Data from: Biodiversity–ecosystem function relationships change in sign and magnitude across the Hill diversity spectrum

# Biodiversity-ecosystem function relationships change in sign and magnitude across the Hill diversity spectrum ## Contributing authors Michael Roswell1 mroswell@umd.edu Tina Harrison2 tinaharrison09@gmail.com Mark A. Genung2 mark.genung@louisiana.edu 1. Dept. of Entomology, University of Maryland, College Park, MD 20742, USA 1. Dept of Biology, University of Louisiana, Lafayette, LA 70503, USA ## Synopsis This repository contains data and code for our submission to the Phil Trans RSB special issue on Biodiversity monitoring, "Biodiversity-ecosystem function relationships change in sign and magnitude across the Hill diversity spectrum". The repo also contains lots of notes and the starts of ideas that are not in the MS. Upon article acceptance, the relevant components will be migrated to a permanent archive (e.g., Dryad & Figshare). ## Keywords abundance, biodiversity, diversity profile, ecosystem function, Hill number, rarity ## Summary Motivated by accelerating anthropogenic extinctions, decades of biodiversity-ecosystem function (BEF) experiments show that ecosystem function declines with species loss from local communities. Yet, at the local scale, changes in species' total and relative abundances are more common than species loss. The consensus best biodiversity measures are Hill numbers, which use a scaling parameter, ℓ, to emphasize rarer versus more common species. Shifting that emphasis captures distinct, function-relevant biodiversity gradients beyond species richness. Here, we surmised that Hill numbers that emphasize rare species more than richness may distinguish large, complex, and presumably higher-functioning assemblages from smaller and simpler ones. In this study, we tested which values of ℓ produce the strongest BEF relationships in community datasets of ecosystem functions provided by wild, free-living organisms. We found that ℓ values that emphasized rare species more than richness most often correlated most strongly with ecosystem functions. As emphasis shifted to more common species, BEF correlations were often weak and/or negative. We argue that unconventional Hill diversities that shift emphasis towards rarer species may be useful for describing biodiversity change, and that employing a wide spectrum of Hill numbers can clarify mechanisms underlying BEF relationships. ## Repo Organization Four directories. Anything used in the published manuscript is contained in "code", "data", or possibly "figures". "Rmds" contains notes and ideas not included directly in the MS. Within the three directories with publication-relevant content, the content for the published MS will be at the top level of the directories, additional files from manuscript preparation may be found in "archive" subdirectories. - "code/" contains .R files for data wrangling, analysis, and producing figures. - "data/" contains files of various sorts, including source and derived binaries, produced and manipulated along the workflow from downloading from a repository to analyses - "figures/" may be empty on git, but is the destination directory of any graph produced by the code - "Rmds" contains .rmd documents comprised of text and code developed for this project. It should be possible to run all scripts in the top level of "code/" from the parent directory to recreate all analyses and figures in the published MS. For archived files, mileage will vary; we recommend reaching out to the authors directly with any questions about this content. ## File organization ``` Hill-BEF | README.md | .gitignore | ----- code | | Download_BEF_data.R # code that pulls datasets from online repositories. | | format_BEF_data.R # format all datasets in similar way | | BEF_correlation_analysis.R # compute correlations and make graphs | | cartoon_fig.R # generate fake data to illustrate methods | ----------- archive | | | towards_general_partition.R # run Tina's partitions on any data (now lefcheck) | | | simulate_correlations_basic.R # explore parameter space for underlying, abstract, non-biological relationships | | | BEF_Hill_Forests_Feb22.R # explores diversity-ef relationships across ell-gradient and spatial scale for tropical forest datasets | | | BEF_HIll_Forests2_Feb22.R # looks v similar to file without 2 in name. | | | Tina_paritition.R # minor changes from Tina's code | ----- data | | lecheck.csv # key data from Lefcheck figshare | | bee_data.rds # data download from Genung et al. 2022 dryad | | bci.rdata # data download from Condit et al. 2019 dryad | | PA_biomass.csv # forest data Pasoh, Malaysia | | VB_biomass.csv # forest data Volcán Brava, Costa Rica | | YA_biomass.csv # forest data Yasuni, Ecuador | | fish_for_analysis.csv # formatted reef fish data | | bees_for_analysis.csv # formatted pollination data | | bci_for_analysis.csv # formatted BCI data | | team_forests_for_analysis.csv # formatted TEAM network forest data | | bef_data_for_analyses.csv # harmonized data for analyses | ----- figures | | # this directory contains many .pdf outputs that can be recreated with code. | ----- Rmds | | Hill_Postulae.Rmd # some general properties of Hill numbers | | Jensens_inequality_with_weights.Rmd # sketch of Jensen's inequality | | empirical_ellBEF.Rmd # notes and snippets used in MS prep | | lefcheck_data_notes.Rmd # super early-stage project notes ``` # Use and licensing: Condit et al. 2019 data are not subject to copyright and are available under a CC 1.0 license from [https://doi.org/10.15146/5xcp-0d46](Dryad) Lefcheck et al. 2021 data are used under a CC BY 4.0 license and are available from [https://figshare.com/articles/dataset/Species_richness_and_identity_both_determine_the_biomass_of_global_reef_fish_communities/16847029?file=31149808](figshare) Genung et al. 2022 data are not subject to copyright and are available under a CC 1.0 license from [https://datadryad.org/stash/dataset/doi:10.5061/dryad.qnk98sfkc](Dryad) The data from Cavanaugh et al. 2014 GEB was originally available from the now-defunct TEAM network. We are republishing these data to make them available again. We reached out to data holders to discuss this. Other materials (e.g. code, figures) present here are freely available under a CC BY 4.0 license. You can cite this dataset by ...(to be updated upon article acceptance)