Data and code for: "Phytoplankton biodiversity is more important for ecosystem functioning in highly variable thermal environments", Bestion et al 2020 PNAS
| Main Authors: | Bestion, Elvire, Haegeman, Bart, Alvarez Codesal, Soraya, Garreau, Alexandre, Huet, Michèle, Barton, Samuel, Montoya, José M. |
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| Format: | Article Journal |
| Terbitan: |
, 2021
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/5078310 |
Daftar Isi:
- ############################################################################################################### Data and code for: Bestion E, Haegeman B, Alvarez Codesal S, Garreau A, Huet M, Barton S, Montoya J.M. 2021. Phytoplankton biodiversity is more important for ecosystem functioning in highly variable thermal environments. Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.2019591118 ############################################################################################################### Composed of 6 datasets, two R files and two text files : -------------------------------------------------------- * datasets (as .csv) - the main dataset: BEF_dataset.csv - the thermal performance dataset from Barton and Yvon-Durocher 2019 : Barton_thermal_performance.csv - the growth curve data at 3 temperatures (20,25 and 30°C) from Barton and Yvon-Durocher 2019 : Barton_growth_curve_parameters.csv and Barton_growth_curve_points.csv - the discrimination accuracy info for the competition between pair of species : table_discrimination_accuracy_species_pairs.csv - the competition between pair of species dataset (for pairs correctly discriminated): competition_species_pairs.csv * code - the functions used in the main analysis : 1_functions_for_Bestion_et_al.R - the R script for the main analysis : 2_analyses_for_Bestion_et_al.R * text files - the R session information with information about package version for reproductibility: R_session_info.txt - the README.txt (this file) Composition of the BEF dataset (BEF_dataset.csv) -------------------------------------------------- Results of the biodiversity-ecosystem functioning experiment, as a csv file, with columns: - date : the date of the measurement - day_fact: the day of the mesurement as a factor (either day 5 or day 15) - temperature: the temperature fluctuation treatment, 3 treatments, either T25 (constant 25°C), T22-28 (fluctuating between 22 and 28°C every other day) or T19-31 (fluctuating between 19 and 31°C every other day) - M : the composition of the community (e.g. DI a community composed of species D and species I, F a community composed only of species F) - R: the richness of the community (1,2,3,4,6 or 12 species) - ln_R: the log transformed richness - P: the partition id (5 independent partitions of the species pool were drawn, following Bell et al 2009) - rep : the replicate id (3 replicates per community within a partition, named 1 to 3) - growth_plate_number: the id of the growth plate (18 24-well plates) - growth_well_number: the well number within a plate (A1 to D6) - sample_identity: an id composed of the temperature treatment, the growth plate number and the growth well number - SA to SL: the species presence-absence status for each of the 12 species (species A to species L), with 1: species present within the community, 0: species absent - cells_per_ml: the abundance in number of cells per ml at the time of the sampling - ln_cells_per_ml: the log transformed abundance - chlo_a_pg_sum_per_ml: the total chlorophyll a content at the time of the sampling in pg.ml-1 - ln_chlo_a_pg_sum_per_ml: the log transformed chlorophyll a - biomass_pgC_sum_per_ml : the total biomass at the time of the sampling in pg C ml-1 - ln_biomass_pgC_sum_per_ml : the log transformed biomass Composition of the thermal performance dataset (Barton_thermal_performance.csv) from Barton et Yvon-Durocher 2019 ------------------------------------------------------------------------------------------------------------------- - Species_name : the scientific name of each species - Species_alpha : a one-letter species id (A to L) used in the BEF experiment - Phylum: the phylum of the species - lnc_mu, Ea_mu, Eh_mu, Th_mu, Topt_mu, Tmax_mu: the parameters of the Schoolfield model for growth rate calculated by Barton et Yvon-Durocher 2019 Composition of the two datasets for the growth curve data from Barton et Yvon-Durocher 2019 --------------------------------------------------------------------------------------------- * Barton_growth_curve_parameters.csv - temperature: the temperature at which the growth was measured (either 20, 25, 27 or 30°C) - Species_name: the scientific name of each species - LOG10Nmax, LOG10N0, mumax: the parameters from the growth function * Barton_growth_curve_points.csv - Species_name:the scientific name of each species - temperature: the temperature at which the growth was measured - day: the day of measurement - LOG10N: the log10-transformed abundance at the day of measurement Composition of the dataset for discrimination accuracy table_discrimination_accuracy_species_pairs.csv --------------------------------------------------------------------------------------------------------- - M: the identity of each of the two-species communities tested in the BEF experiment - A to L: the discrimination accuracy from the randomforest analysis of the species A to L in the community - mean_species: the mean discrimination accuracy - minimum_species: the discrimination accuracy of the species with the worse discrimination accuracy - over_threshold: 0 if the minimum_species is <60% accuracy, 1 if >60% Composition of the dataset for competition species pairs: competition_species_pairs.csv ------------------------------------------------------------------------------------------ - temperature: the temperature fluctuation treatment (T25, T22-28, T19-31) - focal_species: the identity of the focal species (A to L) - second_species: the identity of the second species (B to L) - abundance_focal_species_in_monoculture: the cell abundance of the focal species when grown in monocultures - abundance_focal_species_in_biculture: the cell abundance of the focal species when grown in bicultures