DOI: 10.5061/dryad.08kprr5dm
title: Data and code for: Evolutionarily distinct species in frugivore networks have fewer links and more specialized partners

description: Ecological networks describe the complex set of interconnections among
 species and their environment, and network structure can inform the
 stability, resilience, and functioning of ecosystems. Increasing attention
 is being paid to the mechanisms that determine species interactions.
 Phylogeny has informed our understanding of connections within networks,
 mostly by describing the strength of phylogenetic conservation of
 interactions. Here, we examine how the phylogenetic position of a species
 relates to its functional position within a network, testing the
 relationship between phylogenetic and network topologies. Time
 period: Early 20th century to present. We used a large dataset of
 frugivore interactions to calculate partner degree and degree, and bird
 and plant phylogenies to calculate local evolutionary distinctiveness
 (ED), evolutionary distinctiveness calculated on a community-level
 phylogeny. We then fit binomial Bayesian models to estimate the effect of
 evolutionary distinctiveness on partner degree and degree, comparing the
 effects of known bird traits from AVONET. The partners of both high ED
 birds and plants are less likely to interact with other members of the
 community, and birds with high ED tend to interact with fewer plant
 species. In birds, the effect size of ED is comparable to or larger than
 measured bird traits. Our analysis illustrates how phylogenetic
 relationships affect present-day ecologies and underscores the unique
 ecological contribution of evolutionary outliers.
description: ZanneTreeTrim.tre and EricsonBirdTreeTrim.tre are trimmed
 versions of phylogenies from Zanne et al. 2014 and Jetz et al. 2014,
 respectively. Phylogenies were pruned to include only species represented
 in the Fricke and Svenning (2020) dataset.
description: # Data and code for: Evolutionarily distinct species in frugivore networks
 have fewer links and more specialized partners
 [https://doi.org/10.5061/dryad.08kprr5dm](https://doi.org/10.5061/dryad.08kprr5dm) ## Description of the data and file structure In this analysis, we model the relationship between local evolutionary distinctiveness (ED) and two metrics of species positions in networks: partner degree and degree. We additionally examine the relationship between local ED of partners between phylogenies. We find that species with higher local ED tend to have fewer connections and that their partners tend to be more specialized ## Files and variables: ### File: ZanneTreeTrim.tre **Description:**  A phylogeny of plants from Zanne et al. (2014), trimmed to only contain species represented in the interaction networks from Fricke and Svenning (2020). ### File: birdsynonyms.csv **Description:** A dictionary of bird binomial synonyms. The binomial Latin names of species can change when species relationships are revised; this file contains information to fix discrepancies between the species interaction networks and the bird phylogeny. ##### Variables * Row: Row number * original: Accepted bird species identity used in networks in Fricke and Svenning (2020). * synonym: Synonym species identity represented in Ericson backbone phylogeny from Jetz et al. (2014). ### File: README.txt **Description:** Readme containing information about files, code, and instructions to reproduce analyses. ## Code/software Accompanying R code can be run in the open source language R. Analyses were conducted with R  version 4.3.2. **Dependencies (version number when analyses were conducted)** * tidyverse 2.0.0 * cli 3.6.3 * modelr 0.1.11 * bipartite 2.20 * picante 1.8.2 * ape 5.8-1 * cmdstanr 0.7.1 * brms 2.20.4 * tidybayes 3.0.6 * ggplot2 3.5.1 * ggdist 3.3.1 * cowplot 1.1.3 * magick 2.8.2 * taxize 0.9.100 ## Setting up for analysis Working directory should include folders named 'data', 'output', and 'plots.' 'output' should contain folders 'models', 'stats', and 'summaries.' Run 1_file_downloads.R to download necessary files from various repositories. This includes downloading the large collection of bird phylogenies from birdtree.org and subsetting it to the six used in the analysis, producing 'data/EricsonBirdTreeTrim.tre.' Run 2_synonymization.R to create 'data/birdsynonyms.csv', a species dictionary to match network species IDs to phylogeny species IDs. This step may be skipped as the file is included in the .zip file. Run 3_analysis.R to perform all initial analyses and create publication plots. Analyses may be performed on different subsets of the data by changing the 'subset_type' variable. 1. subset_type="all" performs analyses on all networks 2. subset_type="comp" repeats analyses on the subset of networks labeled as comprehensively sampled, as defined in the Fricke and Svenning data (as opposed to networks produced by focusing on few members of a community) 3. subset_type="fleshy" performs analyses on the subset of networks in which all plants are fleshy-fruited (as opposed to networks where some plants produce dry fruit, which may have different coevolutionary relationships with their consumers) 4. subset_type="quant" performs analyses on the quantitative subset of networks, in which the number of interactions between each species pair is reported (as opposed to binary reports of whether interactions were observed or not) Different analyses make use of the run_model() function, which is defined in the models.R depending on the modeltype and subset_type variables. To see specifications for each model or to make changes, consult the models.R file. The available model types are combinations of the model dependent variable ("degree", "partnerdegree", or partner evolutionary distinctiveness ("partnerED")), the focal taxa of the model ("bird" or "plant"), and for plant-focal degree or partner degree models, whether data should include all networks regardless of frugivore taxa ("alltaxa") or only those in which birds are the frugivores ("birdtaxa"). * "degree_bird", "partnerdegree_bird","degree_plant_alltaxa", "degree_plant_birdtaxa", "partnerdegree_plant_alltaxa", "partnerdegree_plant_birdtaxa", "partnerED_bird," and "partnerED_plant" Other functions used in 3_analysis.R are defined in network_functions.R. Some of these functions were taken from Fricke and Svenning 2020, and are indicated as such in the file. ## Access information Data was derived from the following sources: * Fricke and Svenning 2020 ([https://doi.org/10.5061/dryad.44j0zpcbx](https://doi.org/10.5061/dryad.44j0zpcbx)) * Zanne et al. 2014 ([https://doi.org/10.5061/dryad.63q27](https://doi.org/10.5061/dryad.63q27)) * Jetz et al. 2014 (birdtree.org)