DOI: 10.5061/dryad.pvmcvdnx7
title: Data for: Legacy of the lost and pressure of the present: Malagasy plant seeds retain megafauna dispersal signatures but downsize under human pressure

description: Ongoing declines of large-bodied frugivores limit the dispersal of
 large-seeded plants, contributing to their (local) demise and ‘downsizing’
 of seeds across assemblages. However, the extent to which human pressure
 leads to contemporary seed downsizing, and whether extinct megafrugivores
 have left imprints on seed size, remains unclear. Here, we integrate trait
 and distribution data for 2,852 endozoochorous plant species, 48 extant
 and 15 extinct frugivore species across 361 assemblages on Madagascar.
 Using structural equation models, we show that assemblages with a higher
 human footprint, a cumulative index of human pressure, have smaller
 maximum seed sizes, especially through downsizing of extant frugivores.
 Furthermore, among assemblages with ‘mega-seeded’ plants (i.e., seeds that
 cannot be swallowed by any extant Malagasy frugivore), larger seed sizes
 are associated with larger past megafrugivores, reflecting the legacy of
 past interactions.  Human-driven seed downsizing highlights
 broader implications in the erosion of important ecosystem functions such
 as forest carbon storage.
description: # Data for: Legacy of the lost and pressure of the present: Malagasy plant
 seeds retain megafauna dispersal signatures but downsize under human
 pressure Dataset DOI: [10.5061/dryad.pvmcvdnx7](10.5061/dryad.pvmcvdnx7)
 ## Description of the data and file structure This dataset includes Table
 S1-S3, all raw data, and R scripts used for all analyses in the paper
 “Legacy of the lost and pressure of the present: Malagasy plant seeds
 retain megafauna dispersal signatures but downsize under human pressure”.
 ## Table S1-S3 ### File:
 Table_S1_-_3241_endozoochorous_plant_species_and_fruit_seed_traits.xlsx
 ##### **Description:** Taxonomy and fruit/seed traits of
 3,241 endozoochorous plant species from Albert-Daviaud et al. (2020).
 ##### Variables * Column A-C: species taxonomy * Column D: whether there’s
 filtered occurrence data from Ralimanana et al. (2022) * Column E-G:
 original fruit and seed traits data collected by Albert-Daviaud et al.
 (2020) * Column H-AA: 20 independently imputed seed width datasets from
 Albert-Daviaud et al. (2020) ### File:
 Table_S2_-_frugivores_species__frugivory_and_body_masses.xlsx #####
 **Description:** Taxonomy, frugivory, and body masses of
 48 extant frugivores and 15 extinct megafrugivores. ##### Variables Sheet
 1: 48 extant frugivores  * Column A-E: species taxonomy  * Column
 F: percentage of fruits in the diet of the species  * Column G: reference
 for the source of frugivory data * Column H: body mass (in kg), averaged
 across available data from Wilman et al. (2014), Galán-Acedo et
 al. (2019), and Razafindratsima et al. (2018) Sheet 2: 15
 extinct megafrugivores * ​Column A-B: species taxonomy * Column C: body
 mass (in kg) * Column D: reference for the source of body mass data ###
 File: Table_S3_-_assemblage-level_data.xlsx ##### **Description:** Species
 richness, largest seed widths, largest body masses, human
 footprint, and environmental data in 649 assemblages of plants and
 frugivores across Madagascar. ##### Variables * Column A: Assemblage ID *
 Column B-C: Coordinates of the assemblage * Column D: percentage of
 terrestrial area * Column E: species richness of endozoochorous plant
 species  * Column F: species richness of extant frugivore species * Column
 G: 95th percentile maximum body mass of extant frugivores (in kg,
 log-transformed) * Column H: species richness of extinct frugivore species
 * Column I: 95th percentile maximum body mass of extinct frugivores (in
 kg, log-transformed) * Column J: averaged human footprint value (2009),
 adapted from Venter et al. (2016) * Column K-L: the first two principal
 components of the principal component analysis (PCA) of 26 abiotic
 variables (for a complete overview of variables, see Table S4) * Column M:
 whether at least one mega-seeded plant species occurs in the assemblage *
 Column N-AG: 20 versions of 95th percentile maximum plant seed width using
 20 independently imputed seed width datasets (in mm, log-transformed) ##
 Full raw data and R Code (madagascar_seed_downsizing.zip) #####
 **Description:** This compressed folder contains all the data, code, and
 versions of all R packages necessary to reproduce the analyses presented
 in the paper. All scripts were run under R version 4.5.0 In this folder:
 **“rawdata.RData”** contains all raw data used for the analyses in this
 project, which include species, trait, distribution, and relevant
 environmental data of 2,852 endemic endozoochorous plant species, 48
 extant frugivore species, and 15 extinct frugivore species.
 **“1_-_data_compile.R”** compiles all raw data from
 "rawdata.RData" to assemblage-level data
 **“2_-_data_analyse.R”** takes the compiled assemblage-level data from
 "1-_data_compile.R" and conducts structural equation modelling
 (SEM), spatial autoregressive (SAR) modelling, and simulations of
 randomised communities to test the robustness of the final SEMs.
 **“3_-_plot.R”** takes the compiled data from
 "1-_data_compile.R" and generates all figure drafts used in the
 manuscript (both main text and supporting document) in the corresponding
 order. It also includes annotations linking each SEM model from
 "2-_data_analyse.R" to its corresponding path diagram figure in
 the manuscript.