DOI: 10.5061/dryad.0000000gp
title: Data from: Persistent body size bias in the fossil record of Cenozoic North American mammals

description: Body size is a key organismal trait with profound implications ranging
 from individual physiology to large-scale macroecological or
 macroevolutionary phenomena. Among extant terrestrial vertebrates, peak
 diversity commonly occurs at small body size. Similarities between the
 body size distributions of fossil and extant mammals have been used to
 argue that fossil record signals are robust, yet preservation and
 collector biases disproportionately favour the sampling of large taxa and
 likely underrepresent small-sized diversity. Here, we quantify the effects
 of these biases on the body size distributions of North American mammals
 through the Cenozoic. We assess how these distributions have changed with
 new palaeontological discoveries and evaluate sampling standardisation as
 a potential correction for body size bias. Our results show bias in the
 mammal record to be persistent and severe. Sampling standardisation has no
 consistent effect on recovered distribution shape, likely because sample
 coverage estimators cannot account for changes in the scope of the
 sampling universe driven by a combination of historical worker interest
 and the preservational characteristics of a small pool of formations.
 Short of a novel standardisation method that can account for publication
 biases, deriving non-artefactual fossil body size signals may ultimately
 depend on targeted, systematic sampling of exceptional deposits.
description: # Data from: Persistent body size bias in the fossil record of Cenozoic
 North American mammals Dataset DOI:
 [10.5061/dryad.0000000gp](10.5061/dryad.0000000gp) ## Description of the
 data and file structure README for: **Correcting bias in the body size
 distribution of North American Cenozoic mammals** Data for this project
 can be broken into two categories: that for the primary analyses, and a
 supplementary section used to derive new mass regressions for two mammal
 groups. These are described, respectively, below. For Code, those needed
 for the supplementary section are included within “Files and Variables”;
 the remaining scripts are used for all primary analyses and are found in
 “Code/software.” ## Files and variables #### PRIMARY ANALYSIS (all
 contained in mass_csvs.zip to preserve directory structure when running
 code) **File: full_mass_dataset.xlsx** **Description:** an excel workbook
 which contains the list of all measurements and/or mass groupings used to
 calculate and categorize mammal body mass in this study. It also includes
 references for the source of the measurements per each species and any
 relevant notes. The data from this workbook comprises all of the .csv
 files listed in this section; the variables it contains will therefore be
 listed for each of those entries. **File: mammal_body_mass_refs.pdf**
 **Description:** is the associated bibliography for the above dataset
 **File: extant_mass_add.csv** **Description:** contains body mass data for
 extant mammal species, it is sourced by *add_body_size.R* **Variables:**
 operational_taxon_name: binomial name (genus + species) of a species in
 the dataset higher_classification: a coarser taxonomic grouping (typically
 order) for that species family_or_subclade: a finer taxonomic grouping
 (typically family) for that species mass_kg: body mass, in kg for that
 species **File: multituberculate_mass_add.csv** **Description:** contains
 measurement data used to calculate body mass for multituberculates, it is
 sourced by *add_body_size.R* **Variables:** operational_taxon_name:
 binomial name (genus + species) of a species in the dataset
 higher_classification: a coarser taxonomic grouping (typically order) for
 that species family_or_subclade: a finer taxonomic grouping (typically
 family) for that species m1_length_mm: length of the lower first molar of
 that species, in mm m1_max_width_mm: maximum width of the lower first
 molar of that species, in mm m1_area_mm2: area of the lower first molar of
 that species, in mm^2^ **File: proboscidean_mass_add.csv**
 **Description:** contains measurement data used to calculate body mass for
 proboscideans, it is sourced by *add_body_size.R* **Variables:**
 operational_taxon_name: binomial name (genus + species) of a species in
 the dataset higher_classification: a coarser taxonomic grouping (typically
 order) for that species family_or_subclade: a finer taxonomic grouping
 (typically family) for that species femur_length_mm: length of the femur
 of that species, in mm **File: main_dataset_mass_add.csv**
 **Description:** contains measurement data used to calculate body mass for
 all other mammalian groups in the dataset, it is sourced by
 add_body_size.R **Variables:** operational_taxon_name: binomial name
 (genus + species) of a species in the dataset higher_classification: a
 coarser taxonomic grouping (typically order) for that species
 family_or_subclade: a finer taxonomic grouping (typically family) for that
 species m1_length_mm: length of the lower first molar of a species, in mm
 m1_max_width_mm: maximum width of the lower first molar of a species, in
 mm m1_area_mm2: area of the lower first molar of a species, in mm^2^
 m2_length_mm: length of the lower second molar of a species, in mm
 m2_max_width_mm: maximum width of the lower second molar of a species, in
 mm m2_area_mm2: area of the lower second molar of a species, in mm^2^
 average_molar_length_mm: the average length of the molars of a species of
 "creodont"; either two or three molars depending on taxonomic
 classification (see full_mass_dataset.xslx) lower_tooth_row_length_mm: the
 length of the lower tooth row (molars and premolars) of a species of
 rodent femur_length_mm: the length of the femur of a species, in mm
 humerus_length_mm: the length of the humerus of a species, in mm NOTE: all
 entries listed as "NA" in this table indicate that a particular
 measurement variable is **not** used to calculate body mass for that
 species, and enable the mass estimation script to work correctly (see
 Code/software). **File: na_mass_bins.csv** **Description:** contains body
 mass categorization data for taxa with no available measurement
 information, it is sourced by the function *unmassed_taxa_binning.R*
 **Variables:** operational_taxon_name: binomial name (genus + species) of
 a species in the dataset higher_classification: a coarser taxonomic
 grouping (typically order) for that species family_or_subclade: a finer
 taxonomic grouping (typically family) for that species mass_bin_coarse:
 estimated mass grouping of that species according to the coarse framework
 of "small" (&lt;1 kg), "medium" (1-30 kg), and
 "large" (&gt;30 kg) body mass categories mass_bin_fine:
 estimated mass grouping of that species according to the finer framework
 of order-of-magnitude body mass categories comparison: the group or taxon
 used to justify the assignment of the above mass categories, on the basis
 of similar size or other close relationship **File:
 mammal_synonyms_raw.csv** **Description:** contains synonymy data manually
 taken from the PBDB website
 ([www.paleobiodb.org](http://www.paleobiodb.org/)) to account for the
 synonymization of species through historical research time, it is sourced
 by *get_historical_opinions.R* **Variables:** taxon_group: a unique number
 given to each valid taxon in the table taxon_name: the name replacing an
 earlier, invalid designation for the taxon synonym_name: an earlier,
 invalid designation for the taxon synonymy_pubyr: the year of the
 publication which synonymized the entry in synonym_name into the entry in
 taxon_name notes: any further information on complications with a
 particular synonymy, or on synonymies not listed on the PBDB website which
 need to be instated given the literature (this variable is not used in any
 of the scripts and is purely for user information) **Additional Dataset of
 Smith et al. (2003):** The script *summary_figure.R* needs to source body
 mass data for extant and Pleistocene-extinct North American mammals, from
 the dataset of Smith et al.
 ([https://doi.org/10.1890/02-9003](https://doi.org/10.1890/02-9003)).
 Their dataset will need to be downloaded and titled
 **"smith_2003_modern_dataset.csv"**, and added to the
 *mass**_**csvs* folder. #### SUPPLEMENTARY REGRESSION CALCULATION (all
 contained in supplementary_regressions.zip) **File:
 pholidotamorph_dataset.csv** (in subfolder regression_csvs)
 **Description:** contains the measurement data used to derive novel body
 mass regressions for fossil pholidotamorphs. Includes references and notes
 columns which are quickly pruned by *pholidotamorph_mass_regression.R*
 after sourcing it **Variables:** taxon: binomial name (genus + species) of
 a species in the dataset higher_classification: a coarser taxonomic
 grouping (typically order) for that species family: the family to which
 that species belongs fossoriality: a classification of life ecology for
 that species, either semi-fossorial or strictly fossorial, or in the case
 of pangolins, also potentially arboreal or terrestrial body_mass_g: the
 body mass for that species, in g femur_length_mm: the length of the femur
 for that species, in mm humerus_length_mm: the length of the humerus for
 that species, in mm source: the reference(s) for all measurement data
 derived (this variable is not used in any of the scripts and is purely for
 user information) notes: any further information on how data was obtained
 or tabulated (this variable is not used in any of the scripts and is
 purely for user information) NOTE: all entries listed as "NA" in
 this table indicate that a particular measurement (humerus length or femur
 length) was not available for that species from the references cited in
 "source", and enable *pholidotamorph_mass_regression.R* to work
 correctly. **File: pholidotamorph_refs.pdf** (in subfolder
 regression_csvs) **Description:** is the associated bibliography for the
 above dataset **File: proboscidean_dataset.csv** (in subfolder
 regression_csvs) **Description:** contains the measurement data used to
 derive novel body mass regressions for fossil proboscideans. Includes
 references column which is pruned by *proboscidean_mass_regression.R*
 after sourcing it **Variables:** taxon: binomial name (genus + species) of
 a specimen in the dataset family: the family to which that specimen
 belongs (Gomphotheriidae, Mammutidae, or Elephantidae)
 humerus_max_length_cm: the maximum length (as opposed to the length in
 articulation) of the humerus for that specimen, in cm femur_length_cm: the
 length of the femur for that specimen, in cm shoulder_height_mm: the
 estimated in-flesh shoulder height for that specimen, in cm
 estimated_mass_kg: the estimated body mass for that specimen, in kg
 reference: the reference for all measurement and mass data derived (this
 variable is not used in any of the scripts and is purely for user
 information) NOTE: all entries listed as "NA" in this table
 indicate that a particular measurement (humerus length or femur length)
 was not available for that specimen from the references cited in
 "reference", and enable *proboscidean_mass_regression.R* to work
 correctly. **File: proboscidean_refs.pdf** (in subfolder regression_csvs)
 **Description:** is the associated bibliography for the above dataset
 **File: pholidotamorph_mass_regression.R** (in subfolder
 regression_scripts) **Description:** computes the novel regressions to
 calculate mass in fossil pholidotamorphs, along with associated statistics
 **File: proboscidean_mass_regression.R** (in subfolder regression_scripts)
 **Description:** computes the novel regressions to calculate mass in
 fossil proboscideans, along with associated statistics ### ##
 Code/software The script “*run_all.R*” sources all of the following
 scripts in analysis_scripts in order, enabling a complete run of all
 analyses. Default settings and required packages for the entire analysis
 are also given in this script. (all contained in analysis_scripts.zip to
 preserve directory structure when running code) #### REQUIRED SCRIPTS FOR
 ALL ANALYSES: *pbdb_mammal_download.R* downloads North American mammal
 occurrence data from the Paleobiology Database, creating the basic data
 object *add_body_size.R* computes body masses for taxa in the download
 using several allometric regressions and compiles an occurrence-mass data
 object used in all subsequent analyses *get_historical_opinions.R* creates
 recombination and synonymy tables that track changes in historical
 opinions of taxon status for discovery curves (analyses relying on species
 diversity through historical research time– i.e., the discovery curves)
 #### **SUB-FOLDERS (all .zip files):** “define_regions” contains a script
 and csvs necessary to filter downloaded mammal data to occurrences from
 North America. It is sourced by *pbdb_mammal_download.R* NOTE:
 "define_regions" is hosted as supplementary material on Zenodo
 [https://doi.org/10.5281/zenodo.17158415](https://doi.org/10.5281/zenodo.17158415). Please ensure this file is downloaded and extracted as an unzipped folder into the base directory used to run these analyses. “geoMST_functions” contains scripts necessary to perform spatial analysis. It is sourced by *spatial_analysis.R* “functions” contains three scripts which are sourced by most of the analyses. These are: *unmassed_taxa_binning.R* computes body size categories (either coarse small/medium/large or order-of-magnitude) for taxa which do not have a body mass computable by *add_body_size.R* *chao_shen_coverage.R* computes the Chao and Shen (2010) version of Good’s *u* for sample coverage analyses *drop_obsolete_occs.R* in the case of occurrences where remains where initially identified as one taxon and subsequently reattributed to another, this removes the obsolete, older occurrence with the now-incorrect attribution #### ANALYSES: *calculate_bsfds.R* computes the face-value and sampling standardized body size distributions *coverage_dist_plot.R* computes the distribution of sample coverages across body mass category in each time bin at present day *coverage_through_time.R* computes the level of sample coverage through historical research time for the different body mass categories and time bins (note: this does not implement a historical recombination/synonymization procedure) *plot_dcs.R* computes all discovery curves (raw time-ordered, vs. occurrences, vs. references, sampling-standardized time-ordered, vs. occurrences) for the different mass categories and time bins. *plot_description_curve.R* computes time-ordered curves of species diversity for the different mass categories and time bins using dates of species description, in order to account for an error in the reporting of oldest occurrences caused by a problematic reference in the PBDB. *plot_raw_bsfds_time.R* computes a plot of face-value body size distributions for the different time bins for the years 1900, 1930, 1950, 2000, and 2024, in sequence. *skew_mass_through_time.R* computes the value of skew and median mass through historical research time for the different body mass categories (note: this does not implement a historical recombination/synonymization procedure) *spatial_analysis.R* computes spatial coverage (as summed MST length) through research time for the different body mass categories and time bins (note: this does not implement a historical recombination/synonymization procedure) *short_historical_analyses.R* computes the counts of collections, formations, and references through research time for the different body mass categories and time bins (note: this does not implement a historical recombination/synonymization procedure) *willwood_plot.R* computes a [non-annotated] plot comparing the body size distribution of the exceptionally-well-sampled Willwood Formation to other major occurrence-contributing Formations from the North American Cenozoic, both those favoring the preservation of large and small taxa. *summary_figure.R* computes the [non-annotated] summary figure (main text figure 3), which compares the body size distributions for the entire Neogene and Paleogene to those of extant North American mammals and extant North American mammals *plus* Pleistocene-extinct taxa [megafauna]. ## Access information Data was derived from the following sources: * The literature, using all references listed in the associated .pdf documents