DOI: 10.5061/dryad.bcc2fqz79
title: Data from: Unveiling the food webs of tetrapods across Europe through the prism of the Eltonian niche

description: 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.
description: 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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description: "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.