DOI: 10.5061/dryad.p2ngf1w0g
title: Data for beta diversity analysis of insect herbivory evolution

description: Modern ecosystems display complex associations of plants-insects that
 underwent a long evolutionary process since the appearance of
 mid-Paleozoic vascular plants. Although several major hypotheses explain
 the evolution of these plant–insect associations, the initial pattern of
 modern insect herbivory is poorly understood. To understand the antiquity
 of modern patterns of terrestrial arthropod herbivory, functional feeding
 group–damage type (FFG-DT) data were used to analyze a 305-million-year
 interval from Late Pennsylvanian to present, in which 134 plant
 assemblages were used to assess turnover (replacement of some species by
 other species between sites) and nestedness (difference in composition
 when no species are replaced between sites) in pairwise comparisons of
 DTs. Results of beta diversity analyses indicate the prototype pattern for
 modern insect herbivory was established on gymnosperm-dominated plant
 assemblages by late Middle Jurassic, antedating angiosperm dominance by 60
 million years. Turnover among plant groups and FFGs declined in earlier
 late Paleozoic whereas during the later Cenozoic nestedness generally
 increased. Insect feeding on gymnosperms showed one pattern of change with
 low turnover and high nestedness whereas a bimodal pattern characterized
 angiosperms. Ferns and angiosperms exhibited less DT functional breadth
 (host-plant “specificity” by herbivores) than gymnosperms, reflecting
 major differences in links between insect herbivores and their
 host-plants. This fundamental trophic shift is consistent with the Mid
 Mesozoic Parasitoid Revolution, implying top-down control of herbivores by
 their consumers rather than bottom-up regulation of food sources that
 shaped the modern herbivory pattern. These findings provide a data-rich
 account of the ecological origins of modern herbivory.
description: All the related raw data, figures and extended analyses are
 provided in the three datasets. Note: Some Triassic data from South Africa
 are not yet publicly available elsewhere and are still being processed.
 Researchers interested in using these data should contact Dr. Conrad
 Labandeira directly.
description: # Data from beta diversity analysis of insect herbivory evolution ##
 Description of the data and file structure ### Dataset_S1.zip The insect
 herbivory data collected from Paleozoic to Cenozoic plant assemblages is
 displayed in Dataset S1, titled "`Data Collection from Paleozoic to
 Cenozoic`," in an Excel file. It includes 180 plant assemblages,
 though only 168 have data on Damage Types (DTs) and Functional Feeding
 Groups (FFGs). The richness of DTs assigned to each FFG is also provided.
 1\) For detailed information about each plant assemblage, the following is
 included: * *Assemblage* represents the name of all plant assemblases or
 locality we can search before 2024, as referenced in the cited literature,
 such as the "Kimin", or "Iceland 9-8Ma";  *
 *Abbreviation* means the brief name of each plant assemblage, Since the
 NMDS figure shows the association between insect herbivory groups (FFGs)
 and plant assemblages, it uses abbreviated names for simplicity, as the
 figure cannot display all full names; * *Country* means the modern place
 that those plant assemblage, as fossil assemblages are distributed
 globally and have shifted over time due to continental movement; and *
 "*Age*",  "*Period*" and "Time" means the
 geologic age of each plant assemblage, based on the International
 Chronostratigraphic Chart, * "*Source*": typically provided in
 the citations 2\) For detailed insect herbivory information of each plant
 assemblage, all data are classified by the Functional Feeding Group-Damage
 Type (FFG-DT) system (Conrad Labandeira et al., 2007, the reference can be
 found in the main text description).This includes: * "*leaves*",
 means the plant specimens examined for each plant assemblage, and the
 ratio of the plant specimens damaged by insect is listed as *
 "*herbivorized specimens* (%)", the insect herbivory usually
 contains: * Damage Types (DT) and * Functional Feeding Groups (FFG), the
 specific FFGs include * "*HF*", Hole Feeding; *
 "*MF*", Margin Feeding; * "*SK*", Skeletonization; *
 "*SF*", Surface Feeding; * "*OV*", Oviposition; *
 "*PS*", Piercing and Sucking; * "*MIN*", Mining; *
 "*GAL*", Galling; * "*SP*", Seed Predation; *
 "*WB*", Wood Boring; * "*PA*", Pathogen. The *
 "*specilized DT*" means the ratio of specialist DTs to the total
 DTs * "*Source*": related citations are provided Some values may
 not be available ("na") 1. The designation (freq) represents the
 DTs’ frequency, and (herb) are the herbivorized specimens in the article,
 without total examined specimens providing, and the results that can be
 found in associated references. The italics 1 represent the present, not
 the DT richness, of that FFG in the plant assemblage, such as Fotan plant
 assemblage (Dong et al., 2019). 2. Due to the updated, unpublished version
 of the Damage Guide, there have been minor changes in DT assignments, in
 which there has been removal of a DT from one functional feeding group and
 reassigned to another functional feeding group. Nevertheless, the data
 listed here shows little difference with the results from the raw data,
 such as FFG richness. ### Dataset_S2_v5.zip Dataset S2 contains raw data
 for 134 plant assemblages (both fossil and modern floras), used in the
 analysis of DT trend, beta diversity, NMDS analysis, and specificity
 analysis (Dataset S3). The raw data includes "paleozoic",
 "mesozoic", "cenozoic" three folders, separately. Each
 CSV file corresponds to a plant assemblage listed in Dataset S1. For
 example, the "Daohugou" plant assemblage has rows for DT
 species, and columns for the plant hosts, with 0/1 values indicating the
 presence or absence of each DT. Additionally, 53 plant assemblages from
 the Carnian stage of the Triassic in South Africa have been incorporated.
 These assemblages were briefly described in Labandeira et al. (2018).
 Please note that these data are still part of Dr. Conrad Labandeira’s
 ongoing research and have not yet been formally published. Should you wish
 to use this dataset, we kindly ask that you contact him directly prior to
 use. Three modern insect herbivory data css files from Dr. Lauren Schmidt
 are uploaded. All these dataset belong to Lifang Xiao (1,2,3), Dong Ren
 (2), Conrad Labandeira (2,3), and Lauren Azevedo-Schmidt (4). Affiliations
 are as follows: 1. Guangdong Key Laboratory of Animal Conservation and
 Resource Utilization, Guangdong Public Laboratory of Wild Animal
 Conservation and Utilization, Institute of Zoology, Guangdong Academy of
 Sciences, Guangzhou 510260, People’s Republic of China 2. College of Life
 Science, Capital Normal University, Beijing 100048, People’s Republic of
 China 3. Department of Paleobiology, National Museum of Natural History,
 Smithsonian Institution, Washington, DC 20013 4. Department of Entomology
 and Nematology, University of California Davis, Davis, CA 95616 ###
 Dataset_S3.zip All related analyses results and figures are attached in
 Dataset S3. The dataset includes: 1\) the "dtrich_age", a
 dot-line trend chart showing the richness of DTs and FFGs across 131
 fossil plant assemblages and three modern plant assemblages. Each
 datapoint represents the frequency of DT richness for the DT totals plant
 assemblage (left column) and (right columns) for each of its 12 FFGs. The
 three focal, mid-Mesozoic plant assemblages of Daohugou (165 Ma),
 Dawangzhangzi (125 Ma), and Rose Creek (103 Ma) are indicated by arrows at
 right. The wide DT totals column at left defined by the raw data (open
 circles), mild lumping (open squares), full lumping (open diamonds), and
 overlap of all three symbols show as open polygons, representing analogous
 DTs for each plant assemblage. Horizontal lines in the DT totals column
 represent 95% confidence intervals. The narrow columns (black dots) from
 left to right, represent the DT richness for each FFG of margin feeding
 (MF), hole feeding (HF), skeletonization (SKE), and surface feeding (SF),
 oviposition (OVI), piercing and sucking (P&S), mining (MIN), galling
 (GAL), borings (BOR), seed predation (SP), and pathogens (PAT). The
 relative data is saved as data.frame, which the terms consistent with
 those in Dataset S1.  2) the "ternary",  a three-phase diagram
 illustrating the null distribution and early versions of damage type
 comparisons among 131 fossil and modern plant assemblages across seven
 time intervals.  A composite null distribution of pairwise comparisons of
 damage types seen in 131 fossil and three modern plant assemblages from
 pooled data at (A), subsequently partitioned into seven indicated time
 intervals at (C)–(I). At upper right at (B) are hypothetical examples of
 turnover and nestedness. In each grid, the two rows represent two host
 plants, the six columns represent six damage types; blue squares indicate
 the presence of a damage type and white squares indicate an absence. At
 right bottom of (B) the mean DT richness and minimum sample coverage is
 shown, whereby the color and size of each datapoint indicates the mean DT
 richness for two host plants from the same plant assemblage. The higher
 the coverage rate, the more widely distributed the DT is in the plant
 assemblage. The opacity of each datapoint indicates the minimum to maximum
 sample coverage; the basic sample coverage is 0.85–0.99 percent. All plant
 assemblages were “standardized” by the three categories of raw data
 (circles), the “mild lumping” (triangles), and “full lumping” (diamonds).
 All 134 plant assemblages consisted of leaves that reached the broadleaved
 standard of a sample coverage of 85% or higher or alternatively with
 specimen numbers greater than 20 for each plant host species. Average
 values for similarity (1-β), turnover β(Turnover), and nestedness
 β(Nestedness) are indicated for each time interval. The relative data is
 saved as ternary, with terms of turnover, Nestedness, and Ubeta etc.,
 which were generated using the R package "betapart.",
 representing the diversity of insect herbivory. 3\) the
 "compareNT", a bar chart comparing turnover and nestedness
 values across 134 plant assemblages, including resampled data for major
 plant hosts from fossil and modern plant assemblages. Mean values and 95%
 confidence intervals are indicated for beta diversity metrics, generated
 by resampling and subsampling of data for the major plant hosts from
 fossil and modern plant assemblages. Dark purple columns represent data
 resampled 1000 times and dark green columns represents data resampled 500
 times. The solid horizontal line represents the raw data. Nine
 representive plant assemblages are show at main text*. *The relative data
 is saved as "compareNT", which also include terms of turnover,
 Nestedness, and Ubeta etc., and generated using the R package
 "betapart". The "NA" represents the data not
 available. 4\) the "igs-age-type", a cumulative kurtosis chart
 showing the functional breadth of DTs across geological time, categorized
 by plant type (ferns, gymnosperms, angiosperms). At "type" , the
 left-top panel represents the damage-type functional breadth based on
 geological time of the Paleozoic (oldest), Mesozoic, and Cenozoic
 (youngest) eras. At "*cmp*", the left bottom panel represents
 damage-type functional breadth based on major plant taxa. At
 "*type_cmp*", the panel at right, represents damage-type
 functional breadth based on major plant taxa through the three geologic
 eras. In each panel the horizontal axis represents the logarithm of the DT
 frequency. Each dot represents the frequency of a DT on each plant host.
 Box plots represent the data distribution (including mean values and
 floating ranges). The higher the peak value, the more the data are
 concentrated along the X-axis. The relative data is saved as
 "igs-age-type", including the DT species, host, and specificity
 of each plant assemblage. 5\) the "NMDS", Nonmetric
 multidimensional scaling (NMDS) plots showing the relationships of the
 major plant clades/groups and their functional feeding groups for plant
 assemblages from the late Paleozoic to Mesozoic in (A), and all plant
 assemblages from late Paleozoic, Mesozoic, Cenozoic, and modern in (B).
 Each data point represents the DT richness on foliage specimens that is
 represented with areal coverage higher than 0.85 percent or otherwise
 consisting of more than 20 specimens for a plant species. Pathogens,
 borings, and seed predation FFGs are not included, as these FFGs are not
 documented in all plant assemblages. Ellipse outlines are 84% confidence
 intervals. Abbreviations and details of all plant assemblages can be found
 in *Dataset S1*.  The analysis was conducted using R, and the R code is
 provided in a text file. ## Sharing/Access information ## Code/Software
 The data analysis was conducted using R, with several key packages
 including "ternary," "betapart," "vegan,"
 "dplyr," "purrr," "scico,"
 "ggplot2," "gridExtra," and others. Several functions
 were used to calculate data coverage, as well as for data resampling and
 subsampling.