Investigating the biotic and abiotic drivers of body size disparity in communities of non-volant terrestrial mammals
Data files
Sep 13, 2024 version files 280.30 MB
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EltonTraits.zip
2.39 MB
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gmted2010.zip
277.79 MB
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mammal_variance.R
109.13 KB
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README.md
6.51 KB
Abstract
Aim
The species that compose local communities possess unique sets of functional and ecological traits that can be used as indicators of biotic and abiotic variation across space and time. Body size is a particularly relevant trait because species with different body sizes typically have different life history strategies and occupy distinct niches. Here we used the body sizes of non-volant (i.e., non-flying) terrestrial mammals to quantify and compare the body size disparity of mammal communities across the globe.
Location
Global
Time period
Present
Major taxa studied
Non-volant terrestrial mammals
Methods
We used IUCN range maps of 3,982 terrestrial mammals to identify 1,876 communities. We then combined diet data with data on climate, elevation, and anthropogenic pressures to evaluate these variables’ relative importance on the observed body size dispersion of these communities and its deviation from a null model.
Results
Dispersion is significantly greater than expected in 54% of communities and significantly less than expected in 30% of communities. The number of very large species, continent, range sizes, diet disparity, and annual temperature collectively explain >50% of the variation in observed dispersion, whereas continent, the number of very large species, and precipitation collectively explain >30% of the deviation from the null model.
Main conclusions
Climate and elevation have minimal predictive power, suggesting that biotic factors may be more important for explaining community body size distributions. Continent is consistently a strong predictor of dispersion, likely due to it capturing the effects of climate, human-induced extinctions, and more. Overall, our results are consistent with several plausible explanations, including, but not limited to, competitive exclusion, unequal distribution of resources, within-community environmental heterogeneity, habitat filtering, and ecosystem engineering. Further work focusing on other confounding variables, at finer spatial scales, and/or within more causal frameworks is required to better understand the driver(s) of these patterns.
This repository contains the R code and (some) data files required to produce all of the analyses and plots in:
‘Investigating the biotic and abiotic drivers of body size disparity in communities of non-volant terrestrial mammals’
William Gearty, Lawrence H. Uricchio, and S. Kathleen Lyons
Before running the code
Before running this R script, we suggest that you download this folder and set it as your R working directory. Most data must be downloaded from external repositories and unzipped to specific folders before the analyses can be performed (see specifics below). Required data files should then load when called in each script, and plot files will save within the same folder.
Running the code
Run mammal_variance.R to perform all analyses and produce all plots from the manuscript. Note that the analyses can take a few days to run completely.
Required R packages
Unless otherwise stated, the following packages can all be installed from CRAN:
deeptime
dggridR
ggforce
ggtern
grid
maptools (was retired in 2023; still available on R-Forge)
moments
MuMIn
parallel
patchwork
quantreg
relaimpo
rgbif
sf
spData
spDep
stringr
terra
tidyverse
viridis
These scripts have been tested using R version 4.3.3
Copyright (C) 2024 The R Foundation for Statistical Computing.
Included Data
The EltonTraits database ("EltonTraits.txt") contains species-level foraging attributes for mammals (and birds). The publication describing this database is available here: https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/13-1917.1. The database is available on figshare here: https://doi.org/10.6084/m9.figshare.c.3306933.v1. Thanks to the CC0 license, a copy of the database is also included here in the zipped folder "EltonTraits.zip". This folder should be unzipped and the "EltonTraits.txt" file should be moved to the root directory of the project. Metadata for this file is included in the "metadata.htm" file within this zipped folder. The original sources for the mammal functional trait data are documented in the "MamFuncDatSources.txt" file within the zipped folder.
The elevation data ("gmted2010.zip") are coped from the USGS Global multi-resolution terrain elevation data 2010 (GMTED2010): https://www.usgs.gov/coastal-changes-and-impacts/gmted2010. The data (mean statistic, 30 second resolution) can also be downloaded as a zip folder here: https://topotools.cr.usgs.gov/gmted_viewer/gmted2010_global_grids.php. These files should be unzipped and placed into a folder named "gmted2020". Metadata are available within the "gmted2010_fgdc_metadata.html" file and are also available here: https://topotools.cr.usgs.gov/gmted_viewer/gmted2010_fgdc_metadata.html. All GMTED2010 data products are publicly available; there are no restrictions or access constraints.
External Data Needed for Analyses
The IUCN range maps for terrestrial mammals ("MAMMALS_TERRESTRIAL_ONLY.zip") should be downloaded from the IUCN here: https://www.iucnredlist.org/resources/spatial-data-download. The files should be unzipped and placed into a into a folder named "MAMMALS_TERRESTRIAL_ONLY". All forms of reposting, and any sub-licensing, reselling, or other forms of redistribution of IUCN Red List Data in their original format, either whole or in part, alone or combined with other data, including within Derivative Works, are strictly prohibited without the prior written permission of IUCN.
Taxonomy ("taxonomy.csv") and synonym ("synonyms.csv") files for IUCN terrestrial mammals should be downloaded from the IUCN website here: https://www.iucnredlist.org/search?dl=true&permalink=6da36cdc-5f19-46e7-b980-aeb06b2b6208. To download the files, click the "Download" dropdown, select "Search Summary", then submit a request for the data. All forms of reposting, and any sub-licensing, reselling, or other forms of redistribution of IUCN Red List Data in their original format, either whole or in part, alone or combined with other data, including within Derivative Works, are strictly prohibited without the prior written permission of IUCN.
The Human Footprint Index data are available from the NASA Socioeconomic Data and Applications Center. The dataset from 1993 is available here: https://sedac.ciesin.columbia.edu/data/set/wildareas-v3-1993-human-footprint. The dataset from 2009 is available here: https://sedac.ciesin.columbia.edu/data/set/wildareas-v3-2009-human-footprint. Metadata is available at both of those locations under the "Metadata" tabs. The datasets are available as individual .tif files under the "Data Download" tabs. These two files should be moved to the root directory of the project.
The Millenium Assessment's deforestation hotspot data are available from the NASA Socioeconomic Data and Applications Center here: https://sedac.ciesin.columbia.edu/data/set/ma-rapid-land-cover-change. Metadata is available at this location under the "Metadata" tab. The dataset can be be downloaded as a zip folder under the "Data Download" tab. These files should be unzipped and placed into a folder named "def_hot_for".
The bioclimatic variable data are available at WorldClim. The 30 second resolution dataset (v. 2.1) can be downloaded from the WorldClim website here: https://www.worldclim.org/data/worldclim21.html. Metadata is available at that location, and license information is available here: https://www.worldclim.org/about.html. The data can be downloaded as a large zip folder containing several .tif files. Once downloaded, the files should be unzipped and placed into a folder named "WorldClim".
