DOI: 10.5061/dryad.k59m37f
title: Data from: Inferring predator-prey interactions in food webs

description: 1. Food webs are a powerful way to represent the diversity, structure, and
 function of ecological systems. However, the accurate description of food
 webs requires significant effort in time and resources, limiting their
 widespread use in ecological studies. Newly published methods allow for
 the inference of feeding interactions using proxy variables. Here, we
 compare the accuracy of two recently described methods, as well as
 describe a composite model of the two, for the inference of feeding
 interactions using a large, well-described dataset. 2. Both niche and
 neutral processes are involved in determining whether or not two species
 will form a feeding link in communities. Three different models for
 determining niche constraints of feeding interactions are compared, and
 all three models are extended by incorporating neutral processes, based on
 relative abundances. The three models compared here infer niche processes
 through 1) phylogenetic relationships, 2) local species trait
 distributions (e.g. body size), and 3) a composite of phylogeny and local
 traits. 3. We show that all three methods perform well at predicting
 individual species interactions, and that these individual predictions
 scale up to the network level, resulting in food-web structure of inferred
 networks being similar to their empirical counterparts. 4. Our results
 indicate that inferring food-web structure using phylogenies can be an
 efficient way of getting summary webs with minimal data, and offers a
 conservative test of changes in food-web structure, particularly when
 there is low species turnover between sites. Inferences made using traits
 requires more data, but allows for greater understanding of the mechanisms
 underlying trophic interactions. A composite model of the two methods
 provides a framework for investigating the importance of how phylogeny,
 trait distributions, and relative abundances, affect species interactions,
 and network structure.
description: Adjacency_matricesThis folder contains 21 binary adjacency matrices. The first column contains the row names of the matrix. The columns represent taxa as consumers, and the rows represent taxa as resources. Aij = 1 when column j consumes resource i, and 0 otherwise. The original matrices can be found in Thompson and Townsend, 1999, 2004. (DOI: 10.2307/3546998; DOI: 10.1080/00288330.2004.9517265). Adjacency matrices are modified from originals as described in main text. Briefly, the taxa have been aggregated to resolve naming discrepancies, and only the predator-prey interactions have been retained.Taxa_dry_weight_abundanceThis file contains estimated dry weight and numerical densities for 17 stream communities in New Zealand. Dry weight estimates and numerical densities were calculated as described in main text. Columns: "food.web" indicates which community the data come from. "taxa" is a character string for each taxon found in the community which has data on dry weights and abundance. "dw" is the estimated dry weight in grams for a given taxa. "no.m2" is the estimated number of individuals per meter squared.niche_forbidden_taxaThis is a small table of taxa which are considered to be "niche forbidden" e.g. do not consumer animal prey. See main text for details.other_feeding_interactionsThis file contains data on published feeding interactions from New Zealand streams. Each row represents a consumer-resource interaction, and contains phylogenetic information for both the consumer and resource. The "res." prefix in columns indicates that column refers to the resource, and the "con." prefix refers to data on the consumer. The "source.id" column indicates the original citation for where the data came from.taxonomyThis file contains phylogenetic information for taxa in this study. The "name" column matches taxa names used in the study. i.e. not all taxa are resolved to the same level, and this is used to access other phylogenetic information. The "minimum.res.method" and "minimum.con.method" are specific to the WebBuilder analysis. See main text for more details.