliz.be/imis?dasid=8216

Hijmans R (2023). terra: Spatial Data Analysis. R package version 1.7-3, https://CRAN.R-project.org/package=terra

Oksanen J, et al. (2022). vegan: Community Ecology Package. R package version 2.6-4, https://CRAN.R-project.org/package=vegan

R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/

WoRMS Editorial Board (2023). World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. doi:10.14284/170

Code and methodology

See docs/benthos-trends-dataprep and docs/benthos-trends-turnover in this repository for a full description of methodology including relevant code.

Citation and download link

This product should be cited as:

Webb, T.J. (2023) Temporal turnover of macrobenthos in European seas. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project Phase IV (EMFF/2019/1.3.1.9/Lot 6/SI2.837974), funded by the by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund.

Available to download in:

https://www.vliz.be/imis?dasid=8229

Authors

Tom Webb