Data and code from: Nutrient legacies from elephant megacarcasses create coldspots of biodiversity and hotspots of ecosystem processes
Data files
Sep 23, 2026 version files 72.10 MB
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16S_Sample_Data.csv
9.54 KB
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16S_Sequence_Table.csv
16.13 MB
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16S_Taxonomy_Table.csv
10.34 MB
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Bacterial_Diversity.Rmd
5.50 KB
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Bacterial_Sensitivity_Analysis.Rmd
3.63 KB
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Carcass_Metadata.csv
1.46 KB
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DPM.csv
136.67 KB
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DPM.Rmd
3.23 KB
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Fungal_Diversity.Rmd
5.05 KB
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Fungal_Sensitivity_Analysis.Rmd
3.77 KB
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Grass_Foliar_Isotopes.csv
10.28 KB
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Grass_Foliar_Isotopes.Rmd
6.03 KB
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Grazing.csv
194.83 KB
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Grazing.Rmd
5.81 KB
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ITS_Sample_Data.csv
9.54 KB
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ITS_Sequence_Table.csv
7.88 MB
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ITS_Taxonomy_Table.csv
5.39 MB
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Megacarcass_16S_Phyloseq_Rarefied.rds
20.27 MB
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Megacarcass_ITS_Phyloseq_Rarefied.rds
11.27 MB
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Plant_Composition.csv
342.16 KB
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Plant_Diversity.Rmd
9.01 KB
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README.md
13.73 KB
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Soil_Ions.csv
16.32 KB
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Soil_Isotopes.csv
10.32 KB
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Soil_Nutrients.Rmd
14.97 KB
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Soil_Respiration.csv
10.08 KB
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Soil_Respiration.Rmd
3.62 KB
Abstract
Terrestrial megafauna (animals >1,000 kg) have substantial impacts on ecosystems while alive; yet, we know little about the impacts of these ecosystem engineers after they die. Similar to whale carcasses in the ocean, terrestrial megacarcasses may leave ecological legacies via the nutrient pulses they create on the landscape. Here, we investigated the impact of elephant megacarcasses on savanna ecosystems in the Kruger National Park, South Africa. To determine how elephant carcasses affect below- and aboveground biodiversity and ecosystem processes, we collected soil and plant samples from 40 elephant carcass sites (pairing “on carcass” and “off carcass” samples) ranging from 8 days to 7.7 years postmortem. We found that elephant carcasses released enormous pools of nutrients into savanna soils, increasing ammonium by 31x, nitrate by 7x, and phosphorus by 3x on average. These extreme ammonium concentrations were negatively correlated with the biodiversity of plants and soil microbes, which were suppressed at elephant carcass sites. Despite these decreases in biodiversity, ecosystem processes were strongly elevated at elephant carcass sites, with soil microbial respiration and herbivore grazing each >3x higher at carcasses (for 1-2 years and 7+ years, respectively). These results demonstrate that elephant megacarcasses generate coldspots of biodiversity but hotspots of ecosystem processes that persist for 7+ years of carcass age, unveiling a cryptic ecological function of megaherbivores that is extreme in both magnitude and duration relative to smaller carrion. As humans drive terrestrial megafauna towards extinction, we risk losing not only their ecosystem engineering abilities while they are alive but also the ecological legacies their carcasses create after death.
Dataset DOI: 10.5061/dryad.q2bvq841g
Description of the data and file structure
These datasets and scripts can be used to run the analyses and produce the figures in the associated manuscript (Reed et al. 2026). These data were collected at 40 elephant megacarcass sites ranging from 8 days to 8 years postmortem in the Kruger National Park, South Africa. The sites were split across sandy, nutrient-poor granitic soils (N = 13) and clayey, nutrient-rich basaltic soils (N = 27). Eight of the 40 sites had been sampled during the 2023 wet season and published in previous work (Reed et al. 2025, Biogeosciences). The rest were newly identified. In 2024, we sampled 27 sites (N = 12 on granitic and 15 on basaltic soils). In 2025, we performed repeat sampling on 24 of those sites and added 13 new sites (N = 64 carcasses sampled across both years, with 40 unique sites). In both years, sampling was performed towards the end of the wet season (late February to early April).
Here, we provide data for soil and leaf nutrient concentrations, grazing intensity, herbaceous biomass, plant composition, and soil microbial (16S and ITS) sequencing data, as well as scripts for data analysis. All data here are published for the first time.
Files and variables
File: Carcass_Metadata.csv
Description: This dataset contains metadata for samples collected at elephant carcass sites in the Kruger National Park during March/April 2024 and 2025.
- Carcass.ID: Numeric ID used to identify carcass sites.
- Section: Kruger National Park section
- Soil.Type: granitic or basaltic
- Date.Death: Date that the elephant died
File: Soil_Ions.csv
Description: This dataset contains data on soil ion concentrations at 0.5, 2.5, and 15m distances from the carcass center. Soil samples were collected with a 10 cm auger and were pooled across transects to yield one composite sample per distance per site.
- Year: Year the sample was collected (2024 or 2025)
- Sample.Date: Date the sample was collected (dmy)
- Carcass.ID: Numeric ID used to identify carcass sites.
- Distance.m: Distance from carcass center
- NO3.mgkg: Soil nitrate concentration in mg/kg
- NH4.mgkg: Soil ammonium concentration in mg/kg
- PBray1.mgkg: Soil phosphorus concentration in mg/kg. One cell contains an "NA" indicating no phosphorus concentration data for that sample.
- pH: Soil pH
- Notes: Laboratory notes
File: Soil_Isotopes.csv
Description: This dataset contains data on soil δ15N at 0.5, 2.5, and 15m distances from the carcass center. Soil samples were collected with a 10 cm auger and were pooled across transects to yield one composite sample per distance per site.
- Year: Year the sample was collected (2024 or 2025)
- Sample.Date: Date the sample was collected (dmy)
- Carcass.ID: Numeric ID used to identify carcass sites.
- Distance.m: Distance from carcass center
- N15: Soil δ15N
File: Soil_Respiration.csv
Description: This dataset contains data on soil microbial respiration rates at 0.5, 2.5, and 15m distances from the carcass center. Soil samples were collected with a 10 cm auger and were pooled across transects to yield one composite sample per distance per site.
- Year: Year the sample was collected (2024 or 2025)
- Sample.Date: Date the sample was collected (dmy)
- Carcass.ID: Numeric ID used to identify carcass sites.
- Distance.m: Distance from carcass center
- ugCO2.hr: Soil respiration rate as micrograms of CO2 released per hour per gram of dry soil
- Notes: Laboratory notes
File: Grass_Foliar_Isotopes.csv
Description: This dataset contains data on grass foliar nitrogen concentrations at 0.5, 2.5, and 15m distances from the carcass center. Grass samples were collected preferentially from a common and abundant species (Urochloa trichopus), with Megathrysus maximus as a secondary choice when U. trichopus was not available. Samples were pooled across transects to yield one composite sample per distance per site.
- Year: Year the sample was collected (2024 or 2025)
- Sample.Date: Date the sample was collected (dmy)
- Carcass.ID: Numeric ID used to identify carcass sites.
- Plant.Species: Species of grass comprising sample. "NA" indicates that there was insufficient grass biomass to collect a sample at that site and distance.
- Distance.m: Distance from carcass center
- N.per: Foliar nitrogen (%). "NA" indicates that there was insufficient grass biomass to collect a sample at that site and distance.
- N15: Foliar δ15N. "NA" indicates that there was insufficient grass biomass to collect a sample at that site and distance.
File: Plant_Composition.csv
Description: This dataset contains plant species composition data at elephant carcass sites. We place a 1x1m quadrat centered at 0.5, 2.5, and 15m along each transect. We identified every plant within each quadrat to species level (when possible), visually estimated its percent aerial cover within the quadrat to the nearest 1%, and categorized each species as grass, forb, woody, or other (dead or non-plant).
- Year: Year the sample was collected (2024 or 2025)
- Sample.Date: Date the sample was collected (dmy)
- Carcass.ID: Numeric ID used to identify carcass sites.
- Transect: North, South, East, or West
- Distance.m: Distance from carcass center
- Species: Plant species or description of non-plant material (e.g., bones, bare soil, leaf litter, carcass tissue)
- Full.Classification: Plant species classification based on the South African National Biodiversity Institute and (secondarily) Plants of the World Online.
- Percent.Cover: Percent cover of each species within the quadrat estimated to the nearest 1%
- Veg.Type: Category of plant (grass, forb, woody, other)
File: DPM.csv
Description: This dataset contains herbaceous vegetation height data at elephant carcass sites measured with a disc pasture meter (DPM). Measurements were taken at 1-m intervals along each of the four transects.
- Year: Year the sample was collected (2024 or 2025)
- Sample.Date: Date the sample was collected (dmy)
- Carcass.ID: Numeric ID used to identify carcass sites.
- Transect: North, South, East, or West
- Distance.m: Distance from carcass center
- DPM.cm: Vegetation height measurements from a disc pasture meter in cm. "NA" indicates that a DPM measurement was not taken at that site, transect, and distance, typically due to the presence of a tree.
File: Grazing.csv
Description: This dataset contains grazing intensity data at elephant carcass sites. Measurements were taken at 1-m intervals along each of the four transects. We selected the grass tuft closest to the transect tape and gave it a grazing intensity score ranging from 0 (completely intact) to 5 (completely grazed to the soil surface).
- Year: Year the sample was collected (2024 or 2025)
- Sample.Date: Date the sample was collected (dmy)
- Carcass.ID: Numeric ID used to identify carcass sites.
- Transect: North, South, East, or West
- Distance.m: Distance from carcass center
- Plant.Species: Species of grass. "NA" indicates that there was no grass to sample at that site, transect, and distance.
- Graze.Score: Grazing intensity measurement ranging from 0 (completely intact) to 5 (completely grazed to the soil surface). "NA" indicates that there was no grass to sample at that site, transect, and distance.
File: 16S_Sample_Data.csv
Description: This dataset contains sample metadata specifically for analysis of soil bacterial (16S) sequencing data.
- Sample.ID: Laboratory sample ID for each soil sample used for 16S sequencing
- Year: Year the sample was collected (2024 or 2025)
- Sample.Date: Date the sample was collected (mdy)
- Distance.m: Distance from carcass center
- Carcass.ID: Numeric ID used to identify carcass sites.
- Section: Kruger National Park section
- Soil.Type: granitic or basaltic
- Date.Death: Date that the elephant died
- Years.Postmortem: Years between the date of death and the sampling date
File: 16S_Sequence_Table.csv
Description: This dataset shows the number of sequence reads for each bacterial sequence in each soil sample. The first column contains each unique 16S sequence that can be matched to taxonomic information in 16S_Taxonomy_Table.csv. Each of the other columns is a different soil microbial sample that can be matched to sample metadata in 16S_Sample_Data.csv. Cells contain the number of reads per sequence per sample.
File: 16S_Taxonomy_Table.csv
Description: This dataset contains taxonomic information for each unique 16S bacterial sequence, including Kingdom, Phylum, Class, Order, Family, Genus, and Species (when known -- otherwise indicated as "NA").
File: Megacarcass_16S_Phyloseq_Rarefied.rds
Description: This is a rarefied phyloseq object for 16S sequencing data that can be used in the Bacterial_Diversity.Rmd script (rarefaction depth = 2,003).
File: ITS_Sample_Data.csv
Description: This dataset contains sample metadata specifically for analysis of soil fungal (ITS) sequencing data.
- Sample.ID: Laboratory sample ID for each soil sample used for ITS sequencing
- Year: Year the sample was collected (2024 or 2025)
- Sample.Date: Date the sample was collected (mdy)
- Distance.m: Distance from carcass center
- Carcass.ID: Numeric ID used to identify carcass sites.
- Section: Kruger National Park section
- Soil.Type: granitic or basaltic
- Date.Death: Date that the elephant died
- Years.Postmortem: Years between date of death and sampling date
File: ITS_Sequence_Table.csv
Description: This dataset shows the number of sequence reads for each fungal sequence in each soil sample. The first column contains each unique ITS sequence that can be matched to taxonomic information in ITS_Taxonomy_Table.csv. Each of the other columns is a different soil microbial sample that can be matched to sample metadata in ITS_Sample_Data.csv. Cells contain the number of reads per sequence per sample.
File: ITS_Taxonomy_Table.csv
Description: This dataset contains taxonomic information for each unique ITS fungal sequence, including Kingdom, Phylum, Class, Order, Family, Genus, and Species (when known -- otherwise indicated as "NA").
File: Megacarcass_ITS_Phyloseq_Rarefied.rds
Description: This is a rarefied phyloseq object for ITS sequencing data that can be used in the Fungal_Diversity.Rmd script (rarefaction depth = 1,129)
Code/software
File: Soil_Nutrients.Rmd
R Markdown script to run analyses and produce figures associated with soil nutrient concentrations. Uses Carcass_Metadata.csv, Soil_Isotopes.csv, and Soil_Ions.csv.
File: Soil_Respiration.Rmd
R Markdown script to run analyses and produce figures associated with soil microbial respiration. Uses Carcass_Metadata.csv and Soil_Respiration.csv.
File: Grass_Foliar_Isotopes.Rmd
R Markdown script to run analyses and produce figures associated with grass foliar nitrogen. Uses Carcass_Metadata.csv and Grass_Foliar_Isotopes.csv.
File: Plant_Diversity.Rmd
R markdown script to run analyses and produce figures associated with plant Shannon diversity, including Shannon diversity measurements and correlations with soil nutrients. Uses Carcass_Metadata.csv, Plant_Composition.csv, and Soil_Ions.csv
File: Bacterial_Diversity.Rmd
R Markdown script to run analyses and produce figures associated with 16S Shannon diversity, including Shannon diversity measurements and correlations with soil nutrients. Uses Carcass_Metadata.csv, Megacarcass_16S_Phyloseq_Rarefied.rds, and Soil_Ions.csv. The phyloseq package (McMurdie & Holmes, 2013) must be downloaded and installed to run this code.
File: Bacterial_Sensitivity_Analysis.Rmd
R Markdown script to run a sensitivity analysis to determine whether bacterial Shannon diversity model outputs are sensitive to rarefaction depth. Uses 16S_Taxonomy_Table.csv, 16S_Sequence_Table.csv, and 16S_Sample_Data.csv. The phyloseq package (McMurdie & Holmes, 2013) must be downloaded and installed to run this code.
File: Fungal_Diversity.Rmd
R Markdown script to run analyses and produce figures associated with ITS Shannon diversity, including Shannon diversity measurements and correlations with soil nutrients. Uses Carcass_Metadata.csv, Megacarcass_ITS_Phyloseq_Rarefied.rds, and Soil_Ions.csv. The phyloseq package (McMurdie & Holmes, 2013) must be downloaded and installed to run this code.
File: Fungal_Sensitivity_Analysis.Rmd
R Markdown script to run sensitivity analysis to determine whether fungal Shannon diversity model outputs are sensitive to rarefaction depth. Uses ITS_Taxonomy_Table.csv, ITS_Sequence_Table.csv, and ITS_Sample_Data.csv. The phyloseq package (McMurdie & Holmes, 2013) must be downloaded and installed to run this code.
File: DPM.Rmd
R Markdown script to run analyses and produce figures associated with DPM measurements (including conversion from DPM to herbaceous biomass). Uses Carcass_Metadata.csv and DPM.csv.
File: Grazing.Rmd
R Markdown script to run analyses and produce figures associated with grazing intensity, including correlations between grazing intensity and foliar nitrogen. Uses Carcass_Metadata.csv, Grazing.csv, and Grass_Foliar_Isotopes.csv