DOI: 10.5061/dryad.qnk98sfqb
title: Data on arthropod abundance in tropical forest restoration plots with high or low plant phylogenetic diversity

description: Consideration of plant phylogenetic diversity in ecological restoration
 carries substantial potential, as communities with a greater diversity of
 lineages with older evolutionary histories can increase the diversity of
 niches and thus are likely to recover larger species networks than
 communities clustered in specific clades with reduced variation in
 functional traits. In this study, we experimentally assessed how arthropod
 communities were affected by the phylogenetic diversity of a set of
 tropical tree species. We established 12 experimental restoration plots
 with either high or low plant phylogenetic diversity, while maintaining
 constant the number of plant species. After one and three years,
 arthropods with different feeding habits (herbivores, predators,
 pollinators, and detritivores) were collected and identified as
 morphospecies or operational taxonomic units using metabarcoding
 techniques. We provide insights on the influence of plant phylogenetic
 diversity on arthropod abundance and species diversity, particularly among
 predator, pollinator, and detritivore common and dominant species, which
 increased with plant phylogenetic diversity. The trend, however, was the
 opposite for the diversity of herbivore common and dominant species, which
 decreased as plant phylogenetic diversity increased. These findings
 highlight the importance of considering plant species richness when
 designing restoration strategies, but also their evolutionary histories,
 as the same number of plant species can produce different outcomes for
 higher trophic levels, as a function of their phylogenetic
 relationships. 
description: Between July 2018 and January 2019, we established 12 restoration
 plantings (15 × 15 m) within the active cattle pastures, with a minimum
 distance of 50 m among the plots. To manipulate the phylogenetic diversity
 of the plantings, we used a total of 43 tropical tree species. In half of
 the plots, we established plant assemblages with high phylogenetic
 diversity (HPD), incorporating 27 phylogenetically distant species from 23
 families, widely distributed across the phylogeny of the regional pool of
 species (see below). In the remaining plots, we established plantings with
 low plant phylogenetic diversity (LPD), with 27 species from 10 families
 clustered within the phylogeny and with more recent common
 ancestors. We collected arthropods from the
 experimental plots in September 2019 and 2021 (~ 1 and 3 years after
 establishment of restoration plots), using distinct methods for each
 arthropod guild. To capture pollinators, we used pan traps comprising
 three plastic containers painted in blue, yellow, and white, each filled
 with 200 ml of soapy water. This variety of colors is recommended to
 attract the greatest diversity of pollinators, as different taxa have
 distinct preferences for different colors (Leong, et al., 1999, Padrón, et
 al., 2020). Two sets of traps were placed on each plot, one in the middle
 of the upper right quadrant and the other at the plot´s center. To collect
 adult lepidopterans, we used one Van Someren- Rydon trap with a bait made
 with a mixture of pineapple fermented with beer, positioned at the plot´s
 center. Sweep nets and manual surveys were employed along four
 perpendicular transects positioned every two meters within each plot to
 collect herbivores and predators from the canopies of saplings and
 surrounding vegetation. For detritivores and other crawling arthropods,
 two pitfall traps were placed in the middle of the lower left quadrant, as
 well as in the center of each plot. These diverse traps enabled the
 collection of resident organisms colonizing the plots but also those
 passing through the vegetation islands. After 72 hours, specimens were
 collected from all traps and stored with 70% undenatured ethanol, except
 for lepidopterans which were collected after 24 hours in the Van
 Someren-Rydon traps. These specimens were subsequently frozen and stored
 in glassine paper bags. After taxonomic and/or molecular identification
 (see below), organisms were classified based on their feeding habits,
 using available ecological literature for the most specific taxonomic
 level. We classified organisms that consumed any part of plants (including
 seeds) as herbivores, except for adult Lepidoptera specimens and other
 floral visitors, which were classified as pollinators. Organisms that feed
 on other animals were classified as predators, and those involved in the
 consumption of decomposing organic matter or associated with the cycling
 of soil nutrients were classified as detritivores. Organisms that could
 not be classified were excluded from subsequent analyses.
 We systematically grouped all collected organisms based on their
 respective order, family, and when feasible, assigned them to genus and
 species. In cases where precise taxonomic identification was unattainable,
 we categorized the specimens as morphospecies. For molecular
 identification, we sorted specimens into two distinct groups: i) those
 obtained from color and Van Someren-Rydon traps, and ii) those captured
 with pitfall traps, manual surveys, and sweep nets. Specimens were
 categorized into small (<em>&lt; </em>3 mm), medium
 (&gt; 3 mm and &lt; 15 mm) and large (&gt; 15mm) size classes,
 according to the criteria outlined by Galvez-Reyes, et al. (2021). Whereas
 the entire body was used for small arthropods, medium-sized arthropods
 were dissected to select the thorax (including the head), and only two
 legs were selected for large arthropods. After placing specimens or their
 parts in falcon tubes according to their size class, we extracted DNA from
 the composite arthropod samples of each size category and group, to
 perform a metabarcoding analysis (i.e. sensu Yu et al., 2012), following a
 modified protocol by Galvez-Reyes, et al. (2021) using a DNeasy® Blood and
 Tissue Kit (Qiagen). We used primers B_F 5’ CCIGAYATRGCITTYCCICG 3'
 (Shokralla, et al., 2015) and Fol-degen-R 5’ TANACYTCNGGRTGNCCRAARAAYCA
 3' (Yu, et al., 2012) to amplify a 418-base pair region located at
 the 5’ end of the mitochondrial COI gene. This specific region is part of
 the standard barcode region for metazoans. For the construction of
 metabarcoding libraries, individual samples (n =104) were pooled and
 grouped in equimolar proportions based on their designated category
 (pollinators or crawling arthropods), resulting in the generation of 60
 final libraries (one library per sample). DNA samples, along with negative
 control, were sequenced using an Illumina Miseq 2x300 bp platform at
 Illumina (RTL Genomics). Additional details on bioinformatic read
 processing are elaborated in Supplementary Information A1.
description: # Data on arthropod abundance in tropical forest restoration plots with
 high or low plant phylogenetic diversity
 ## Description of the data
 and file structure Data sets contents 1. Abundance of arthropods
 (predators, herbivores, pollinators and detritivores) 2. Arthropod Species
 Abundance by Rank (to calculate species rank abundance curves) 3.
 Arthropod Species Abundance by treatment and year (by guild: Predators,
 herbivores, Pollinators and Detritivores)- To calculate number of Hills 4.
 Arthropod Species Abundance by treatment and year (to calculate species
 composition differences for both, Morphospecies and OTUs) *in all cases:
 HPD=High Phylogenetic Diversity and LPD = Low Phylogenetic Diversity
 Experimental Procedure: The study was carried out within 'Los
 Amigos' cattle ranch, located in the buffer zone of the Los Tuxtlas
 biosphere reserve (18°32’56” N, 94°59’58” W) in Veracruz, México. The
 climate in this area is warm and humid with mean temperatures ranging from
 24 to 26°C and total precipitation ranging from 2,000 to 4,000 mm (Soto,
 2004). The vegetation in this region includes evergreen tropical forest
 with a high level of fragmentation surrounded by an agricultural and
 cattle ranching landscape (Von Thaden, et al., 2018). The ranch itself has
 cattle pastures, bordered by remnants forests Between July 2018 and
 January 2019, we established 12 restoration plantings (15 × 15 m) within
 the active cattle pastures, with a minimum distance of 50 m among the
 plots. To manipulate the phylogenetic diversity of the plantings, we used
 a total of 43 tropical tree species. In half of the plots, we established
 plant assemblages with high phylogenetic diversity (HPD), incorporating 27
 phylogenetically distant species from 23 families, widely distributed
 across the phylogeny of the regional pool of species (see below). In the
 remaining plots, we established plantings with low plant phylogenetic
 diversity (LPD), with 27 species from 10 families clustered within the
 phylogeny and with more recent common ancestors (Supplementary information
 Table S1). In each plot we planted between 1 and 7 seedlings (between 30 -
 70 cm tall) from each species in a 1 × 1 m grid, resulting in a total of
 196 individuals per plot. However, due to plant mortality, between 21 and
 28 species (15 to 19 non-pioneer species and 10 to 12 pioneer species)
 remained in each plot, but contrasts in phylogenetic diversity between
 both treatments were maintained (Supplementary information Table S1,
 Santos-Gally and Boege, 2022). We collected arthropods from the
 experimental plots in September 2019 and 2021 (~ 1 and 3 years after
 establishment of restoration plots), using distinct methods for each
 arthropod guild. To capture pollinators, we used pan traps comprising
 three plastic containers painted in blue, yellow, and white, each filled
 with 200 ml of soapy water. This variety of colors is recommended to
 attract the greatest diversity of pollinators, as different taxa have
 distinct preferences for different colors (Leong, et al., 1999, Padrón, et
 al., 2020). Two sets of traps were placed on each plot, one in the middle
 of the upper right quadrant and the other at the plot´s center. To collect
 adult lepidopterans, we used one Van Someren- Rydon trap with a bait made
 with a mixture of pineapple fermented with beer, positioned at the plot´s
 center. Sweep nets and manual surveys were employed along four
 perpendicular transects positioned every two meters within each plot to
 collect herbivores and predators from the canopies of saplings and
 surrounding vegetation. For detritivores and other crawling arthropods,
 two pitfall traps were placed in the middle of the lower left quadrant, as
 well as in the center of each plot. These diverse traps enabled the
 collection of resident organisms colonizing the plots but also those
 passing through the vegetation islands. After 72 hours, specimens were
 collected from all traps and stored with 70% undenatured ethanol, except
 for lepidopterans which were collected after 24 hours in the Van
 Someren-Rydon traps. These specimens were subsequently frozen and stored
 in glassine paper bags. After taxonomic and/or molecular identification
 (see below), organisms were classified based on their feeding habits,
 using available ecological literature for the most specific taxonomic
 level. We classified organisms that consumed any part of plants (including
 seeds) as herbivores, except for adult Lepidoptera specimens and other
 floral visitors, which were classified as pollinators. Organisms that feed
 on other animals were classified as predators, and those involved in the
 consumption of decomposing organic matter or associated with the cycling
 of soil nutrients were classified as detritivores. Organisms that could
 not be classified were excluded from subsequent analyses. We
 systematically grouped all collected organisms based on their respective
 order, family, and when feasible, assigned them to genus and species. In
 cases where precise taxonomic identification was unattainable, we
 categorized the specimens as morphospecies. For molecular identification,
 we sorted specimens into two distinct groups: i) those obtained from color
 and Van Someren-Rydon traps, and ii) those captured with pitfall traps,
 manual surveys, and sweep nets. Specimens were categorized into small
 (*&lt; *3 mm), medium (&gt; 3 mm and &lt; 15 mm) and large (&gt; 15mm)
 size classes, according to the criteria outlined by Galvez-Reyes, et al.
 (2021). Whereas the entire body was used for small arthropods,
 medium-sized arthropods were dissected to select the thorax (including the
 head), and only two legs were selected for large arthropods. After placing
 specimens or their parts in falcon tubes according to their size class, we
 extracted DNA from the composite arthropod samples of each size category
 and group, to perform a metabarcoding analysis (i.e. sensu Yu et al.,
 2012), following a modified protocol by Galvez-Reyes, et al. (2021) using
 a DNeasy® Blood and Tissue Kit (Qiagen). We used primers B_F 5’
 CCIGAYATRGCITTYCCICG 3' (Shokralla, et al., 2015) and Fol-degen-R 5’
 TANACYTCNGGRTGNCCRAARAAYCA 3' (Yu, et al., 2012) to amplify a
 418-base pair region located at the 5’ end of the mitochondrial COI gene.
 This specific region is part of the standard barcode region for metazoans.
 For the construction of metabarcoding libraries, individual samples (n
 =104) were pooled and grouped in equimolar proportions based on their
 designated category (pollinators or crawling arthropods), resulting in the
 generation of 60 final libraries (one library per sample). DNA samples,
 along with negative control, were sequenced using an Illumina Miseq 2x300
 bp platform at Illumina (RTL Genomics). Additional details on
 bioinformatic read processing are elaborated in Supplementary Information
 A1.