DOI: 10.5061/dryad.3ffbg79zh
title: Stably coexisting communities deliver higher ecosystem multifunctionality

description: Linking the processes determining species coexistence and effects of
 biodiversity on ecosystem functioning is important for a mechanistic
 understanding of how species loss impacts ecosystems. There are good
 theoretical reasons to expect stably coexisting communities to deliver
 higher ecosystem functioning, as niche differences should promote
 coexistence and complementarity, however, there is still little empirical
 evidence to demonstrate this relationship. We present a novel experimental
 approach to tackle this question, in which we first measured interaction
 coefficients and intrinsic growth rates for 12 grassland species and used
 population models to estimate coexistence5. We then assembled 48
 three-species communities, predicted to differ in their degree of
 coexistence and measured seven above and belowground functions. Here we
 extend findings demonstrating that biodiversity increases
 multifunctionality to show that amongst communities with the same initial
 diversity, multifunctionality is higher when all the species are predicted
 to coexist. Decomposing coexistence into the influence of niche and
 fitness differences showed that multifunctionality was high in niche
 differentiated communities but also in those with a single highly
 competitive species. We further examined the effect of indirect
 interactions, which provide an alternative mechanism of coexistence in
 multispecies communities, and found that they also provided an alternative
 route to high multifunctionality. Our results point the way to a
 unification of coexistence and biodiversity theory and to a more
 mechanistic understanding of the functional effects of biodiversity
 change.
description: # Structural_coexistence_multifunctionality In this folder you may find
 the data and code for the analysis of "Stably coexisting communities
 deliver higher ecosystem multifunctionality". ## What can you find in
 this project? ### a) data.zip Please refer to the METADATA text file that
 regroups all information on the data folder, and contains a list of
 abbreviations for each variable that can be found in this folder. ####
 *coexistence and experimental design* In the data folder, you can find a
 subfolder called "species alphas and lambdas" containing all
 competition matrices used during the analysis, as text files which names
 start with "biommatrix", and their associated standard errors,
 which are named "SE_biommatrix". The species intrinsic growth
 rates are also present in this folder under the name starting with
 "biomintrinsic". These matrices are derived over the whole year
 2020 (combining June and August sampling for this year), or only for June
 2020 sampling, as this month was used to compute predictions for 2022
 species evenness and years to extinction. Two text files,
 "plot_info" and
 "structural_coexistence_experimental_design", describe the
 organisation of the plots in our study, which species compose them and
 what are their predicted coexistence strength and mechanisms. The
 "structural_coexistence_experimental_design" file itself is
 derived from another text file "all_triplets_experiment" which
 lists structural coexistence values for all possible triplets from our
 pool of species. The environment image
 "structural_coexistence_image" also contains the same
 information but pre-loaded for convenient sourcing. #### *ecosystem
 functions* A set of ecosystem functions and data sampled in our triplet
 experiment may be found in this data folder. Each text file name starts
 with the month and date of its sampling. The functions measured are: *
 biomass in May and August 2022 * betaglucosidase, in May and August 2022 *
 phosphatase in May and August 2022 * herbivory damage in May 2022 *
 pathogen damage in May 2022 * root biomass in August 2022 * decomposition
 in April 2023 Aside from these ecosystem functions, the percentage cover
 of each species present in the plot was also recorded in June and August
 2022. ### b) R functions This repository contains two folders that
 regroups functions from previous studies: * the folder
 "anisoFun_functions.zip" contains functions from the paper:
 "Structural asymmetry in biotic interactions as a tool to understand
 and predict ecological persistence.", by Allen‐Perkins, Alfonso, et
 al., *Ecology Letters* (2023). This code was used to compute the minimum
 distance to exclusion variable, a measure of coexistence strength. * the
 folder "structural_coexistence_functions.zip" contains a set of
 functions from the paper: "A structural approach for understanding
 multispecies coexistence." by Saavedra, Serguei, et al., *Ecological
 Monographs* (2017). This code was slightly adapted by me and it was used
 to compute all measure of coexistence mechanisms: niche and fitness
 differences as well as indirect interactions. ### c) code #### *main
 analyses* This project contains a set of original code. These code files
 are numbered from (1) to (5) and they contain the main analyses of the
 study. Each file can be run independently, as they all source all files
 that are needed to run the analysis. However, the code was build in this
 specific order and the logic of the analysis might be easier to follow if
 each file is read in this order. #### *extra code* Finally, the repository
 contains some files that are satellites to the main analyses. These files
 don't need to be read for the main analysis to function, as their
 output is already saved in the "data" folder. * The first one,
 "structural_coexistence_control_nitrogen.qmd" is a quarto
 document that I used to compute all coexistence mechanisms and minimum
 distance to exclusion for the set of 48 triplets in this experiment. The
 format of the code file is different because this was a file created
 before the start of the experiment, in 2021. * The second one,
 "time_to_extinction_tool_no_SE.R" was authored by Oscar Godoy
 and modified by me, in order to compute the predicted evenness and
 abundances for our communities. Its output are the text files
 "bh_predicted_evenness_15y_2022",
 "abundances_predictedBH_all_plots" and
 "years_to_extinction_triplets", they are analysed in the main
 code file number (5). * The third one,
 "multimembership_function.R" contains functions that I used to
 run multimemberships models more effectively. ## Contact information If
 you wish to get more information on the code or if you have questions,
 feel free to contact me using this email address:
 *[caroline.daniel@unibe.ch](mailto:caroline.daniel@unibe.ch)*