DOI: 10.5061/dryad.gf1vhhmzt
title: Century-long trends in plant diversity of temperate mountain vegetation are modulated along elevation gradient

description: Understanding how multiple global change drivers interact to shape forest
 plant communities requires a long-term perspective that extends beyond the
 last few decades. Mountain forests, with their strong climatic and
 management gradients, enable the assessment of how global and local
 drivers jointly shape long-term plant diversity patterns. Our objective
 was to detect trends in taxonomic diversity and species distributions
 along the elevational gradient in response to three main drivers of global
 change: climate change, nitrogen deposition, and historical human
 management. Therefore, we resurveyed 56 vegetation plots first recorded in
 the 1920s in temperate montane forests in the Tatra Mountains (Poland),
 spanning ~650 m elevational gradient. We quantified changes in species
 richness and Shannon diversity, community indicator values, species
 turnover, and species elevational optima. Plant diversity increased over
 the course of the century. The increases were strongest at lower
 elevations and weakened upward, with little change or even declines at the
 highest sites. Community indicator values shifted towards higher soil
 moisture and nitrogen and lower grazing pressure. Nitrogen-demanding
 generalist plants increased in frequency, while several oligotrophic or
 acid-tolerant taxa typical of species-poor spruce stands declined. We
 found no consistent warming signal (thermophilization) in the understory
 communities. Community change was more strongly correlated with soil
 reaction and human management legacy than with direct climatic trends. The
 patterns match the cessation of intensive pastoralism in the mid-20th
 century and the recovery of stands previously converted to spruce
 plantations at lower elevations. Species-level responses included frequent
 downward shifts of elevational optima among species typical for
 broadleaved forests, consistent with reduced grazing pressure and changing
 stand structure. The century-long changes in these montane forest plant
 communities were primarily governed by former human management and its
 cessation after establishment of the national park, which outweighed the
 direct community-level effects of recent climate warming. This study
 advances ecological understanding by showing that reliable interpretation
 of biodiversity trends requires very long data records and explicit
 accounting for management history alongside contemporary drivers such as
 climate change and atmospheric deposition.
description: # Century-long trends in plant diversity of temperate mountain vegetation
 are modulated along elevation gradient
 [https://doi.org/10.5061/dryad.gf1vhhmzt](https://doi.org/10.5061/dryad.gf1vhhmzt) ## Description of the data and file structure This dataset contains data analysed as part of a study entitled: "Century-long trends in plant diversity of temperate mountain vegetation are modulated along elevation gradient". The dataset contains five tables and one RMarkdown document. Please refer to the manuscript for a detailed rationale and explanation of these analyses. The data included in this database below includes information from two surveys: historical data from the 1920s and recent data from the 2020s, covering 250 species (which may have been observed during one or both sampling periods) across 56 study sites. Analysis structured as follows: **1)** Calculation of mean annual temperatures for meteorological station in Zakopane; **2)** Estimation of relocation error; **3)** Taxonomic diversity (species richness, Shannon diversity index, regression to mean); **4)** Analyses of Ecological Indicator Values (EIV) and Disturbance Indicator Values (DIV). **5)** Modelling of altitudinal optima; **6)** Permutational Multivariate Analysis of Variance and Similarity Percentages; ### Files and variables #### File: plotsChanges.csv **Description:** The file contains information on the changes that have occurred in the study plots ##### Variables * Key: plot ID/plot "Key" * Error: relocation error of plot * Altitude: altitude of plot in m a.s.l. #### File: siteXenvironment.csv **Description:** environmental variables of analysed plots ##### Variables * Altitude: altitude of plot in m a.s.l. * Aspect..degrees.: aspect of plot in degrees * Slope..degrees.: slope of plot in degrees * Longitude: Longitude * Latitude: Latitude * Key: plot ID/plot "Key" * Age: period of the studies - can be "Historical" (from 1920s) or "Recent" (surveyed in 2020s) #### File: siteXspecies.csv **Description:** Table with species abundance; sites in rows and species in columns. Species are coded in Latin names with a dot between the generic and species name (and sometimes a lower rank). #### File: siteXspecies01.csv **Description:** Same as siteXspecies.csv but with presence/absence data. Species are coded in Latin names with a dot between the generic and species name (and sometimes a lower rank) #### File: speciesXtraits.csv **Description:** Table with Ecological Indicator Values for European Flora (EIVE) and Disturbance Indicator Values for European Flora (DIVE); species in rows and environmental variables in columns. Species are coded in Latin names with a dot between the generic and species name (and sometimes a lower rank) ##### Variables * Moisture: value of ecological indicator value for soil moisture * Nutrients: value of ecological indicator value for soil nitrogen * Reaction: value of ecological indicator value for reaction * Light: value of ecological indicator value for light availability * Temperature: value of ecological indicator value for species thermal conditions * Disturbance.Severity: value of disturbance indicator value for disturbance severity * Disturbance.Frequency: value of disturbance indicator value for disturbance frequency * Grazing.Pressure: value of disturbance indicator value for grazing pressure * Soil.Disturbance: value of disturbance indicator value for soil disturbance #### File: Century-long_trends_in_plant_diversity.md **Description:** RMarkdown document, which will guide you through all the major analyses that have been prepared for the manuscript #### File: Generalized_Dissimilarity_Model.md **Description:** RMarkdown document to guide you through the analyses that have been added to the manuscript on Generalized Dissimilarity Models. ## Code/software All analyses and figures were calculated and drawn in R 4.1.2 (R Development Core Team 2021). We used packages for data wrangling, statistical analyses, and graphical presentation, including: dplyr, ggplot2 , ggpubr, vegan, eHOF, tidyr, FD and 'gdm'.