Impacts of Pleistocene extinctions on the biomass and energy use of local mammal assemblages around the world
Data files
Sep 05, 2025 version files 2.90 MB
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Appendix_S1_-_Pre-extinction_samples___records.xlsx
526.53 KB
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Appendix_S2_-_Post-extinction_samples___records.xlsx
484.04 KB
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Appendix_S3_-_Species.xlsx
99.82 KB
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R_script_and_raw_data_files.zip
1.78 MB
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README.md
10 KB
Abstract
Many of the world's megafaunal species went extinct during the late Quaternary, leading to dramatic reductions in community and ecosystem functioning. While the nature and severity of the extinctions are well documented on global and continental scales, less is known about local-scale impacts. We quantified the biomass and energy use of 292 pre-extinction and 360 post-extinction fossil assemblages from around the globe to determine effects on large mammal communities. Assemblage energy use was calculated from metabolic rates obtained for 562 individual species, and was compared to species richness along with indicators of taphonomy, archaeology, and biogeography, using three analytical methods: least-squares orthogonalization regression, spatial autoregression, and linear mixed effects model analysis. Globally, total biomass and energy use are greatly reduced in post-extinction assemblages. Human-accumulated assemblages are further homogenised post-extinction due to their high abundances of domesticated species. The presence of domesticates greatly altered the biomass and energy use of assemblages post-extinction, producing strong energetic variation across continents that differs considerably to pre-extinction patterns. This fundamental anthropogenic alteration of communities further exacerbated the impacts of Pleistocene extinctions, even in less severely impacted regions. The results show how human activities have altered mammalian communities for many thousands of years.
Impacts of Pleistocene extinctions on the biomass and energy use of local mammal assemblages around the world
This study calculated the energy use and biomass of 652 late Quaternary fossil assemblages from across the globe and found that both were greatly reduced following the Pleistocene megafaunal extinctions. In addition, the high abundances of domesticated species present in many post-extinction assemblages altered the geographic variation of energy use patterns, further exacerbating the extinction impacts.
There are three appendix files as well as a zip folder containing the R code and raw data files used to conduct the analyses. The R script will automatically read all data files directly into R.
The three appendices are as follows:
Appendix S1 - Pre-extinction samples + records: complete lists of all 292 pre-extinction fossil samples and 3218 pre-extinction sample records (species-plus-sample combinations) that were downloaded from the Ecological Register and used in the analysis.
Appendix S2 - Post-extinction samples + records: complete lists of all 360 post-extinction fossil samples and all 2964 post-extinction sample records (species-plus-sample combinations) that were downloaded from the Ecological Register and used in the analysis.
Appendix S3 - Species: the complete list of all 562 large mammal species that were present in the 652 fossil samples alongside their body masses and basal metabolic rates (BMR). The 181 sp. records and eight unique familial indet. records that were included are also listed.
The R script and raw data files zip folder contains the following files:
R SCRIPT.R: The R script to conduct the analyses presented in the study.
All_register.txt: The 9103 individual species by site records present in the Ecological Register download.
All_samples.txt: The 683 samples that were present in the Ecological Register download.
ALL Fossil Species BMR.txt: the body masses and basal metabolic rates for all 754 large mammal species present in the dataset, including all sp. and some indet. records.
Species BMR.txt: the body mass and basal metabolic rate (BMR) for all 147 species with directly measured metabolic rates.
baarCoords.txt: The coordinates used to generate the BAAR map projections in Figs. 3 and 4 of the main text.
Baar_continental_cells.txt.gz: The continental cells used to generate the BAAR map projections in Figs. 3 and 4 of the main text.
The column names in the appendix files are as follows:
Sample number: The number of the sample as recorded in the Ecological Register database.
Created (date and time): The date and time the sample was entered into the database.
Sample name: The name of the sample in the database, usually corresponding to the name of the fossil site and the layer/unit (if applicable).
Country: The country where the sample is located.
State/Province: The main first-level country subdivision (usually a state or province) where the sample is located. This is usually only recorded when it is reported in the reference publication. If it was not reported, then the cell is left blank.
Ecozone: The biogeographical realm where the sample is located (i.e. the Afrotropics, Australasia, Indomalaya, Nearctic, Neotropics, Palearctic).
Latitude: The latitude of the sample.
Longitude: The longitude of the sample.
Sampling methods: The main sampling methods used during the excavation of the sample (i.e. quarry, screenwash, surface). This is usually, but not always reported by the manuscript. If no sampling methods are provided, then it says 'not stated'.
Time interval: The time period of the sample (i.e. ‘Late Pleistocene’, ‘Holocene’, or ‘Pleistocene – Holocene’) based on the sample’s date or date range.
Section Number: A number indicating that the sample is part of a larger stratigraphic sequence whereby each layer/unit forms its own individual sample. The section number is the same for each sample that belongs to the same section and usually corresponds to the publication reference number as recorded in the Ecological Register database. An “NA” value means that the sample does not belong to a larger stratigraphic sequence.
Unit number: The number of the specific layer/unit within the larger stratigraphic sequence. Applies only to samples with a section number. NA = not applicable.
Unit order: The order of the unit numbering (i.e. ‘above to below’ or ‘below to above’) indicating whether the layers/units are numbered from top to bottom or bottom to top. Applies only to samples with a section number (see above). NA = not applicable.
Age (Ma): The age of the sample in units of millions of years (the standard in the database). If a date range applies to the sample, the value reflects the midpoint of the range.
Maximum Age (Ma): The maximum age of the sample in millions of years. Applies only to samples with a date range. NA = not applicable.
Minimum Age (Ma): The minimum age of the sample in millions of years. Applies only to samples with a date range. NA = not applicable.
Age basis: The dating method used to obtain the dates for the sample according to the reference publication or another paper where the dates were obtained. If no dating methods were stated then it says 'not stated'.
Taphonomic context(s): The primary accumulation mode(s) of the assemblage represented by the sample as stated in the reference publication. If none were stated, then it says 'none stated'.
Archaeological features: A list of any archaeological features found or present within the assemblage represented by the sample (e.g. stone or bone tools, hearths, burials, ceramics, structures, etc.). If no archaeological features were reported, then it says 'none reported'.
Number of individuals: The total number of identified specimens present in the entire sample. Does not include specimens of unidentified material.
Number of species: The total number of unique species identified within the sample.
Ecological group: The designated ecological group of a particular species as recorded in the Ecological Register. The six groups in this dataset are: ‘carnivore’, ‘rodent’, ‘primate’, ‘ungulate’, ‘other large mammal’, and ‘other small mammal’.
Species name (genus + species): The scientific binomial of the identified species present in the sample.
Subspecies: A subspecific epithet of a species indicating that the remains are of a particular subspecies of that species. This usually only applies to certain subspecies that differ notably from other members of the species (e.g. are domesticated). If no subspecies is designated, then this field is left blank.
Count (NISP): The total number of identified specimens (NISP) of a particular species present in the sample (i.e. its abundance).
Mass (g): The average adult body mass of the identified species measured in grams.
Log10 mass: The common logarithm (to the base 10) of the body mass (in grams) of the identified species.
Mass source: The source of the body mass value listed under ‘Mass (g)’. Masses obtained from the ‘Ecoregister’ are based on published measurements of wild, adult individuals. ‘EoL’ = Encyclopedia of Life.
BMR (W): The basal metabolic rate (BMR) of the identified species measured in watts (i.e. joules per second).
BMR (kJ per day): The basal metabolic rate (BMR) of the identified species measured in kilojoules per day.
BMR (ml.O2.h): The basal metabolic rate (BMR) of the identified species measured in millilitres of oxygen consumption per hour (ml O2 h-1).
Log10 BMR (ml.O2.h): The common logarithm (to the base 10) of the basal metabolic rate (BMR) of the identified species (specifically of the values measured in ml O2 h-1).
BMR source: The source of the basal metabolic rate values listed in the ‘BMR’ columns.
Additional column names that are present only in the 'raw data files' are as follows:
synonym: a currently invalid taxonomic name for the species listed in the 'species_name' column. Synonyms are rarely listed, usually only occurring in a few instances where the now synonymous name was (or is still) very commonly used, or the name was updated due to recent taxonomic studies. As a result, this field is mostly blank.
reference_no: the Ecological Register reference number of the paper where the data for the sample was obtained from. Every sample in the register is tied to a scientific publication, and each reference publication is allocated a unique reference number.
contributor: the name of the person who contributed the sample data to the Ecological Register.
enterer: the name of the person who entered the sample into the Ecological Register.
region: the geographic region (e.g. Europe) that the sample belongs to. This is often not recorded and therefore is usually left blank.
land mass: a categorical field describing whether the sample is from a continent (e.g. Africa), a large oceanic island (e.g. Borneo), a coastal island, etc.
altitude value: the value of the altitude recorded at the location of the sample.
altitude unit: the units that the altitude value is measured in (usually metres).
extant or extinct: a simple binary indicating whether the species is currently alive today or has died out.
genus: the scientific genus name that the species belongs to.
species: the specific epithet of the species.
All other colums in the raw data files are the same as described in the appendices, or are simply not relevant to the current dataset (i.e. they are simply the raw files that were downloaded from the Ecological Register, which is primarily focused on modern ecological samples, not fossil data. As a result, a number of extra columns are included in the raw data files that contain no data as those columns are simply not applicable to fossil data - and thus are not relevant to this study).