DOI: 10.5061/dryad.83bk3jb1w
title: Data from: Limited directional change in mountaintop plant communities over 19 years in western North America

description: Plant communities on mountain summits are commonly long-lived,
 cold-adapted perennials with low dispersal ability. These characteristics
 in tandem with limited area to track suitable conditions make these
 mountain communities potentially highly vulnerable to climate change, and
 indicators of climate change impacts. We investigated temporal changes in
 plant communities on 29 arid mountain summits across eight study regions
 in California and Nevada, USA over 19 years. We analyzed community
 dynamics in terms of species richness, turnover, gain and loss of
 functional groups, and relative abundance of functional groups. First,
 across all summits and regions, we found no change in species richness
 over time. Second, there was relatively high species turnover (21.7%)
 between the five-year survey intervals, but turnover was not significantly
 different from random expectation. Within functional groups, forbs had the
 greatest proportion of gains and cushions had the greatest proportion of
 losses. Third, qualitative abundance categories presented a small but
 consistent signal of decrease in the relative abundance of cushions,
 graminoids and shrubs/trees over the study period. Across a broad
 geographic scale and nearly two decades, community patterns were widely
 similar, suggesting that climate change has not impacted local
 colonization or extirpation of mountaintop species in this arid region.
 These findings support observed differences in response to climate change
 between temperature-limited and water-limited regions globally, and
 highlight the lagged and variable nature of high elevation systems. Our
 findings fill a major data gap on alpine plant community responses to
 climate change in the western United States and bolster the importance of
 long-term ecological monitoring with rapid climate change.
description: # Limited directional change in mountaintop plant communities over 19
 years in western North America Repository for code, data, and figures
 related to Goff et al. manuscript: "Limited directional change in
 mountaintop plant communities over 19 years in western North America"
 ## File Manifest: ### code: 04_richness_model_figure1d.R - Performs
 species richness analysis, including statistical analysis and creating
 manuscript Figure 1d.
 05_turnover_binomial_model_figureS2_figureS4_tableS2.R - Performs turnover
 analysis, using a modified function "turnover" in the package
 code to compute turnover between pairs of sequential surveys on the same
 peak, and feeding this data into statistical analysis. These results are
 used to create supplemental Figure S2 and S4, as well as table S2
 05A_modify_codyn_turnover.R - makes one small modification to the source
 code of codyn (Hallet et al. 2013), so that gains and losses are not
 proportional to the total species richness of a given replicate. Also
 creates a function to calculate total richness separately.
 06_func-gr_gain-loss_binomial_figure2.R - Performs another set of turnover
 analyses for each functional group (forb, cushion, graminoid, shrub/tree),
 again uses this for statistical analysis. Outputs are Figure 2.
 07_abundance_models_figure3_figuresS3_tableS3-S4.R - Statistical analysis
 of change in abundance ranks (r!, r, s, c, d) of the four functional
 groups using cumulative link models. This script creates Figure 4, and
 supplementary materials Figure S3, and Tables S3 and S4.
 08_climateNA_and_logger_data_figure1bc_figureS1.R - This script visualizes
 the mean annual temperature, mean annual precipitation and climatic
 moisture deficit for the 8 target regions included in this study, which is
 used to create panels b and c in Figure 1. This script also conducts a
 statistical analysis of changes in the three climate variables of interest
 from 2004-2022. Next, we create a model for soil temp change over time
 from the logger data, make figure S1, showing logger data over time for
 each tr. 08A_climate_and_elevation_setup.R - Imports and preps GLORIA
 summit data for Climate NA, including downloading elevations using the
 elevatr package. 09_turnover_null_model.R - This script is used to create
 a null turnover model to use as a basis for comparison for the turnover
 model created in script 05_. ### data: plot_elevation_information.csv
 contains the following columns: target_region - target region codes peak -
 peak codes elevation_m - elevation in meters latitude - latitude in
 decimal degrees longitude - longitude in decimal degrees SAScleandata.csv
 - This is the clean summit-area-section data used for the analyses in this
 manuscript, containing the following columns: country - country code (us
 for United States of America) target_region - target region code
 consistent with GLORIA international peak - peak codes year - survey year
 aspect - north, east, south or west-facing sides of the summit data_type -
 summit area section from the GLORIA international protocol contour - 5
 meters or 10 meters vertical distance from the summit species - vascular
 plants and cover classes cf - meaning confer, and relating taxonomic
 uncertainty for a given observation abundance - includes percentages in
 the old data that were removed from these analyses, and the five
 categorical abundance classes (r!, r, s, c, d) that were used in the
 abundance analyses. pct_cover - refers to a percent cover ocular estimate,
 which was not used in these analyses functionalgroupsheetV2.csv -
 Functional group assignments (forb, graminoid, cushion, shrub/tree) for
 all species included in this study. This data includes the following
 columns: species - lists all species in the study functional_group - codes
 each species into one of the four functional groups (forb, cushion,
 shrub/tree, graminoid). ggb_geo_elev_forClimNA_1901-2022MSY.csv - Raw
 output of climate data for each peak from ClimateNA, including MAT (mean
 annual temperature in degrees C) and MAP (mean annual precipitation in
 millimeters) for each peak (id2). Also includes each peak's elevation
 and latitude/longitude in decimal degrees, NAD84 datum.
 sas_supplemental_species_data_organized.xlsx - This Excel sheet is not to
 be used in subsequent reanalysis of this data, it is instead a formatted
 version of the complete list of species that appear in this study (rows),
 and what year, peak and target region each of these species was seen on,
 with green shaded boxes with "1" indicating present.