DOI: 10.5061/dryad.wstqjq30w
title: Data and code from: Phenotypic plasticity masks evolutionary change in grassland plant traits in response to land use abandonment

description: Traditionally-managed grasslands are among the most biodiverse habitats in
 Europe, but are threatened by land use abandonment. While the negative
 impacts of grazing and mowing cessation on species richness are well
 documented, little is known about potential evolutionary changes within
 species. Yet, intraspecific functional diversity is critical for
 successful grassland restoration and ensuring adaptive potential to future
 climate change. To disentangle the heritable and non-heritable components
 of population-level response to land use change in semi-natural
 grasslands, we examined 22 populations of a common grass, Briza media,
 from grazed sites and sites where grazing was abandoned, with resulting
 tree and shrub encroachment. We measured a range of traits under field
 conditions and following clonal propagation under common garden
 conditions. Field surveys revealed that abandonment resulted in litter
 accumulation, greater shading by woody and herbaceous vegetation, and
 lower temperature and moisture fluctuations compared with grazed sites.
 Plants responded to conditions at abandoned sites with phenotypic
 plasticity in traits that enhanced competitive ability for light (greater
 height and specific leaf area) but reduced tissue protection against
 stress (lower dry matter content). However, when the same genotypes were
 measured after clonal propagation in common conditions, countergradient
 variation was apparent, with heritable shifts towards increased tissue
 protection in populations from abandoned sites. When measured under field
 conditions, trait diversity was higher in sites with higher levels of
 shading and productive sites with higher variation in light conditions.
 However, high heritable trait diversity was instead characteristic of
 grazed sites with high densities of flowering B. media individuals. These
 findings demonstrate that land use change can cause evolutionary shifts
 and changes in heritable trait diversity that are masked in the field by
 phenotypic plasticity. Hence, the assessment of functional trait variation
 based on field observations is not a reliable way to assess the genetic
 variation essential for population adaptive potential.
description: # Data and code from: Phenotypic plasticity masks evolutionary change in
 grassland plant traits in response to land use abandonment Dataset DOI:
 [10.5061/dryad.wstqjq30w](https://doi.org/10.5061/dryad.wstqjq30w) ##
 Description of the data and file structure All data analyses were done in
 R Studio Version 2023.06.0+421 (2023.06.0+421). Before you start using the
 script, please run all data files first, because some graphs and tables
 contain information from several csv files.  To make all data work,
 please, run the following packages: library(lme4), library(car),
 library(performance), library(ggplot2), library(vegan),
 library(tidyverse), library(marginaleffects), library(ggplot2),
 ibrary(ggsci), library(patchwork), library(ggpubr), library(hypervolume).
 The input files to replicate the statistical analyses are the following:
 `Briza_field_2022data_correct.csv` This is the main file that contains
 data for plant above and belowground traits measured in the field and
 common conditions after 8 months of propagation in commin garden. To
 analyse data from it, we used ANOVA and lmer. `fieldAMF_colonisation.csv`
 This is an additional file that contains information about the percent of
 AMF (Myc in data) colonisation. For each site (SiteID), there are five
 replicates, and we were using the ink-vinegar method described in
 Vierheilig et al. 1998.   `light_data.csv` This is an additional file that
 contains information about canopy openness and mean proportion of
 photosynthetically active radiation below compared with above the
 herbaceous vegetation that we measured using fish-eye pictures and Gap
 Light Analyzer (GLA) 2.0, Version 2.0 (Frazer et al., 1999). 
 `list_of_variables1.txt` This is an additional file that contains
 information about variables that we have in all data sets. 
 `Site_means.csv` This is an additional file that contains information
 about means and coefficient of variation of site characteristics such as
 soil properties (content of phosphorus, pH, bulk density, etc.), light
 characteristics (canopy openness, soil temperature), and vegetation
 (density of flowering Briza media, plant litter mass, etc.). A more
 detailed list of variables can be found in list_of_variables1.txt.
 `soil_data.csv` This is an additional file that contains information about
 physical (bulk density) and chemical (pH, P, N, C) soil properties. 
 `Vegetation_data.csv` This is an additional file that contains information
 about vegetation data for our sites. The number of the 0.25 x 0.25 m plot
 (1, 2, 3), species richness in 0.25 x 0.25 m plots, density of vegetative
 B. media shoots in 0.25 x 0.25 m plots, and density of flowering *B.
 media* individuals in 2 x 2 m plots.  The R script to run all analyses is
 the file `full_script_fordryad.r`. At the beginning of the script, you can
 find all the packages that will be needed and the data files. If you use
 RStudio, you'll find a "Show Document Outline" button.
 Clicking it will reveal a menu with all table and figure numbers in the
 text for easy navigation. ## Code/software R Studio Version 2023.06.0+421
 (2023.06.0+421).