Data from: Population re-establishment and spatial dynamics of crowberry (Empetrum nigrum ssp. hermaphroditum), a foundation species in restored alpine ecosystems
Data files
Sep 13, 2024 version files 65.90 MB
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ece370242-sup-0002-FileS1.zip
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README.md
Abstract
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.
README: 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
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.
Methods
This dataset contains positional and age data of a population sample of Empetrum nigrum ssp. hermaphroditum (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 Empetrum individuals collected in the field by survey-grade GNSS equipment from contiguous transects, processed in ArcGIS and R.
Empiric and modelled age data of Empetrum individuals: empiric data obtained from counting of growth rings on root collar cross-sections from sampled Empetrum individuals, modelled data based on individuals' crown size (principal crown diameter).
For details, see article in Ecology and Evolution (open access).