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Data from: Unveiling the food webs of tetrapods across Europe through the prism of the Eltonian niche

Citation

O'Connor, Louise et al. (2020), Data from: Unveiling the food webs of tetrapods across Europe through the prism of the Eltonian niche, Dryad, Dataset, https://doi.org/10.5061/dryad.bcc2fqz79

Abstract

Aim

Despite the recent calls on integrating the interaction networks into the study of large‐scale biodiversity patterns, we still lack a basic understanding of the functional characteristics of large interaction networks and how they are structured across environments. Here, building on recent advances in network science around the Eltonian niche concept, we aim to characterize the trophic groups in a large food web, and understand how these trophic groups vary across space.

Location

Europe and Anatolia.

Taxon

Tetrapods (1,136 species).

Methods

We combined an expert‐based metaweb of all European tetrapods with their spatial distributions and biological traits. To understand the functional structure of the metaweb, we first used a stochastic block model to group species with similar Eltonian niches, and then analysed these groups with species’ functional traits and network metrics. We then combined these groups with species distributions to understand how trophic diversity varies across space, in function of the environment, and between the European ecoregions.

Results

We summarized the 1,136 interacting species within the metaweb into 46 meaningful trophic groups of species with a similar role in the metaweb. Specific aspects of the ecology of species, such as their activity time, nesting habitat and diet explained these trophic groups. Across space, trophic diversity was driven by both biotic and abiotic factors (species richness, climate and primary productivity), and the representation of trophic groups differed among European ecoregions.

Main conclusions

We have characterized the Eltonian niche of species in a large food web, both in terms of species interactions and functional traits, and then using this to understand the spatial variation of food webs at a functional level, thus bringing together network science, functional ecology and biogeography. Our results highlight the need to integrate multiple aspects of species ecology in global change research. Further, our approach is strongly relevant for conservation biology as it could help predict the impact of species translocations on trophic diversity.

Methods

The network of potential trophic interactions between all European tetrapod species (hereafter, the metaweb) was built using a combination of expert knowledge, published information and field guides (a list of references is found below). Trophic interactions between a predator and its prey were identified from published accounts of their observation, morphological similarities between potential prey and literature‐referenced prey and, in the absence of this information, the diet of the predator's sister species.

The trophic links for mammals were compiled from the Handbook of the Mammals of the World composed of nine volumes (Wilson and Mittermeier 2009–2019). Furthermore, we considered multiple books on the mammalian fauna of the single countries and all volumes of Mammalian Species (published by the American Society of Mammalogists) available for species included in the database. The trophic links for breeding birds were compiled from the Handbook of the Birds of Europe, the Middle East and North Africa (9 volumes; Cramp et al. 1977–1994), the Handbook of the Birds of the World (16 volumes; del Hoyo et al 1992–2013), and the Handbook of the Birds of the World Alive website (del Hoyo et al. 2014). The trophic links for amphibians and reptiles were compiled from the Handbuch der Reptilien und Amphibien Europas (Arntzen et al. 1999; Bohme 1984; Fritz 2001; Grossenbacher and Thiesmeier 2003; Thiesmeier et al. 2004) plus multiple books and papers on the herpetofauna of the single countries. Trophic links for each species were compiled by the authors using a standardized data input protocol in MS Excel. For each species, we included in the database all trophic links reported in the publications using the highest possible taxonomic detail. Most of the time the information was available at the level of family or higher; for instance, the food habits of Falco tinnunculus (the common kestrel) are described as: “in Europe up to 90% voles, with some mice and shrews; open area passerines normally less important […]; also lizards and insects […]”, therefore we included as potential prey species all mammals of the families Arvicolinae, Muridae, and Soricidae, all birds of the family Alaudidae, and all reptiles of the family Lacertidae.

 The metaweb contained 1,136 tetrapod species and a total of 50,408 potential trophic interactions. In this metaweb, 883 basal species did not prey on European tetrapod species (i.e. basal species here could feed on plants, detritus, invertebrates, fish, domestic animals or were coprophagous), 213 intermediate consumer species had both prey and predator species among European tetrapods and 40 top predator species had no predator species. The metaweb had a connectance of 0.0385.

To build trophic groups, we used a stochastic block model (SBM) on the metaweb of potential trophic interactions (R‐package mixeR version 1.8 Daudin et al., 2008; Miele, 2006)), following previous studies (Baskerville et al., 2011; Gauzens et al., 2015; Kéfi et al., 2016; Mariadassou, Robin, & Vacher, 2010). The SBM is a random graph model with several groups of nodes (also known as ‘group model’ in Allesina and Pascual (2009) or ‘block model’ in Newman and Leicht (2007)). A parameter of this model is an aggregated graph with groups of nodes, linked to one another through edges that represent the probability of connection between any two nodes in the corresponding groups. Consequently, two nodes belonging to the same group have the same probability of connection with all other nodes in the graph. Given a network, the statistical machinery of the SBM aims to recover the groups defining similar groups of species in terms of the interactions they have with each other (Gauzens et al., 2015). The goodness of fit of the model is assessed using the integrated classification likelihood (ICL) information criterion. Applied to the metaweb, the SBM inferred groups of species such that two species belonged to the same group if they had the same probability of interacting with all other species in the metaweb ‐ in other words, they potentially preyed on similar sets of species, and were potentially preyed upon by similar sets of species. Using the SBM, we partitioned the species in the metaweb along a range of 10–60 groups, hereafter referred to as trophic groups. We defined the optimal number of groups based on the partitioning of the metaweb that maximized the ICL criterion. We then computed the average trophic level of each trophic group (R‐package NetIndices (version 1.4.4; Soetaert, Kipyegon Kones, & van Oevelen, 2015)).

 

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Usage Notes

"Metaweb_adults.csv" is the adjacency matrix that represents the metaweb of all potential trophic interactions between European tetrapods at the adult stage. Element (i,j) of this matrix is equal to 1 if species i (in row) is a potential predator of species j (in column), and 0 if there is no potential trophic interaction.

Species are referenced with an Id that is associated to their latin name in the text file "Spp_Id.txt"

"SBMgroups_spp.csv" presents the output of the stochastic block model, with the optimal partitioning of the metaweb into 46 trophic groups. This table lists the species and the trophic group they belong to. 

 

 

Funding

Agence Nationale de la Recherche