DOI: 10.5061/dryad.7m0cfxq2h
title: The interplay between defaunation and phylogenetic diversity affect leaf damage by natural enemies in tropical plants

description: Natural enemies play an important role in controlling plant population
 growth and vegetation dynamics. Tropical rainforests host the greatest
 diversity of herbivores, from large mammalian ungulates to microscopic
 pathogens, generating and maintaining plant diversity. By feeding on the
 same resources, large mammalian herbivores may interfere with plant
 consumption and leaf damage by important enemy guilds such as invertebrate
 herbivores and pathogens, triggering indirect trophic cascades. However,
 the impact of local extinctions of large herbivores on plant-enemy
 interactions is relatively unknown. We experimentally tested the effects
 of defaunation of large mammalian herbivores (e.g., peccaries, tapirs,
 brocket deer; hereafter, large herbivores) on leaf damage of 3,350
 understory plants in tropical rainforests of Brazil. We examined leaf
 damage in 10,050 leaves from 333 morphospecies by assigning the area
 consumed or damaged by five guilds of insect herbivores and leaf pathogens
 within 86 paired open-closed plots and investigated the joint effects of
 defaunation and plant phylogenetic diversity. Plants released from large
 herbivores had 9% less leaf damage; this difference was due to the lower
 leaf pathogens incidence (29%) rather than insect herbivory. Evolutionary
 Distinctness was similarly and positively correlated with leaf damage in
 all treatments, suggesting additive effects of defaunation and
 phylogenetic diversity. Total and pathogenic leaf damage (but not insect
 damage) decreased with plant richness across treatments, and large
 herbivores' exclusion resulted in increased plant species richness.
 This suggests that large herbivores' exclusion leads to a dilution of
 total and pathogens’ leaf damage by increasing plant species richness. Our
 results suggest that large herbivores' indirect effects decrease the
 dilution potential of plant communities against pathogens and rather
 reinforce their top-down impact on vegetation, demonstrating a previously
 overlooked cascading effect of large herbivore extinction on forest
 ecosystems. Synthesis: The extinction of large mammalian herbivores can
 lead to a decrease in pathogen-driven leaf damage, a previously unknown
 indirect effect in forest ecosystems, which might have consequences for
 plant fitness and ultimately for plant diversity. Large herbivores and
 plant pathogens might have synergistic effects in regulating the diversity
 of plant communities in some of the most diverse ecosystems on Earth.
description: Our study was carried out in a multi-site, long-term experiment
 (DEFAU-BIOTA), distributed at four study sites located in protected areas
 of the Atlantic Forest in the state of São Paulo, Brazil. The four sites
 have different compositions of large herbivore communities, but
 nevertheless, a rich assemblage of species can be found in all of them. 
 Due to different human pressures, sites differ in the presence of the
 largest ground-dwelling mammal species, the white-lipped peccary
 (<em>Tayassu pecari</em>) and the tapir (<em>Tapirus
 terrestris</em>) (Galetti et al., 2017). Although both species are
 present at site Itamambuca [ITA], only white-lipped peccaries are present
 at Ilha do Cardoso State Park [CAR]; at Carlos Botelho State Park [CBO]
 only tapirs are found, and neither of the species are present at Vargem
 Grande [VGM]. In each site, we installed 15 paired
 plots (5 m long x 3 m wide) in 2009–2010, but some of the plots collapsed
 over time; as a result, the data in this work were collected in nine
 paired plots in ITA, 10 in CBO and 12 in CAR and VGM, summing up 86 plots.
 Each pair consists of a closed, exclusion plot of medium and large mammals
 (hence simulating defaunation), and an open plot allowing free access to
 these animals (control). Each plot was subdivided into eight subplots of 1
 m<sup>2</sup>, in which three subplots were randomly chosen
 and all plants larger than 0,1 m and smaller than 1 m were marked,
 identified at the lowest possible taxonomic level, and accessed without
 disturbance to estimate leaf damage. We evaluated the
 leaf damage of all marked plants within each selected subplot in July,
 August, and November 2019. For each individual plant, we randomly chose
 three mature leaves (when possible; otherwise, we count on the available
 number per individual, that is, one or two leaves) to estimate their leaf
 damage according to the percentage of leaf area lost and/or damaged. Next,
 we visually assigned the following leaf damage categories for each
 selected leaf: 0 (intact), 1 ( 1–6% of lost and/or damaged leaf area), 2
 (6–12%), 3 (12–25%), 4 (25–50 %), 5 (50–75%) and 6 (75–99%). We proceed
 with this categorization of damage considering four feeding guilds of
 insect herbivores (internal and external chewers, galls and leaf miners),
 the guild of pathogens, and the total leaf damage caused by all groups,
 given that each leaf may be affected by more than one type of
 damage.
description: # The interplay between defaunation and phylogenetic diversity affect leaf
 damage by natural enemies in tropical plants
 This dataset is the
 original data sampled from a defaunation experiment, in which large
 mammalian herbivores were excluded, using a paired design of open-closed
 plots. The dataset contains the raw records of leaf damage caused by
 plants' natural enemies, using the herbivory index described in the
 main text, and before any averaging and/or analyses. The variables
 included in the dataset are as follows: * local: protected area in which
 the data was collected, ie., Itamambuca [ITA], Ilha do Cardoso State Park
 [CAR]; Carlos Botelho State Park [CBO]; Vargem Grande [VGM]. * plot:
 sequential number (1 to 86) identifying the pairwise plots studied within
 each local. * treatment: each pairwise plot is composed of two treatments
 = open (or the control plot, in which large mammals have open access) and
 closed (fenced, in which large mammals are excluded). * plotID = unique
 code for each plot, combining the local, plot and treatment information. *
 ID_plant = unique code for each individual seedling or sapling within each
 plot. This code is part of DEFAU-BIOTA long-term experimental study, and
 it is maintained by Prof. Galetti' group. * N_leaf = sequential
 number (1 to 3) to identify the leaf sampled in each individual plant. *
 binary_data = indicating whether the N_leaf has any type of damage y
 natural enemies (1), or not (0). NA = leaf not present in the plant. *
 perc_leaves_wdamage = percentage of leaves with any type of leaf damage
 per individual plant, considering the total leaves sampled, i.e., if there
 were either three, two or one leaf available to be sampled and all of then
 have damage, then it equals 100% and the value is 1; if two leaves out of
 three have damage, then the value is equal 0.66%; if one leaf out of
 three, then is 0.33%; one leave out of two = 0.5%; and if no leaf has
 damage, it is 0%. * leaf_damage = categorical value corresponding to the
 leaf damage category assigned for each sampled leaf: 0 (intact), 1 (1 - 6%
 of lost and/or damaged leaf area), 2 (6 - 12%), 3 (12 - 25%), 4 (25 - 50
 %), 5 (50 - 75%) and 6 (75 - 99%). NA = leaf not present in the plant. *
 ME = leaf damage category assigned to external chewers. NA = leaf not
 present in the plant. * bin_me = presence (1) or absence (0) of damage by
 external chewers in that leaf. * perc_me = percentage of leaves with ME in
 the corresponding individual plant. * MI = leaf damage category assigned
 to internal chewers. NA = leaf not present in the plant. * bin_mi =
 presence (1) or absence (0) of damage by internal chewers in that leaf. *
 perc_mi = percentage of leaves with MI in the corresponding individual
 plant. * PAT = leaf damage category assigned to pathogens. NA = leaf not
 present in the plant. * bin_pat = presence (1) or absence (0) of damage by
 pathogens in that leaf. * perc_pat = percentage of leaves with PAT in the
 corresponding individual plant. * MIN = leaf damage category assigned to
 leaf miners. NA = leaf not present in the plant. * bin_min = presence (1)
 or absence (0) of damage by leaf miners in that leaf. * perc_min =
 percentage of leaves with MIN in the corresponding individual plant. * GAL
 = leaf damage category assigned to galls. NA = leaf not present in the
 plant. * bin_gal = presence (1) or absence (0) of damage by galls in that
 leaf. * perc_gal = percentage of leaves with GAL in the corresponding
 individual plant.