Data from: Ecosystem age drives food web architecture of glacier retreat-formed fishless ponds in Greenland
Data files
Sep 15, 2025 version files 74.66 KB
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community_cons.csv
592 B
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community2.csv
7.26 KB
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Data1.csv
34.58 KB
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Data2.zip
1.90 KB
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Environmental_variables.csv
758 B
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GLM_analysis.csv
1.52 KB
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López-Rodríguez_et_al._2024_FINAL_R_script.R
22.41 KB
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README.md
5.65 KB
Abstract
Here, we studied the topology of food webs in newly created Arctic ponds formed by deglaciation, analyzing potential drivers such as environmental variables in 16 fishless ponds of contrasting ages (8 young, <50 years; 8 old, >150 years) located on the rapidly retreating west coast of Greenland. Using gut content analysis of zooplankton and benthic macroinvertebrates, we constructed food webs and examined how food web metrics related to pond age and environmental variables. We also tested for differences in beta diversity and nestedness of prey and consumers between pond age classes. In young ponds, food items of zooplankton and macroinvertebrates represented a subset of those found in old ponds. Food webs in old ponds exhibited higher taxonomic richness, greater linkage density, and lower connectance, indicating greater stability. Pond age was the main explanatory factor for most food web metrics, followed by productivity proxies (total nitrogen and phytoplankton chlorophyll-a). While food webs in old ponds were not significantly associated with environmental variables, in young ponds, connectance and trophic niche overlap were significantly related to TN and Chl-a. These contrasting patterns suggest that food web topology becomes more complex and less dependent on environmental conditions as ponds age.
Dataset DOI: 10.5061/dryad.n5tb2rc81
Description of the data and file structure
Samples were obtained during a single survey of ponds located on the western coast of Greenland. Pond age was estimated at the landscape level using current and historical ice-sheet maps and aerial photographs measuring distance to the ice front, rather than at the level of individual systems. Half of the ponds (n = 8) were located in an area where the glacier had retreated within the past 50 years (“young ponds”), while the other half were situated in an area deglaciated for at least 150 years (“old ponds”). Macroinvertebrates and zooplankton were sampled to reconstruct the food webs of each pond based on gut content analyses. These data were linked via GLMs to the ecosystem age and to morphometric and environmental variables.
The datasheets correspond to:
- A diet matrix from one pond (as an example) for calculating food web metrics.
- A compressed folder containing the files necessary for the representation of the food webs. This compressed folder must be decompressed before running the script, as the R scripts assume the folder is located in the same directory from which they are executed.
- A presence/absence species matrix for both prey and consumers (for beta diversity calculations).
- A sheet containing environmental data.
- A sheet integrating environmental data and food web metrics (for GLM analysis).
Files and variables
File: Environmental_variables.csv
Description: Environmental, age and morphometric characteristics of the 16 Greenlandic ponds studied
Variables
- System: Id Pond
- Age: Pond age (young or old)
- Area: Pond Area, m2
- Depth: maximum water depth (m)
- Chl-a: chlorophyll-a water concentration (µg L-1)
- TN: total nitrogen concentration in water (µg L-1)
- TP: total phosphorus concentration in water (µg L-1)
- T: water temperature (°C)
- K: electrical conductivity (µS cm-1)
- pH: water pH
File: GLM_analysis.csv
Description: Environmental, age and morphometric characteristics of the 16 Greenlandic ponds studied. Additionally, the dataset includes community-level variables such as food web metrics
Variables
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System: Pond id
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Age: Pond age class
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Area (m2): pond surface area (m2)
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TP (µg/L): total phosphorus concentration in water (µg L-1)
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TN (µg/L): total nitrogen concentration in water (µg L-1)
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Chl-a (µg/L): chlorophyll-a water concentration (µg L-1)
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pH: water pH
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Depth (m): maximum water depth (m)
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Cond (µS/cm): electrical conductivity (µS cm-1)
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Temp (C): water temperature (°C)
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Number of links: Result of the species accumulation curve, where the number of items consumed by the consumers in each system was standardized by the number of stomach analyzed. That is, the expected number of total items consumed per pond.
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Max. trophic level: Maximum trophic position for each pond
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Connectance: Number of effective connections divided by the total number of possible links (taxa).
C= 2L/S(S-1), where L is the number of effective connections and S is the number of taxa in the web.
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Linkage density: Calculated as the number of links for each taxa. LD= L/S, where L is the number of links in the web and S is the number of taxa.
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Trophic niche overlap: Use of the same food item by two or more taxa or individuals. At global level, it is calculated as the average of all occurring overlaps.
File: community2.csv
Description: presence/absence matrix of food items in all sampling sites was constructed (for beta diversity calculations).
File: Data1.csv
Description: Diet matrix from one pond (as an example) for calculating food web metrics. The first row and the column headers correspond to the species in the network (both consumers and food items). The values within the matrix indicate the relative abundance of each dietary item.
File: community_cons.csv
Description: presence/absence matrix of cpnsumers in all sampling sites was constructed (for beta diversity calculations).
File: Data2.zip
Description: Compressed folder containing the files necessary for the representation of the food webs. This compressed folder must be decompressed before running the script, as the R scripts assume the folder is located in the same directory from which they are executed.
Files in the compressed folder:
1- nodes: Taxonomic identity of every species in the food web. Nodes: species present in the food web; Category: trophic position of each species in the food web.
2- trophic.links: list of interactions (-edge list-, where each row represents a trophic interaction from a consumer to a resource). Resource: Food items; Consumer: consumers
3- properties: Input file needed by the Cheddar package to import the community dataset and visualize the networks.
File: López-Rodríguez_et_al._2024_FINAL_R_script.R
Description: R script with the code used to perform the analyses.
Code/software
The data analysis was performed using common R packages and functions, as detailed in the methodology of the paper. The analysis included GLM and model selection procedures, all of which are standard approaches in ecological research. These models are implemented with widely used packages for statistical modeling.
Food web metrics were calculated using the bipartite and Cheddar packages. Beta diversity analyses were also performed using the betapart package.
Samples were obtained during a single survey of ponds located on the western coast of Greenland. Pond age was estimated at the landscape level using current and historical ice-sheet maps and aerial photographs measuring distance to the ice front, rather than at the level of individual systems. Half of the ponds (n = 8) were located in an area where the glacier had retreated within the past 50 years (“young ponds”), while the other half were situated in an area deglaciated for at least 150 years (“old ponds”).
Stomach contents of macroinvertebrates and zooplankton were analyzed to reconstruct food webs. Using the relative abundance of food items by taxon and by system, we built diet matrices for each pond (file: data1.csv) to calculate trophic network metrics (connectance, linkage density, and trophic niche overlap). For graphical representation of networks, we also constructed edge lists for each pond, where each row represents a trophic interaction from a consumer to a resource (file: data2, folder with spreadsheets for network reconstruction).
Based on consumer identifications by pond, we created a presence/absence matrix of consumers across sites (file: community cons.csv). Similarly, based on the food items found in guts, we created a presence/absence matrix of prey items across sites (file: community2.csv). From these matrices, we calculated overall beta diversity (βsor) and its components (turnover, βsim, and nestedness, βnes).
Morphometric and environmental variables were measured in each pond: surface area and maximum depth (measured in situ), water pH, temperature, and electrical conductivity at the central point, as well as water samples for chemical analyses. Indicators of trophic state included total phosphorus (TP, μg L⁻¹), total nitrogen (TN, μg L⁻¹), and phytoplankton chlorophyll-a (Chl-a, μg L⁻¹) concentrations, as proxies of potential productivity. Differences between pond age groups were tested using two-tailed Mann–Whitney–Wilcoxon tests at α=0.05 (file: Environmental variables.csv).
Relationships between food web metrics (number of food items, maximum trophic level, connectance, linkage density, and trophic niche overlap) and environmental, age, and morphometric variables were analyzed using Generalized Linear Models (GLM) (file: GLM_analysis.csv).
All analyses were conducted in R using standard packages and functions, as described in the methodology section of the article. The accompanying script provides an example of each type of analysis; full details are available in the published paper.