DOI: 10.5061/dryad.xgxd254r9
title: Interspecific trait differences drive plant community responses on serpentine soils.

description: Serpentine ecosystems are characterised by multiple environmental
 stressors: high levels of trace metals such as nickel (Ni), low
 availability of macronutrients and low water retention. These harsh
 environmental conditions exert a strong selective force on the vegetation,
 but their effect on community assembly processes and the functional trait
 composition remains unknown. In 26 plots on four serpentine sites on
 Lesbos Island (Greece), we measured six leaf functional traits related to
 resource acquisition and stress resistance on the 20 most abundant plant
 species. We quantified the proportion of variance explained by inter- and
 intraspecific traits difference and tested if individual species show
 changes in trait values explained by soil Ni content. We investigated the
 adaptive value and the community level changes for each trait along the
 natural soil Ni gradient using a mixed model approach and functional
 diversity analyses. We also tested the role of the abundant serpentine
 endemic and Ni-hyperaccumulating species Odontarrhena lesbiaca in
 driving these patterns. Intraspecific variation explained by soil Ni
 content is smaller than 4%, and most of the variance is explained by
 interspecific differences in trait values. Most species do not show
 significant changes in trait values in response to soil Ni. At the
 community level, low specific leaf area and small and thick leaves are
 selected on high Ni soils. Functional diversity analyses suggest a shift
 towards a stress tolerance syndrome (thick and small leaves with low SLA
 values), and an increase in functional diversity on Ni rich soils.
 However, these patterns are driven by the increasing abundance
 of O. lesbiaca. The endemic Ni hyperaccumulator has a stress
 tolerance strategy with small thick leaves and low SLA, while the
 community of broadly distributed species show an increase in trait values
 related to dominance and fast growth. Synthesis. Intraspecific variation
 in leaf trait responds little to soil metal toxicity. Endemic species
 harbour unique trait values compared to species with broad distribution
 which should justify their conservation as a priority.
description: # Interspecific trait differences drive plant community responses on
 serpentine soils.
 [https://doi.org/10.5061/dryad.xgxd254r9](https://doi.org/10.5061/dryad.xgxd254r9) ## Description of the data and file structure Plant species abundance, functional traits and related environmental data associated with the article "Interspecific trait differences drive plant community responses on serpentine soils" in Journal of Ecology.  This file contains the raw data, R scripts and ready-to-use data in a .RDS file containing all data used in the study.  The five R scripts contain all necessary code to reproduce all results and figures included in the study. The four numerated R files (1. Data preparation, 2. Exploratory analyses, 3 Community trait analyses and 4. Intraspecific trait variation) should be run in the order 1 to 4. The Functions.R file contains functions that are called by the other four scripts. dataserpentine.RDS contains all data used to reproduce the study and that are also provided as raw data. The "raw_data" file contains 4 spreadsheets with respectively 1) the abundance of each species in each plot, 2) the traits measured on each individual plant, 3) the life cycle of each plant species and 4) soil variables measured in each plot. **Files and variables:** raw_data contains four files in .xlsx format. **Description** **TraitsITV.xlsx** * Sp: the species code used throughout the analyses and script. * site: code for each site studied: Amp (Ampeliko), Lout (Loutra), Oly (Olympos) and Vat (Vatera). * samplenu: sample identifier. * species: binomial name of each species. * LL: leaf length in cm. * LW: leaf width in cm. * LeafArea: leaf area in cm<sup>2</sup>. * LDMC: leaf dry matter content (in g kg<sup>-1</sup>). * SLA: specific leaf area (in m<sup>2</sup> kg<sup>-1</sup>), the area of a leaf divided by its dry mass. * LT: leaf thickness (in μm), calculated as 1/(SLA*LDMC)*10000. * C: leaf carbon content (in % of dry mass). * N: leaf nitrogen content (in % of dry mass). **soil.xlsx** * ID: identifier for each site. * Site: code for each site studied: Amp (Ampeliko), Lout (Loutra), Oly (Olympos) and Vat (Vatera). * Plot: code for each plot. * Ca: soil calcium content (in % dry mass). * Fe: soil iron content (in % dry mass). * K: soil potassium content (in % dry mass). * Mg: soil magnesium content (in % dry mass). * Co: soil cobalt content (in mg kg<sup>-1</sup>). * Cr: soil chromium content (in mg kg<sup>-1</sup>). * Cu: soil copper content (in mg kg<sup>-1</sup>). * Mn: soil manganese content (in mg kg<sup>-1</sup>). * Na: soil sodium content (in mg kg<sup>-1</sup>). * Ni: soil nickel content (in mg kg<sup>-1</sup>). * P : soil phosphorus content (in mg kg<sup>-1</sup>). * Zn: soil zinc content (in mg kg<sup>-1</sup>). * Richness: observed species richness (number of different species) counted in each plot. * Greenbiom: dry weight (in g) of the biomass of living material. * SumBiomObs: dry weight (in g) of the biomass of plant species for which functional traits were measured and that are used in the study. * PercBiomObs: proportion of the total biomass in each plot represented by the species on which traits were measured. **abundance.xlsx** * Site: code for each plot studied: Amp (Ampeliko), Lout (Loutra), Oly (Olympos) and Vat (Vatera). * All other columns contain the biomass of each species in each plot (in g of dry weight). Species codes are specified in the traitsITV.xlsx dataset. **Life_cycle.xlsx** (this dataset is for information only and is not used in the code provided and is not included in the .RDS data). * Sp: species code. * species: binomial name of each species * cycle: describes if a species is annual or perennial **Code/Software** R is required to run the script and reproduce the results. The script was created using R 4.4.1. **Access information** Other publicly accessible locations of the data: * [https://github.com/guildelhaye/serpentine_community](https://github.com/guildelhaye/serpentine_community)