Data for: Legacy of the lost and pressure of the present: Malagasy plant seeds retain megafauna dispersal signatures but downsize under human pressure
Data files
Aug 21, 2025 version files 68.84 MB
Abstract
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.
Dataset DOI: 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.