DOI: 10.6084/m9.figshare.26324338
title: <b>EcoTol: a global dataset of plants ecological tolerance to shade, drought, waterlogging, cold and low nutrients coupled with information on functional traits, phylogeny and species distribution</b>

description: <b>Abstract</b>The ability to survive the shortage of an abiotic factor (light, water, nutrients) under competition with other species makes up a species’ ecological tolerance. Understanding the interspecific differences in ecological tolerance can provide insight into composition and performance of actual plant communities. However, data on species ecological tolerances are still scant and/or not readily available.For this reason, we present EcoTol, a dataset including species-level ecological tolerance rankings for shade, drought, cold, waterlogging and low nutrient for 2373 species worldwide. Tolerance scoring in EcoTol is expressed on a three-point scale, and each species is scored as either intolerant, intermediate or tolerant to a given abiotic factor.Since species ecological tolerance depends on many biological, genetic and environmental factors, we collated tolerance data with multiple ancillary information including metadata related to species’ biology, functional traits, species phylogenetic information and species distribution data. Finally, we provide custom R functions to query and subset EcoTol from external data sources and to connect it with updated bioclimatic information.We expect that the comprehensive scope of EcoTol will strongly increase the use of tolerance scores in large scale analyses, allowing exploration of multiple research question spanning from macroecology to trait-based ecology.<b>Contents description</b>The EcoTol_dataset folder includes the following files (described in detail below):<b><i>Main data file:</i></b>- EcoTol.csv<b><i>Ancillary files:</i></b>- LatLong.rds- phylotree3p.tre- R_functions.R- Vignette.pdf<b>Content description by file:</b><b><i>1) EcoTol.csv </i></b>It contains the following information (ordered by their appearance in the dataset):**Usage note**: all the missing values in EcoTol are marked as NA.<b><i>Taxonomic information </i></b>- *Family*. The family to which each species belongs.- *Genus*. The genus to which each species belongs.- *Species*. Species binomial. Note: taxonomic backbone is the World Flora Online.<b><i>Metadata</i></b><i>Woodiness</i>. A categorical variable with three levels: woody, non-woody, variable. Following Wenk et al. (2024), woody refers to those plants that produce secondary xylem (true wood). non-woody are those plants that never produce lignified stems. variable include intermediate cases between woody and non-woody (e.g., plants with lignified stems that do not produce secondary xylem). AngioGymno*. A categorical variable with two levels: Angiosperm, Gymnosperm. To further identify woody and non-woody plants that are either lianas or vines, respectively, we also added a column named ‘SelfSupporting’ that contains binary information (Yes/No). <i>Deciduousness</i>. A categorical variable with two levels: deciduous, evergreen.<i>LeafType</i>. A categorical variable with two levels: broad-leaved (bl), needle-leaved (nl). <i>LifeCycle</i>. A categorical variable with three levels: perennial, annual, other. Following Wenk et al. (2024), 'perennial' refers to plants that lives for three or more growing seasons, with an exact lifespan that is indeterminate. 'annual' refers to plants that live for up to 1 year after germinating, completing its life cycle in a single growing season. 'other' indicates alternative combinations in between 'perennial' and 'annual' (e.g., biennial). <i>LifeForm</i>. A categorical variable with four levels: phanerophyte, therophyte, hemicryptophyte, other. Are classified as 'phanerophyte' those species with surviving buds or shoot apices that are borne on shoots which project into the air (at least &gt; 25 cm from the ground level), as 'therophytes' those plants that complete their life cycle from seed to seed and die within a season, and as 'hemicryptophyte' those species which buds or shoot apices are situated at the level of the soil surface.<i>GrowthForm</i>. A categorical variable with four levels: tree, shrub, herb, other. Plants classified as 'tree' are tall, woody, perennial plants, usually with a single main trunk, and its leaves predominantly elevated above the ground surface. 'shrubs' are those plants that are woody but differ from trees because they are generally short, have leaves distributed almost across the entire plant height, many relatively narrow stems arising at or near ground level (note that the definition of shrub is complex and subject to many different interpretations, see Wenk et al. (2024)). 'herbs' are those seed-bearing plants that do not have a woody above-ground stem.Metadata were compiled from multiple sources including the GIFT database (Weigelt et al., 2020, J. Biogeog. 47, 16-43), published articles (Poorter et al. 2009 *New Phytol.* 182, 565-588; Poorter et al. 2010 *J. Exp. Botany* 61, 2043–2055; Poorter et al. 2019 *New Phytol.* 223, 1073-1105; Puglielli et al. 2021 *New Phytol.* 229, 308-322), and web searches.<b><i>Functional traits </i></b>LA (mm<sup>2</sup>): individual size of a leaf. One-sided projected area of a leaf. Nm (mg g<sup>-1</sup>): leaf nitrogen content per unit dry mass.PH (m): maximum plant height.SLA (mm<sup>2</sup> mg<sup>-1</sup>): specific leaf area. Ratio of leaf area to its dry mass.SSD (mg mm<sup>-3</sup>): stem specific density. Stem dry mass to fresh volume ratio.SM (mg): seed dry mass.Trait values were obtained from Carmona et al. (2021, Nature 597, 683–687).<b><i>Tolerance data </i></b><i>Shade</i>. Shade tolerance. Unit less numerical variable indicating the level of shade tolerance of a species (species ability to survive in consistently shaded habitats). It assumes the following values: 3 = tolerant, 2 = intermediate, 1 = intolerant. <i>Drought</i>. Drought tolerance. Unit less numerical variable indicating the level of drought tolerance of a species (species ability to survive under long-term drought). It assumes the following values: 3 = tolerant, 2 = intermediate, 1 = intolerant.<i>Waterlogging</i>. Waterlogging tolerance. Unit less numerical variable indicating the level of waterlogging tolerance of a species (species ability to survive under long-term waterlogging). It assumes the following values: 3 = tolerant, 2 = intermediate, 1 = intolerant. <i>LowNutr</i>. Unit less numerical variable indicating the level of low nutrient tolerance of a species (species ability to survive in chronically nutrient deprived soils for a long time). It assumes the following values: 3 = tolerant, 2 = intermediate, 1 = intolerant. <i>Cold</i>. Unit less numerical variable indicating the level of freezing tolerance of a species (species ability to survive in habitats with prolonged freezing periods). It assumes the following values: 3 = tolerant, 2 = intermediate, 1 = intolerant. <b><i>2) </i></b><b><i>LatLong.rds</i></b> An R .rds file containing an object of class list. The file contains species occurrences (longitude-latitude combinations) that were obtained from GBIF (accessed in 03/2024) and cleaned following standard procedures (see main text). This file is used to query the CHELSA database (Karger et al., 2018 *Scientific Data* 4, 170122) to retrieve target bioclimatic data using the custom get_clim() function included in the R_functions.R file below.<b><i>3) phylotree3p.tre</i></b> A file containing the phylogenetic tree for all the species in the dataset. The phylogenetic tree was obtained using the phylomaker function of the V.PhyloMaker R package (Jin and Qian 2019, *Ecography* 42, 1353-1359) using the 'scenario 3' (see function help for details).<b><i>4) CHELSA_bioclim.txt</i></b>A text file consisting of two columns. The first one includes the URLs to all the CHELSA bioclimatic data (see https://chelsa-climate.org/bioclim/ for details). The second column includes the 'shortname' for each variable (e.g., bio1). This file is internally used by one of the custom R function (see file below)<b><i>5) R_functions.R</i></b>An R script file containing the custom functions for data handling and matching EcoTol with CHELSA database.<b><i>6) Vignette.pdf</i></b>It contains a worked example of how to use the custom R functions.