Data for: Fundamental interaction niches: towards a functional understanding of ecological networks’ resilience
Data files
Jun 02, 2025 version files 2.33 MB
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animal_df.RData
6.92 KB
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animal_df2.RData
11.54 KB
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case_study_code_for_publication.R
19.49 KB
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hummingbird_occurrences_spatial.RData
760.02 KB
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network_long.RData
294.92 KB
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plant_df.RData
39.81 KB
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plant_occurrences_spatial.RData
1.19 MB
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README.md
13.94 KB
Abstract
Global change will create new species interactions and alter or eliminate existing ones, a process known as interaction rewiring. This rewiring can significantly affect how ecosystems function. To better predict the future structure of ecological networks, it is crucial to assess their ability to adapt to changes. Here, we introduce two concepts: ‘rewiring capacity’ of a single species (the multidimensional trait space of all its potential interaction partners within a region) and ‘rewiring potential’ of a local community (the total trait space covered by interaction partners of the species at the target trophic level locally). To quantify the rewiring capacity and potential, we apply existing methods for determining species' functional interaction niches in a novel way to quantify species’ and communities’ ability to form new interactions and the functional resilience of interaction networks to global change. To illustrate the applicability of these concepts, we assessed the rewiring capacity and potential of interactions between 1,002 flowering plant species and 318 hummingbird species across the Americas. The rewiring capacity and potential metrics offer a new way to understand and quantify ecosystem resilience, allowing us to map how ecological networks respond to global change.
https://doi.org/10.5061/dryad.h9w0vt4sq
Description of the data and file structure
Fundamental interaction niches: towards a functional understanding of ecological networks’ resilience
Code for fitting an interaction prediction model and calculating rewiring capacity and rewiring potential using empirical plant-hummingbird interaction and trait data from the Americas
README file created by Emma-Liina Marjakangas on April 26th, 2025
We illustrate the application of the conceptual framework on network resilience for a mutualistic pollination network of flowering plants and hummingbirds in the Americas.
Files and variables
Filtered data for the analysis are available as data files here (listed below) and as raw data from original sources cited in the manuscript (for references, see "Access information"). Missing values are indicated as NA. For a detailed description of the methodology and the reasons for choosing the traits, see the published article's methods.
File: plant_df.RData
Description: traits of 1002 plant species observed in empirical networks. Variable names and explanations for the file "plant_df.RData":
"Plant_species" = Plant species name.
"Plant_genus" = Plant genus name.
"Plant_family" = Plant family name.
"corolla_length_imputed_mean" = Length of corolla in millimeters. Missing values are imputed based on phylogeny. Vollstädt et al. 2025
"plant_height_max_imputed_mean" = Maximum plant height in meters. Missing values are imputed based on phylogeny. Weigelt et al. 2019
"seed_length_max_imputed_mean" = Mean seed length in millimeters. Missing values are imputed based on phylogeny. Weigelt et al. 2019
"seed_mass_mean_imputed_mean" = Mean seed mass in grams. Missing values are imputed based on phylogeny. Weigelt et al. 2019
"nectar_concentration_imputed_mean" = Nectar concentration in percentages. Missing values are imputed based on phylogeny. Vollstädt et al. 2025
"pollination_syndrome_imputed_mean" = Floral color following the pollination syndrome concept. Approximated as a categorical flower color that indicates pollination syndrome. Continuous average based on multiple observations per species, ranging between 1 and 3. 1 = short-wavelength color of blue and white, and usually insect-pollinated, 3 = long-wavelength color of red and orange, and usually bird-pollinated. Missing values are imputed based on phylogeny. Vollstädt et al. 2025
File: network_long.RData
Description: pairwise interactions between 172 hummingbird species and 1002 plant species and their traits, formatted for fitting generalized boosted regression tree models. Variable names and explanations for file "network_long.RData":
"Plant_species" = Plant species name.
"Animal_species" = Hummingbird species name.
"Network_name" = ID for the sampled network from Dalsgaard et al. 2021
"Latitude" = Latitudinal coordinate for the sampled network from Dalsgaard et al. 2021
"Longitude" = Longitudinal coordinate for the sampled network from Dalsgaard et al. 2021
"Plant_genus" = Plant genus name.
"Animal_genus" = Hummingbird genus name.
"Beak.Length_Culmen" = Length from the tip of the beak to the base of the skull in millimeters. Tobias et al. 2022
"Beak.Depth" = Depth of the beak at the anterior edge of the nostrils in millimeters. Tobias et al. 2022
"Tarsus.Length" = Length of the tarsus from the posterior notch between tibia and tarsus, to the end of the last scale of acrotarsium (at the bend of the foot) in millimeters. Tobias et al. 2022
"Handwing.Index" = 100*DK/Lw, where DK is Kipp’s distance and Lw is wing length (i.e., Kipp’s distance corrected for wing size). Kipp's distance = length from the tip of the first secondary feather to the tip of the longest primary. Tobias et al. 2022
"Tail.Length" = Distance between the tip of the longest rectrix and the point at which the two central rectrices protrude from the skin, typically measured using a ruler inserted between the two central rectrices in millimeters. Tobias et al. 2022
"Mass" = Body mass given as species average (both male and female) in grams. Tobias et al. 2022
"Habitat" = Main habitat associated with, levels: Desert (drylands and other open arid habitats, often sandy with very sparse vegetation); Rock (rocky substrate typically with no/very little vegetation, including rocky outcrops, rocky coastlines, arid stony steppes, rocky mountaintops and mountain slopes); Grassland (open dry to moist grass-dominated landscapes, at all elevations); Shrubland (low stature bushy habitats, included thornscrub, thorny or arid savanna, caatinga, xerophytic shrubland and coastal scrub); Woodland (medium stature tree-dominated habitats, including Acacia woodland, riparian woodlands, mangrove forests, forest edges, also more open parkland with scattered taller trees); Forest (tall tree-dominated vegetation with more or less closed canopy, including palm forest); Human modified (urban landscapes, intensive agriculture, gardens); Wetland (wide range of freshwater aquatic habitats including lakes, marshes, swamps and reedbeds); Riverine (rivers and streams at all elevations); Coastal (intertidal zones within immediate vicinity of beaches, estuaries, brackish to salty marshes, including mudflats, lagoons, alkaline wetlands, coastal dunes and harbours); Marine (pelagic, on sea near coasts, intertidal zone on beaches, pelagic sea cliffs, islets and islands). Tobias et al. 2022
"outcome" = Observed interaction between a pair of plant and animal species in the network data by Dalsgaard et al. 2021 (0 = not observed, 1 = observed once or more often).
"Plant_family" = Plant family name.
"Animal_clade" = Hummingbird species' clade category following the classification of McGuire et al. 2014
"Beak_curvature_bo" = Mean bill curvature in degrees. Dalsgaard et al. 2021
"corolla_length_imputed_mean" = Length of corolla in millimeters. Missing values are imputed based on phylogeny. Vollstädt et al. 2025
"plant_height_max_imputed_mean" = Maximum plant height in meters. Missing values are imputed based on phylogeny. Weigelt et al. 2019
"seed_length_max_imputed_mean" = Mean seed length in millimeters. Missing values are imputed based on phylogeny. Weigelt et al. 2019
"seed_mass_mean_imputed_mean" = Mean seed mass in grams. Missing values are imputed based on phylogeny. Weigelt et al. 2019
"nectar_concentration_imputed_mean" = Nectar concentration in percentages. Missing values are imputed based on phylogeny. Vollstädt et al. 2025
"pollination_syndrome_imputed_mean" = Floral color following the pollination syndrome concept. Approximated as a categorical flower color that indicates pollination syndrome. Continuous average based on multiple observations per species, ranging between 1 and 3. 1 = short-wavelength color of blue and white, and usually insect-pollinated, 3 = long-wavelength color of red and orange, and usually bird-pollinated. Missing values are imputed based on phylogeny. Vollstädt et al. 2025
File: plant_occurrences_spatial.RData
Description: binary data of occurrences of 1002 plant species in 0.5*0.5 degree grid cells in the Americas based on range data, including GIS information of the grid cells. Variable names and explanations for file "plant_occurrences_spatial.RData":
"FID" = Numerical ID for grid cells.
columns 2-1002: binary presence-absence information for each plant species in each grid cell (whether range overlaps with grid cell or not).
"sp_richness" = Number of plant species present in the grid cell (range overlaps with the grid cell).
"geometry" = GIS information for each grid cell to allow spatial analyses and plotting (in simple features format).
File: animal_df.RData
Description: traits of 172 hummingbird species observed in empirical networks. Variable names and explanations for the file "animal_df.RData":
"Animal_species" = Hummingbird species name
"Animal_genus" = Hummingbird genus name
"Beak.Length_Culmen" = Length from the tip of the beak to the base of the skull in millimeters. Tobias et al. 2022
"Beak.Depth" = Depth of the beak at the anterior edge of the nostrils in millimeters. Tobias et al. 2022
"Tarsus.Length" = Length of the tarsus from the posterior notch between tibia and tarsus, to the end of the last scale of acrotarsium (at the bend of the foot) in millimeters. Tobias et al. 2022
"Handwing.Index" = 100*DK/Lw, where DK is Kipp’s distance and Lw is wing length (i.e., Kipp’s distance corrected for wing size). Kipp's distance = length from the tip of the first secondary feather to the tip of the longest primary. Tobias et al. 2022
"Tail.Length" = Distance between the tip of the longest rectrix and the point at which the two central rectrices protrude from the skin, typically measured using a ruler inserted between the two central rectrices in millimeters. Tobias et al. 2022
"Mass" = Body mass given as species average (both male and female) in grams. Tobias et al. 2022
"Habitat" = Main habitat associated with, levels: Desert (drylands and other open arid habitats, often sandy with very sparse vegetation); Rock (rocky substrate typically with no/very little vegetation, including rocky outcrops, rocky coastlines, arid stony steppes, rocky mountaintops and mountain slopes); Grassland (open dry to moist grass-dominated landscapes, at all elevations); Shrubland (low stature bushy habitats, included thornscrub, thorny or arid savanna, caatinga, xerophytic shrubland and coastal scrub); Woodland (medium stature tree-dominated habitats, including Acacia woodland, riparian woodlands, mangrove forests, forest edges, also more open parkland with scattered taller trees); Forest (tall tree-dominated vegetation with more or less closed canopy, including palm forest); Human modified (urban landscapes, intensive agriculture, gardens); Wetland (wide range of freshwater aquatic habitats including lakes, marshes, swamps and reedbeds); Riverine (rivers and streams at all elevations); Coastal (intertidal zones within immediate vicinity of beaches, estuaries, brackish to salty marshes, including mudflats, lagoons, alkaline wetlands, coastal dunes and harbours); Marine (pelagic, on sea near coasts, intertidal zone on beaches, pelagic sea cliffs, islets and islands). Tobias et al. 2022
"Animal_clade" = Hummingbird species' clade category following the classification of McGuire et al. 2014
"Beak_curvature_bo" = Mean bill curvature in degrees. Dalsgaard et al. 2021
File: animal_df2.RData
Description: traits of 318 hummingbird species, including 172 hummingbird species observed in empirical networks and 146 additional hummingbird species occurring in the Americas but not in the empirical networks. Variable names and descriptions are the same as in the file "animal_df.RData".
File: hummingbird_occurrences_spatial.RData
Description: binary data of occurrences of 318 hummingbird species in 0.5*0.5 degree grid cells in the Americas based on range data, including GIS information of the grid cells. Variable names and explanations for file "hummingbird_occurrences_spatial.RData":
"FID" = Numerical ID for grid cells.
columns 2-317: binary presence-absence information for each hummingbird species in each grid cell (whether range overlaps with grid cell or not).
"sp_richness" = Number of hummingbird species present in the grid cell (range overlaps with the grid cell).
"geometry" = GIS information for each grid cell to allow spatial analyses and plotting (in simple features format).
File: case_study_code_for_publication.R
Description: All analyses were conducted in R software (version 4.3.0). This file includes the commented code for the analysis.
Code/software
R software is needed to open and rerun the code files.
Access information
The raw data that support the analyses of this study are all freely available for research purposes, and can either be directly downloaded from the respective websites or are available on demand. References for the raw data sources:
Bird range data: BirdLife International. (2022). Bird species distribution maps of the world. Available at: http://datazone.birdlife.org/species/requestdis.
Empirical network and hummingbird bill curvature trait data: Dalsgaard, B. et al. (2021). The influence of biogeographical and evolutionary histories on morphological trait‐matching and resource specialization in mutualistic hummingbird–plant networks. Functional Ecology, 35, 1120–1133.
Plant range data: Enquist, B.J. et al. (2016). Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity. PeerJ Preprints, 1–32.
Plant trait data: Weigelt, P. et al. (2020). GIFT - A Global Inventory of Floras and Traits for macroecology and biogeography. Journal of Biogeography, 47, 16-43
Plant trait data: Vollstädt, M. et al. (2025). The role of insularity: plants have few ornithophilous traits but are visited by morphologically more distinct hummingbirds in the Caribbean islands. Functional Ecology DOI: 10.1111/1365-2435.70068
Hummingbird checklist data: Lepage, D. (2023). Avibase - The World Bird Database. https://avibase.bsc-eoc.org/checklist.jsp?region=index&lang=FI&list=clements.
Hummingbird clade data: McGuire, J.A. et al. (2014). Molecular Phylogenetics and the Diversification of Hummingbirds. Current Biology, 24, 910–916.
Hummingbird trait data: Tobias, J.A. et al. (2022). AVONET: morphological, ecological and geographical data for all birds. Ecology Letters, 25, 581–597.
The dataset includes a commented code file and filtered and ready-to-use data of plant-hummingbird interactions and traits for running the case study analyses.
We obtained data from 79 complete bipartite plant-hummingbird networks from Dalsgaard et al. (2021) with 1002 plant species, 172 hummingbird species, and 4155 observed pairwise interactions in the Americas. In addition, 10,814 absences of pairwise interactions were inferred from the complete networks if an interaction was not observed between a pair of plant and hummingbird species that occurred in a study site. We transformed the number of observed flower visits to binary presences and absences of interactions to allow the fitting of a probabilistic model. To extend beyond the observed hummingbird species in the 79 networks, we included 146 additional hummingbird species that consume nectar as their main food source (>= 90% in EltonTraits; Wilman et al. 2014) and are included in the checklist of South, Central, or North America (Lepage 2023). We obtained data on the following plant species’ traits: corolla length, floral color following the pollination syndrome concept, nectar concentration, maximum height of the plant, mean seed length, and maximum seed mass (Weigelt et al. 2020; Vollstädt et al. 2025). We use this broad array of plant traits to increase model performance. For those plant species with missing species-level trait data, we imputed traits using an ancestral state reconstruction approach. For this, we constructed a phylogeny using V.Phylomaker (Jin & Qian 2019) and the Smith & Brown (2018) phylogeny as a backbone. We obtained data on the following hummingbird species’ traits: beak length, depth, and curvature, tarsus length, hand-wing index, tail length, body mass, and primary habitat association (Tobias et al. 2022; Dalsgaard et al. 2021). We obtained plant species range maps from the BIEN database (Enquist et al. 2016) or range estimates based on GBIF observations. We obtained hummingbird ranges for both species in the original networks and the additional species from BirdLife International (2022).