DOI: 10.5061/dryad.5x69p8dfw
title: Data from: Fecal biomarkers in soils record landscape-scale wild herbivore abundance

description: In Earth history, our understanding of how large-bodied herbivores shape a
 variety of ecosystem processes is limited by the quality of
 paleoecological proxies for herbivore composition and abundance. Fecal
 stanols are lipids that can be produced by microbes within animal
 digestive systems and that could remedy this dearth of proxies. 
 We use two multi-decadal herbivore exclosures in Kruger National Park,
 South Africa, to constrain whether and how biomarker signatures preserve
 signals of herbivore abundance. Soil samples and dung counts were
 collected along transects across crest, mid-slope, and sodic sites inside
 and outside exclosures. Soils were analyzed for steroid (sterols and
 stanols) concentrations and distributions. We found that stanol
 concentrations were significantly greater in sodic soils outside
 exclosures, where herbivore dung densities were greatest. By contrast,
 sterol concentrations did not differ between treatments. Ratios of stanol
 isomers to sterols, which account for both compound degradation and
 source, increased strongly with herbivore dung counts. Finally, while
 herbivore species compositions influenced steroid distributions, total
 herbivore abundance was their strongest predictor. Further calibration is
 needed, but this work provides strong preliminary evidence that wild
 herbivore populations are quantitatively recorded by fecal biomarker
 distributions.
description: # Data from: Fecal biomarkers in soils record landscape-scale wild
 herbivore abundance
 [https://doi.org/10.5061/dryad.5x69p8dfw](https://doi.org/10.5061/dryad.5x69p8dfw) ## Description of the data and file structure Methods are described in detail in the manuscript. Here we present herbivore dung count data and fecal steroid concentration data from herbivore exclusion experiments in Kruger National Park (South Africa).  ### Files and variables #### File: KNP.HEX.sample.metadata.csv **Description:** Metadata associated with soil samples collected ##### Variables * Sample.name: Name of soil sample collected  * Experiment: Name of experiment NKH stands for Nkhuhlu, and HLG stands for Hlangwini * Treatment: If the sample was collected from an enclosure (EX) where no herbivores were present or a control where herbivores were present (CON) * Soil.Profile: Where the transect was located in the cateanal profile, the crest, mid slope (mid), or sodic zone (sod) * Soil.Depth: The depth the soil sample was collected at either 0-5 cm or 0-1 cm * Replicate: The replicate designation of the transect (A or B)  * big.herb.total: The total dung count of all big (excluding hares, duiker, and porcupine) herbivores across the transect * herb.total: The total dung count of all herbivores across the transect * Carnivore.total: The total dung count of carnivores across the transect * Lat: the Latitude of the start of the transect * Long: the Longitude of the start of the transect #### File: KNP.HEX.compounds.sums.ratios.csv **Description:** Compound sums and ratios measured from soil samples ##### Variables * Sample.name: Name of soil sample collected * total.stanols: The sum of all stanols measured (ng/g soil) * total.sterols: The sum of all sterols measured (ng/g soil) * total.plant.stanols: The sum of all plant stanols (5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5alpha3beta−𝑐𝑎𝑚𝑝𝑒𝑠𝑡𝑎𝑛𝑜𝑙, 5beta3alpha−s𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙, 5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙) measured (ng/g soil) * total.plant.sterols: The sum of all plant sterols (𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑒𝑟𝑜𝑙 + beta−𝑠𝑖𝑡𝑜𝑠𝑡𝑒𝑟𝑜𝑙 + 𝐶𝑎𝑚𝑝𝑒𝑠𝑡𝑒𝑟𝑜𝑙) measured (ng/g soil) * total.beta.stanols: The sum of all beta stanols (5beta3beta−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙, 5beta3alpha−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙, 5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙, 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙) measured (ng/g soil) * total.alpha.stanol: The sum of all alpha stanols (5alpha3beta−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙, 5alpha3beta−𝑐𝑎𝑚𝑝𝑒𝑠𝑡𝑎𝑛𝑜𝑙, 5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙) measured (ng/g soil) * total.betasigma.stanols: The sum of all beta stigmastanols (5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 , 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙) measured (ng/g soil) * total.alphasigma.stanols: The sum of all alpha stigmastanols (5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙) measured (ng/g soil) * PS: The plant steroid ratio (PS) as defined in the EQ5 of the publication: (5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5alpha3beta−𝑐𝑎𝑚𝑝𝑒𝑠𝑡𝑎𝑛𝑜𝑙)/(5alpha, 3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5alpha3beta−𝑐𝑎𝑚𝑝𝑒𝑠𝑡𝑎𝑛𝑜𝑙 + 𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑒𝑟𝑜𝑙 + beta−𝑠𝑖𝑡𝑜𝑠𝑡𝑒𝑟𝑜𝑙 + 𝐶𝑎𝑚𝑝𝑒𝑠𝑡𝑒𝑟𝑜𝑙) * PU: The Pee-eww ratio (PU) as defined in the EQ6 of the publication: (5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙)/(5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑒𝑟𝑜𝑙 + beta−𝑠𝑖𝑡𝑜𝑠𝑡𝑒𝑟𝑜𝑙) * beta.stig.alpha: As defined in EQ3 of the publication: (5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙)/(5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙) * beta_stig.beta_epi_stig: As defined in EQ2 of the publication: 5beta3beta− 𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙/(5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙) * beta_cop.beta_cop_alpha_chlo: As defined in EQ4 of the publication: (5beta3beta−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙)/ (5beta3beta−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙 + 5alpha3beta−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙) * cop.cop_epi: As defined in EQ1 of the publication: 5beta3beta−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙/(5beta3beta−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙) #### File: KNP.HEX.Dung.Counts.csv **Description:** Dung counts for transects that correspond to each soil sample ##### Variables * Sample.name: Name of soil sample collected * elephant: dung counts * impala: dung counts * kudu: dung counts * giraffe: dung counts * buffalo: dung counts * wildebeest: dung counts * waterbuck: dung counts * zebra: dung counts * warthog: dung counts * duiker: dung counts * steenbok: dung counts * bushbuck: dung counts * nyala: dung counts * hippo: dung counts * porcupine: dung counts * hare: dung counts #### File: KNP.HEX.Fecal.Steroids.csv **Description:** ng/g concentrations of fecal steroids measured from soil samples ##### Variables * Sample.name: Name of soil sample collected * Coprostanol: 5beta3beta−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙 (ng/g soil) * Epicoprostanol: 5beta3alpha−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙 (ng/g soil) * Cholesterol: Cholesterol (ng/g soil) * 5alpha.Cholestanol: 5alpha3beta−𝑐ℎ𝑜𝑙𝑒𝑠𝑡𝑎𝑛𝑜𝑙 (ng/g soil) * 5beta.Stigmastanol: 5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 (ng/g soil) * Epi.5beta.stigmastanol: 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 (ng/g soil) * Campesterol: 𝐶𝑎𝑚𝑝𝑒𝑠𝑡𝑒𝑟𝑜𝑙 (ng/g soil) * Campestanol: 5alpha3beta−𝑐𝑎𝑚𝑝𝑒𝑠𝑡𝑎𝑛𝑜𝑙 (ng/g soil) * Stigmasterol: 𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑒𝑟𝑜𝑙 (ng/g soil) * Sitosterol: beta−𝑠𝑖𝑡𝑜𝑠𝑡𝑒𝑟𝑜𝑙 l (ng/g soil) * 5alpha.Stigmastanol: 5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 (ng/g soil) #### File: KNP.HEX.herb.characteristics.csv **Description:** Characteristics of the species of herbivores whose dung was found in the transects ##### Variables * Species: Common name of species * scientific_name: Scientific name of species * diet_preference: Diet preference, b = browser, mf = mixed feeder, g = grazer. Designations after Abraham et al (2021): [https://doi.org/10.5061/dryad.31zcrjdnb](https://doi.org/10.5061/dryad.31zcrjdnb) * digestive_system: Digestive system, R = ruminant, NR = non-ruminant #### File: Wendt_et_al_2024_sum_herb_ratios.csv **Description:** Summary data for lake core samples with historical herbivore density estimates from Wendt et al (2024): [https://doi.org/10.1371/journal.pone.0311950](https://doi.org/10.1371/journal.pone.0311950) ##### Variables * Zoostanol: After Wendt et al (2024), the sum of concentrations of 5β-stanols measured in this study (5β3β-cholestanol, 5β3α-cholestanol, 5β3β-stigmastanol, 5β3α-stigmastanol) (ng/cm3) * PS: The modified (no campestanol) plant steroid ratio (PS) as defined in the EQ5 of the publication: (5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5alpha3beta−𝑐𝑎𝑚𝑝𝑒𝑠𝑡𝑎𝑛𝑜𝑙)/(5alpha, 3beta− 𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑒𝑟𝑜𝑙 + beta−𝑠𝑖𝑡𝑜𝑠𝑡𝑒𝑟𝑜𝑙 + 𝐶𝑎𝑚𝑝𝑒𝑠𝑡𝑒𝑟𝑜𝑙) - PU: The Pee-eww ratio (PU) as defined in the EQ6 of the publication: (5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙)/(5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑒𝑟𝑜𝑙 + beta−𝑠𝑖𝑡𝑜𝑠𝑡𝑒𝑟𝑜𝑙) * Year: Date in AD of sediment sample * Elk num: historical number of elk for that year * Bison num: historical number of bison for that year * kg sum: The summed kilograms of bison and elk biomass. Calculated by multiplying the number of elk by 235 kg and the number of bison by 665 kg. (kg) - million kg sum: The summed millions of kilograms of bison and elk biomass. (millions kg) - num sum: the total number of elk and bison - management: where were the bison during the winter, based on management discussion in Wendt et al. (2024). natural = means bison were not foddered by the lake. Winter restricted = means the bison were foddered by the lake - Stigmastanol: Sum of concentration of all the sigmastanol isomers measured 5β3β-stigmastanol, 5β3α-stigmastanol, 5α3β-stigmastanol (ng/cm3) - stigma ratio: As defined in EQ3 of the publication: (5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙)/(5beta3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5beta3alpha− 𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙 + 5alpha3beta−𝑠𝑡𝑖𝑔𝑚𝑎𝑠𝑡𝑎𝑛𝑜𝑙)