DOI: 10.5061/dryad.8sf7m0d17
title: Data from: Drivers of plant community composition and species richness in Western Greenland

description: The Arctic experiences rapid climate change, but our ability to predict
 how this will influence plant communities is hampered by a lack of data on
 the extent to which different species are associated with particular
 environmental conditions, how these conditions are interlinked, and how
 they will change in coming years. Increasing temperatures may negatively
 affect plants associated with cold areas due to increased competition with
 warm-adapted species, but less so if local temperature variability is
 larger than the expected increase. Here we studied the potential drivers
 of vegetation composition and species richness along coast to inland and
 altitudinal gradients by the Nuuk fjord in western Greenland using
 Hierarchical Modelling of Species Communities (HMSC) and linear mixed
 models. Community composition was more strongly associated with random
 variability at intermediate spatial scales (among plot groups 500 m apart)
 than with large-scale variability in summer temperature, altitude or soil
 moisture, and the variation in community composition along the fjord was
 small. Species richness was related to plant cover, altitude and slope
 steepness, which explained 42% of the variation, but not to summer
 temperature. Jointly, this suggests that the direct effect of climate
 change will be weak, and that many species are associated with
 microhabitat variability. However, species richness peaked at intermediate
 cover, suggesting that an increase in plant cover under warming climatic
 conditions may lead to decreasing plant diversity.
description: The study was conducted at five different sites along the Nuuk
 fjord (Godthåbsfjorden) in western Greenland.  In
 2011–2013, 414 permanent plots were established across the five study
 sites. The plots were circular, with a diameter of 2 m. Three groups of
 six plots were selected for every 100 m increase in altitude. The position
 of the first plot at each altitude was selected by walking uphill straight
 towards a pre-selected point until the isocline was reached (measured
 using a hand-held GPS). Plot centres were placed exactly 10 m apart along
 the isoclines, or slightly more if needed to prevent plots from being
 entirely in water or having an average slope &gt;45°. Plot groups were
 placed exactly 500 m apart. The lowest plots were moved to 20 m a.s.l. to
 avoid exposure to salt. The highest altitudes used in sites 1–5 were 200,
 200, 400, 500 and 500 m a.s.l., respectively, reflecting that the
 mountains are higher further east. The study design was the exact same as
 previously used in Young Sund (Nabe-Nielsen et al. 2017).
 The vegetation survey included a complete inventory of all
 species of vascular plants in each plot. This inventory was conducted in
 2011–2013. Maximum height and diameter were measured for the woody species
 in 2021–2022. The cover of woody species, graminoids, and herbaceous
 plants was assessed for each plot by two independent observers as percent
 cover &lt;2 m from plot centres. Subsequently the two estimates were
 averaged. Plants were named following Böcher <em>et
 al.</em>(1978).
description: # Drivers of plant community composition and species richness in Western
 Greenland Dataset DOI: [10.5061/dryad.8sf7m0d17](10.5061/dryad.8sf7m0d17)
 **Principal Investigator Contact Information** ``` Name: Jacob
 Nabe-Nielsen Institution: Aarhus University  Email: jnn@ecos.au.dk ``` ##
 Description of the data and file structure This dataset contains the data
 required to replicate analyses in Nabe-Nielsen et al. (2025), studying the
 potential drivers of vegetation composition and species richness along
 coast to inland and altitudinal gradients by the Nuuk fjord in western
 Greenland using Hierarchical Modelling of Species Communities (HMSC) and
 linear mixed models. Data originate from five study sites along the Nuuk
 fjord in western Greenland. At each site three groups of six plots were
 selected for every 100 m increase in altitude. Plot centres were placed
 exactly 10 m apart along the isoclines, and plot groups were placed
 exactly 500 m apart. The permanently marked plots were circular, with a
 diameter of 2 m. For each plot a complete inventory of all species of
 vascular plants was conducted in the period 2011–2013. Positions of
 individual plots are provided in the UTM zone 22 N projection.
 **Nuuk_plant_data_231114.xlsx** (located in the "data" folder in
 the file "HMSC_models_and_data.zip") is an Excel-file with four
 sheets containing all the field data used in the publication. The
 sheet **Species data** contains a list of all plant species recorded in
 the 414 vegetation plots. Species: Scientific name of the studied plant
 species N plots: Number of plots where the species was found P001–P414:
 Presence of the species in each of the 414 study plots (presence recorded
 with an 'x') The sheet **Positions and inclin:** plot:  Plot
 numbers (P001–P414), corresponding to the numbers on the metal tags used
 in the field site: Study site number (1–5) alt: Altitude of the plot (in
 m) grp.no: Name of the plot group number within the specific site and
 altitude band (a, b, or c) plot.grp: Name of the plot group (combination
 of site, altitude and grp.no) long.garmin: Longitude, measured using
 Garmin GPS (blank means missing) lat.garmin: Latitude, measured using
 Garmin GPS (blank means missing) x.garmin: East-west position, measured
 using Garmin GPS (UTM zone 22N; blank means missing) y.garmin: North-south
 position, measured using Garmin GPS (UTM zone 22N; blank means missing)
 x.trimble: East-west position, measured using Trimble differential GPS
 (UTM zone 22N; blank means missing) y.garmin: North-south position,
 measured using Trimble differential GPS (UTM zone 22N; blank = missing)
 inclin.down: Average plot steepness (degrees) inclin.dir: Direction of
 slope (i.e., direction downhill), in degrees soil.water.x: Soil water,
 with x taking the values 1-3 (pct. water; missing values shown as NA)
 date1 and date.2: the dates where the plot was visited / variables
 measured The sheet **Hgt and cover 2021-22**: plot: Plot numbers
 (P001-P414) site: Study site (1-5) Taxon: Name of the taxonomic group (or
 'Rock') Max hit: Maximum height of the taxon observed within the
 2-m plot (cm) Max dia: Maximum diameter (mm) of different taxa within the
 2-m plots Cover: How much of the 2-m plot that was covered by the taxon
 (in percent; average of two estimates). ## Code/Software The file
 "HMSC_models_and_data.zip" is a compressed archive contaning the
 field data and the code required to run the HMSC analyses presented in the
 publication, along with directories required for handling input and output
 from the analyses. The archive contains the folders "data",
 "models", and "results", and the R code files
 "S1_define_and_fit_models.R",
 "S2_evaluate_convergence.R",
 "S3_show_parameter_estimates.R". The first file contains code
 for reading in and rearranging the species data stored in "data/Nuuk
 plant data 231114.xlsx". It also reads in the file "data/b for
 Hmsc 231114.RData" **b for Hmsc 231114.RData**: stores covariates
 used in the analysis (rearranged from data stored in the tabs
 "Species data" and "Hgt and inclination 2021-22" in
 the Excel data sheet, and summer temperatures and summer precipitation
 data from the Chelsa database version 2.1 (Karger et al. 2017)). One line
 per plot: plot.grp: Plot group number (see above) plot: Plot number (one
 line per plot, numbered P001 to P414) lon: Longitude of the plot lat:
 Latitude of the plot site: Study site (1-5) alt: Altitude (m) grp.no: Name
 of the plot group number within the specific site and altitude band (a, b,
 or c) date.1: Date of first visit to the plot; collection of vegetation
 composition data (yyyy-mm-dd) date.2: Date of second visit to the plot;
 collection of plant height and cover (yyyy-mm-dd) inclin.down: Plot
 steepness (degrees) inclin.dir.true: Direction of slope (degrees)
 soil.water.mean: Average of three soil water measures (percent soil water)
 Sri: Solar radiation index: Calculated from slope, direction and position
 (see paper) cover.p: Cover values from pin-point data; not used in the
 present data analyses (range 0–1) cover.c: Cover values estimated within
 2-m circle (percent); used in the paper n.spp.per.plot: Number of species
 observed in the plot group (response variable used in the linear analyses)
 max.hgt: Maximum plant height (cm) summer.temp: Mean summer temperature
 (degrees Censius) summer.prec: Mean summer precipitation (mm) cont.idx:
 Continentality index; fraction of distance moved between outer coast and
 inland glacier **S1_define_and_fit_models.R**: Code used to define the
 spatial nesting used in the analysis, with plots nested within plot groups
 nested within sites, and specifies the number of replicates to use.
 Finally the models are fitted using the "sampleMcmc" function
 from the Hmsc package, and the model objects are stored in
 "models/unfitted_models.RData". **S2_evaluate_convergence.R:**
 code for plotting the fitted model objects to evaluate model convergence
 (outputs stored in the "results" directory).
 **S3_show_parameter_estimates.R:** code for producing the plots presented
 in the paper based on the fitted model objects. The **data** folder
 contains the file **unfitted_models.RData**; a list of model outputs used
 in code found in the files S2_evaluate_convergence.R
 and S3_show_parameter_estimates.R. The results folder contains a number of
 produced automatically when running the code in the files
 S2_evaluate_convergence.R and  S3_show_parameter_estimates.R. The files
 are: Fig 4 - Hmsc parameter_estimates.csv, MCMC_convergence.pdf,
 MCMC_convergence.txt, parameter_estimates_Beta_plant model.xlsx,
 parameter_estimates_Omega_plant model_group.xlsx,
 parameter_estimates_Omega_plant model_plot.xlsx,
 parameter_estimates_Omega_plant model_site.xlsx,
 parameter_estimates_VP_plant model.csv,
 parameter_estimates_VP_R2T_Betaplant model.csv,
 parameter_estimates_VP_R2T_Yplant model.csv, parameter_estimates.pdf,
 parameter_estimates.txt, Prop raw var - VPr.csv. The values stored in the
 csv files and the plots in the pdf files make it possible to inspect how
 well the model fits and provides various summaries of the model outputs.
 Contents of all outputs are described in detail in the paper (Nabe-Nielsen
 et al. 2025) and the help files accompanying the Hmsc-package, which is
 available on CRAN
 ([https://cran.r-project.org](https://cran.r-project.org)).  All
 statistical analyses were performed using R version 4.4.1 **Dates of Data
 Collection** ``` 2011-2013. ``` **Data Spatial Scope** The Nuuk fjord
 (Godthåbsfjorden) in western Greenland. **Sharing/Access** This work is
 licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
 license. **Recommended Citation** Nabe-Nielsen, J., Nabe-Nielsen, L.I.
 & Ovaskainen, O. (2025). Drivers of plant community composition and
 species richness in Western Greenland. Ecography.