DOI: 10.5061/dryad.8cz8w9h52
title: Impacts of Pleistocene extinctions on the biomass and energy use of local mammal assemblages around the world

description: 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.
description: 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).