DOI: 10.5061/dryad.fqz612k2z
title: Mutualism and predation have contrasting effects on pine canopy arthropod diversity

description: Predators are recognized to increase prey diversity by suppressing
 competitively dominant species, where mutualists are predicted to reduce
 diversity by promoting a competitively dominant partner. However this
 trend, and the effect of these interactions when they cooccur, remain
 underexplored. We investigated the effects of predation and mutualism on
 the diversity of pine-associated arthropods by excluding insectivorous
 birds and mutualist ants from branches of Pinus ponderosa and sampling
 arthropods during a 2-year period. We identified 92,549 arthropods to the
 species or morphological species level. In the absence of ants, birds had
 no effects on diversity while in the absence of birds, ants decreased
 Simpson diversity and Pieolu's evenness but did not affect species
 richness. However, in the presence of ants, birds increased diversity,
 evenness, and richness. Effects on arthropod composition mirrored
 diversity: birds alone had no effect on composition, ants alone increased
 aphid and aphid predator abundance, but in the presence of ants, birds
 reduced aphid and aphid predator abundance. In summary, we provide
 evidence that mutualists reduce diversity and alter community composition
 in pine-associated arthropods by promoting the dominance of partner
 species, and these interaction together are non-additive, with predator
 effects likely working through the disruption of the mutualism.
description: # Mutualism and predation have contrasting effects on pine canopy
 arthropod diversity
 [https://doi.org/10.5061/dryad.fqz612k2z](https://doi.org/10.5061/dryad.fqz612k2z) ## Description of the data and file structure Work was conducted at the Manitou Experimental Forest in Woodland Park, Colorado, USA (39°06′02″ N, 105°05′32″ W) in mature stands of ponderosa pines at an elevation of 2400 m. In 2001, we selected 21 sites over 750 ha area selecting four adult reproductive trees (84 trees total). In each site (“block” hereafter, "B" in dataset), one tree was allocated to one of four exclusion treatments: birds and ants excluded, birds alone (ants excluded), ants alone (birds excluded), and birds and ants together (Fig. 1a). Two branches per tree, ranging 0.5 to 6.0 m from the ground (2.4 ± 0.8 m, mean ± SE), were sampled for arthropods. For bird exclusions we installed a 2.5-cm opening monofilament netting bag over each branch. For ant exclusions we applied sticky paste (Tanglefoot, Grand Rapids, Michigan, USA) at the base of each tree, while applying a similar amount of paste to half the trunk of trees with ants to account for any affects not associated with excluding ants. During the first week of each month from July to September in 2001 and June to August in 2002, we collected arthropods alternating between the two experimental branches. Branches were beaten with a padded bat to dislodge arthropods into a 1.5 x 1.5 m fabric tub (0.5 m deep) and preserved in 70% ethanol. Each arthropod was identified to species or morphological species. For 2000 there are blocks 1-16, for 2001 and 2002 there are 21 blocks. The treatments are 00, 01, 10, 11. They refer to the 2 x 2 factorial manipulation of birds and ants. First digit refers to presence/absence of birds and second digit refers to presence/absence of Ants (ex. 01 - birds excluded, ants present). Within the file the first line is a legend.  The second line is the block, treatment, month and year. After that there are taxa codes (we’ll decipher those later) and then the abundance of that taxa for each size class (1mm, 2mm, … 20mm). Next to the taxa code is a number either 0 or 1. This indicates winged or not.  It can be either kept as a variable or appended to the taxa code name. For example, “Cinara1J, 0” and “Cinara1J, 1” could be “Cinara1J_0” and Cinara1J_1”. When the taxa code = “x” this is an unused taxa code and can be cut from the dataset. Each data file has a row for every taxa code whether or  not there were any observations for that taxa code. ### Files and variables #### File: compiled\_data.txt **Description:** This is a compiled text file of all collected and identified arthropods from 2000 to 2002.  \**Note on "NA" values: **Taxa were identified to varying levels due to limitations in identification or sample condition. These entries contain "NA" in some of the taxonomic columns to reflect that fine-scale identification was not possible or necessary. This level of identification is consistent with how the data were analyzed: the majority of analyses were conducted at the order level. Therefore, these "NA" values are **not missing data**, but **intentional placeholders** indicating the finest taxonomic resolution available in the study. #### File: PINE\_ARTH\_DATA\_WRANG-6.6.23.Rmd **Description:** This is the code we used to wrangle data, removing unnecessary labels and fields, compiling years, etc.  #### File: TAXA\_FILE\_FEB\_15\_2023\_CORRECTED\_CARLA(11.30.23).csv **Description:** Once data wrangling is complete and taxonomy columns have been added, use this file join to add taxonomy information. \**Note on "NA" values: **This file contains "NA" values in certain taxonomic columns for the same purpose as the compiled_data.txt file, to reflect that fine-scale identification was not possible or necessary for certain samples. ##### Variables * Taxacode: Numeric code * Old_name: True old name of collected arthropod including winged and juvenile status * New_name: Name used for analyses * Class: Taxonomic Class * Order: Taxonomic Order * Suborder: Taxonomic Suborder * Family: Taxonomic Family * Genus: Taxonomic Genus * Species: Taxonomic Species #### File: PINE\_ARTH\_DATA\_ANALYSES-2025.Rmd **Description:** This is the code we used to analyze the data, starting with different methods to test diversity, using a few different types of multivariate analyses, and additional analyses we eventually did not include in the manuscript (indicator species analysis).  ##### Variables * Tax_ID: Identification code for taxonomic species which formerly included winged and juvenile states, but is currently the same as "*New_name" * B: Stands for "Block" and identifies which of the 21 sets of 4 trees was sampled. Single digit blocks are identified by the first digit with the second digit blank.  * TREATMENT: Identifies which of the four treatments the tree within the block received. 1 and 0 represent the presence and absence of birds and ants. The first digit indicates bird presence or absence and the second digit indicated ant presence or absence. i.e. treatment 10 codes for bird presence and ant exclusion, 01 indicates bird exclusion and ant presence, etc.  * month: Month in which arthropods were collected. * sums: Total number of that taxa found within that sample.  * n: Indicates number of branches on the tree arthropods were collected from. Branches were sampled rotating between 2 or the 3 branches under treatment.  * YEAR: Year sample was collected.  * Old_name: Taxa ID with spaces removed from name. * Taxacode: Numeric code for taxa ID * New_name: Taxa ID without winged or juvenile status used for reference when changing Taxa_ID in code. * Class: Taxonomic Class * Order: Taxonomic Order * Suborder: Taxonomic Suborder * Family: Taxonomic Family * Genus: Taxonomic Genus * Species: Taxonomic Species ## Code/software We ran statistical analyses in R software version 4.2.1 (R Core Team 2013). Packages used for analyses include: lmerTest, ggplot2, ggpubr, reshape2, tidyverse, ggrepel, rlist, qdapRegex, vegan, multcomp, lsmeans, asbio, PerformanceAnalytics, iNEXT, devtools.