Data and code from: Phenotypic plasticity masks evolutionary change in grassland plant traits in response to land use abandonment
Data files
Jan 08, 2026 version files 171.17 KB
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Briza_field_2022data_correct.csv
60.22 KB
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fieldAMF_colonisation.csv
2.61 KB
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full_script_fordryad.r
80.91 KB
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light_data.csv
4.13 KB
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list_of_variables1.txt
6.49 KB
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README.md
3.12 KB
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Site_means.csv
6.58 KB
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soil_data.csv
4.85 KB
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Vegetation_data.csv
2.26 KB
Abstract
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.
Dataset DOI: 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).