Data from: Limited directional change in mountaintop plant communities over 19 years in western North America
Data files
Jan 29, 2025 version files 1.29 MB
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functional_group_sheet_V2.csv
7.22 KB
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ggb_geo_elev_forClimNA_1901-2022MSY.csv
239.13 KB
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plot_elevation_information.csv
592 B
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README.md
4.53 KB
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SAS_clean_data.csv
937.15 KB
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sas_supplemental_species_data_organized.xlsx
97.42 KB
Abstract
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.
README: 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.