Trophic and non-trophic seasonal interaction network for boreal forest tetrapods
Data files
Oct 29, 2024 version files 751.62 KB
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communities_eigen.R
1.73 KB
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data_references.csv
137.60 KB
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deltacon.R
1.89 KB
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interaction_data.csv
590.32 KB
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modul_assort_analysis.R
15.22 KB
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README.md
4.85 KB
Abstract
Aim: Understanding the organization of the wide variety of ecological interactions is crucial to advancing our understanding and management of real ecosystems. We aimed to compile a “complete” network of tetrapod trophic and non-trophic interactions for the entire North American boreal forest biome that could be analyzed to gain insights into community organization and function. In particular, we aimed to identify functionally important units (modules) and species within the boreal network, and to compare how these changed seasonally and with the inclusion of non-trophic interactions.
Location: Boreal North America
Time period: 1950 – present day
Major taxa studied: Tetrapods
Methods: We compiled published ecological interactions for boreal tetrapods into a food web (trophic interactions) and inclusive network (trophic and non-trophic interactions). We partitioned interactions by season, creating four networks representing the two network types per season. We examined how the modular structure, composition of modules, assortativity of traits within modules, and importance of different species compared across these networks.
Results: We compiled a network of 5037 ecological interactions between 421 boreal tetrapod species. Most of these interactions (87%) occur in summer. The summer and winter boreal food webs and inclusive networks are modular (i.e., contain subsets of species interacting more with each other than with species outside of the subset). Several species attributes explain which species assort together into modules, including physical and behavioural traits, taxonomic class, and trophic niche. A small set of species come out as most functionally important (central, module hubs, or responsible for the greatest network change when non-trophic interactions are included) across all versions of the network, and other species are important within a certain season or interaction context.
Main conclusions: Potential conservation management units (modules) exist in the boreal forest network, and considering species’ function at the community level highlights new priorities for species-level management.
https://doi.org/10.5061/dryad.547d7wmg9
Contents:
Data:
interaction_data.csv - lists 6465 known trophic and non-trophic interactions between boreal forest tetrapod species, the season in which they occur, and the literature reference code(s) for each interaction
data_references.csv - lists the full references corresponding to each reference code in the interaction data set
boreal_trait_table.csv - lists species traits for the 429 tetrapod species in the data set
R code:
modul_assort_analysis.R - script for the analysis of assortativity of species traits into network modules in Daly et al. [accepted 2024], Global Ecology and Biogeography.
communities_eigen.R - script for module identification analysis in Daly et al. [accepted 2024], Global Ecology and Biogeography.
deltacon.R - script for the analysis of which nodes were responsible for the greatest change in network structure when non-trophic interactions were added to the food web, for summer and winter respectively, in Daly et al. [accepted 2024], Global Ecology and Biogeography.
Description of the data and file structure
interaction_data.csv
Variable descriptions:
interaction_type - trophic or non-trophic. Trophic indicates a feeding interaction. Non-trophic indicates a non-feeding interaction (e.g., communal feeding or nesting, pollination, mobbing, kleptoparasitism, food provision, brood parasitism, etc.)
given_species - the "giver" of the interaction effect. E.g., in a trophic interaction, this is the species that eats the other species. In most cases, this is a tetrapod species. However, species other than terrestrial tetrapods were not included with species-level resolution, and were instead classified into species groups, such as "Graminoids", "Deciduous trees", "Fish", etc.
interaction - specifies the interaction type, and the effect on the "giver" and "receiver" of the interaction in parentheses. For example, (+/-) means that the given_species benefits, and there is a cost to the target_species.
target_species - the "receiver" of the interaction effect. E.g., in a trophic interaction, this is the species that gets eaten. In most cases, this is a tetrapod species. However, species other than terrestrial tetrapods were not included with species-level resolution, and were instead classified into species groups, such as "Graminoids", "Deciduous trees", "Fish", etc.
season - the season that this interaction was documented in. Can take values of "summer" or "winter". Interactions that occur in both seasons are entered twice, with one row for each season.
Ref1, Ref2, Ref3, Ref4, Ref5 - Codes for literature reference(s) that describe the interaction described in that row. The full reference corresponding to each code is listed in the file data_references.csv. Every interaction has one to five associated references. NA values in the columns for the 2nd-5th references mean that we don't have additional references for those interactions.
data_references.csv
Variable descriptions:
reference_ID - reference code used in the file interaction_data.csv
citation - full citation corresponding to the reference code
boreal_trait_table.csv
The trait and attribute data in this spreadsheet come from the AvoNet (Tobias et al., 2022) and AnimalTraits (Herberstein et al., 2022) databases, as well as from Supplementary Data 2 in Mendoza & Araújo (2019).
Tobias, J. A., Sheard, C., Pigot, A. L., Devenish, A. J. M., Yang, J., Sayol, F., Neate-Clegg, M. H. C., Alioravainen, N., Weeks, T. L., Barber, R. A., Walkden, P. A., MacGregor, H. E. A., Jones, S. E. I., Vincent, C., Phillips, A. G., Marples, N. M., Montaño-Centellas, F. A., Leandro-Silva, V., Claramunt, S., … Schleuning, M. (2022). AVONET: Morphological, ecological and geographical data for all birds. Ecology Letters, 25(3), 581–597. https://doi.org/10.1111/ele.13898
Herberstein, M. E., McLean, D. J., Lowe, E., Wolff, J. O., Khan, M. K., Smith, K., Allen, A. P., Bulbert, M., Buzatto, B. A., Eldridge, M. D. B., Falster, D., Fernandez Winzer, L., Griffith, S. C., Madin, J. S., Narendra, A., Westoby, M., Whiting, M. J., Wright, I. J., & Carthey, A. J. R. (2022). AnimalTraits—A curated animal trait database for body mass, metabolic rate and brain size. Scientific Data, 9(1), Article 1. https://doi.org/10.1038/s41597-022-01364-9
Sharing/Access information
Interaction data were derived from the list of references in the file data_references.csv
Code/Software
All code is for R. R packages used are listed at the top of each script.
Using a systematic search, trophic and non-trophic interactions between tetrapod species of the North American boreal forest were extracted from the literature. All extant tetrapods that regularly live, breed, or migrate in the nearly 600 million hectares of the North American boreal biome were included. Wild, non-native species known to occur in self-sustaining populations were included, such as feral horses. Not all are woodland species, as the boreal biome encompasses wetlands, urban areas, meadows, and some agricultural matrix. Given the wide scope of possible non-trophic interactions and varying degrees of ecological importance, the non-trophic interaction search focused primarily on interactions that affected nesting or denning, feeding, and access to territory, because these non-trophic interactions include both summer and winter processes and can affect species distributions and individual survival in an obvious way. We included only recorded ecological interactions. Species other than terrestrial tetrapods were classified into groups, as it was infeasible to include every organism at the species level for this spatial scale, and species-level information was often lacking. We treated these groups as nodes that could be the "giver" or the "receiver" of an interaction, like the species-level nodes in the network.