DOI: 10.5061/dryad.bzkh189k8
title: Data from: Population re-establishment and spatial dynamics of crowberry (Empetrum nigrum ssp. hermaphroditum), a foundation species in restored alpine ecosystems

description: Many ecosystems are defined and shaped by one or a few common, foundation
 species. Even though such species hold a key role in the restoration of
 these ecosystems, the demographic processes involved in their
 re-establishment have rarely been studied. Foundation species'
 population dynamics, re-establishment history, and the abiotic and biotic
 factors that affect individual establishment at restored sites can be
 studied by addressing population spatial patterns and age structure. Such
 an approach to studying population dynamics is particularly relevant for
 long-lived species with low mortality, such as shrubs in alpine areas. We
 studied a population of the foundation species Empetrum nigrum
 ssp. hermaphroditum at an alpine spoil heap site and found evidence of
 population re-establishment starting within a decade after construction.
 High Empetrum densities close to the spoil heap edges indicated
 that short distances to seed sources in the surroundings had a strong
 positive effect on establishment of individuals. Empetrum
 individuals were significantly clustered, which indicated intraspecific
 facilitation. As revealed by spatial analyses of recruits and older,
 established individuals, clustering developed gradually over time, which
 indicated a shift from no interaction to increased facilitation. We
 conclude that intraspecific facilitation promotes Empetrum
 reestablishment at the studied alpine spoil heap. We show that population
 spatial patterns and age structure can be successfully used to unveil the
 re-establishment history of a foundation species in a restoration context.
 Efficient seed dispersal and intraspecific facilitation seem to be
 important factors behind Empetrum's successful re-establishment at
 alpine spoil heaps. Identification of abiotic and biotic factors
 determining foundation species' establishment success at restored
 sites can support planning and improve success of restoration.
description: This dataset contains positional and age data of a population
 sample of <em>Empetrum nigrum</em> ssp.
 <em>hermaphroditum</em> (approx. 2300 individuals) collected
 in autumn 2015-spring 2016 at Fossane spoil heap, Aurland municipality,
 Norway (approx. 60°47'22.0"N 7°23'46.6"E)
 Positional data of <em>Empetrum</em> individuals
 collected in the field by survey-grade GNSS equipment from contiguous
 transects, processed in ArcGIS and R. Empiric and
 modelled age data of <em>Empetrum</em> individuals: empiric
 data obtained from counting of growth rings on root collar cross-sections
 from sampled <em>Empetrum</em> individuals, modelled data
 based on individuals' crown size (principal crown
 diameter). For details, see article in Ecology and
 Evolution (open access).
description: # Data from: Population re-establishment and spatial dynamics of crowberry
 (*Empetrum nigrum* ssp. *hermaphroditum*), a foundation species in
 restored alpine ecosystems
 [https://doi.org/10.5061/dryad.bzkh189k8](https://doi.org/10.5061/dryad.bzkh189k8) ## Description of the data and file structure The data were collected to study population dynamics of crowberry (*Empetrum nigrum* ssp. *hermaphroditum*) at an alpine spoil heap. For details, see published article. ### Files and variables #### File: ece370242-sup-0002-FileS1.zip **Description:** A .zip file with: * Complete datafile (Empetrum_data_dat.RData) containing all individual data: ages, positions, models, etc. described in the article in Ecology and Evolution * R-script for the principal spatial statistical tests in the article (Empetrum_script_scr.R and SubsetMaker_scr.R for a specific user-defined subset-making function to designate recruits and established individuals for bivariate inhomogeneous pair correlation functions). The .RData-file contains many data structures (R dataframes, lists etc.) which stem from various steps in the analyses. Genesis/origin of many of these data structures can be found in the .R-script. Not all data structures are equally relevant for potential future users. Most relevant are following data structures: * Dataframe **dat_emp_trim** (contains the complete **re-establishment dataset**, "trim" means that it is "trimmed" for *Empetrum* individuals outside of transects 1–3 (in planar projection, see Supporting information to the article for details) and individuals with lost positions): * **Variables:** * "Year": sampling year (2015 or 2016) * "Tr": transect (1, 2 or 3) * "Seg_aff": transect segment affiliation (all transects were divided into 5 × 5 m contiguous segments; NB legacy transect ID's are used here, i.e. T1A for transect 1, T6A for transect 2, T5A for transect 3) * "ID": *Empetrum* individual ID * "X": *Empetrum* individual position – X coordinate (EPSG: 25832) * "Y": *Empetrum* individual position – Y coordinate (EPSG: 25832) * "Z": *Empetrum* individual position – Z coordinate (elevation) in m * "Age": *Empetrum* individual age (modelled, raw model output) in years * "Cr1": *Empetrum* individual principal crown diameter (PCD) in cm * "Cr2": *Empetrum* individual largest crown diameter perpendicular to the PCD (LPD) in cm * "Age_alt": *Empetrum* individual age (modelled, rounded to the nearest decimal) in years * Note: dataframe **dat_emp_all** contains all sampled ("untrimmed") individuals. This dataframe has identical variables as **dat_emp_trim**. 'spatstat'-representation of the re-establishment dataset is in object **new_Tall_ppp**. * Dataframe **allo_dat** (contains data on collected Empetrum individuals whose age data (i.e. growth ring counts) and size data were used to build the allometric model, i.e. the **allometry dataset**): * **Variables:** * "ID": Empetrum individual ID (specific for the allometry dataset; NB individuals from this dataset present also in the re-establishment dataset get suffix "_15" there) * "Age_Trial1": Minimum age based on growth ring count (manual, legacy) in years * "AT_2.ObjectJ.": Minimum age based on growth ring count (growth ring counting aided by ObjectJ-plug-in in ImageJ) in years * "D_Cr1": *Empetrum* individual principal crown diameter (PCD; field measurement) in cm * "D_Cr2": *Empetrum* individual largest crown diameter perpendicular to the PCD (LPD; field measurement) in cm * "FD_IJ": Feret diameter (ImageJ, legacy) in cm * "minFD_IJ": minimal Feret diameter (ImageJ, legacy) in cm * "Cr1*_*pic*_*man": PCD-measurement from photograph (manual, legacy) in cm * "Cr2*_*pic*_*man": LPD-measurement from photograph (manual, legacy) in cm * "Cr1*_*line*_*IJ": PCD-measurement from photograph (line method, ImageJ) in cm * "Cr2*_*line*_*IJ": LPD-measurement from photograph (line method, ImageJ) in cm * "Cr1_mod": *Empetrum* individual PCD used in the allometric model ("D_Cr1" or "Cr1*_*line*_*IJ", field measurement preferred) in cm * "Cr2_mod": *Empetrum* individual LPD used in the allometric model ("D_Cr2" or "Cr2*_*line*_*IJ", field measurement preferred) in cm * "Age_mod": *Empetrum* individual age used in the allometric model (ObjectJ-based method for growth ring counting preferred) in years * "Cr_avg": average of "Cr1_mod" and "Cr2_mod" (legacy) in cm * "Cr_mult": product (i.e. multiplication) of "Cr1_mod" and "Cr2_mod" (legacy) in cm^2 * Note: the allometric model itself is stored in object (list) **allo_mod** ## Code/software R is needed to view the data and scripts (R Studio is recommended). To display all statistical tests and models properly, 'spatstat'-package (and its dependencies) is needed. See the published article for specific R-version used (and timestamps in .R-script for 'spatstat'-version). Use headers to navigate through the script. As mentioned earlier, the scripts can explain origin/genesis of most objects in the .RData file. It is not necessary to re-run the scripts to re-create the objects, but both scripts can help to understand the data objects and statistical procedures better.