DOI: 10.5061/dryad.3j9kd51vw
title: Data from: Taphonomic controls on a multi-element skeletal fossil record

description: Animals with multi-element skeletons, including vertebrates, echinoderms,
 and arthropods, are some of the most biodiverse and ecologically important
 animal groups. Understanding the relative impact of the myriad geological
 and biological factors that impact the quality of multi-element skeletal
 fossils is thus crucial for disentangling perceived changes in
 biodiversity through time and shedding light on gaps in the fossil record.
 We have characterised the specimen-level taphonomic history of virtually
 the entire Palaeozoic fossil record of echinoids, the class of echinoderms
 which includes the living sea urchins. We find that the majority of this
 fossil record consists of disarticulated skeletal elements, and as
 preservational quality increases, so does the proportion of specimens that
 can be identified with higher taxonomic precision. We then assessed the
 relative impacts of multiple geological and biological factors on our
 specimen quality, identifying that fine-grained host matrix, as well as
 siliciclastic lithology, are the biggest factors in determining the
 quality of fossil echinoid preservation, while aspects intrinsic to
 specific taxonomic groups also play a role. Differential sampling of the
 fossil record seems to play little role in influencing the distribution of
 taphonomic grades, and fluctuations in the North American record of
 Siliciclastic rocks are positively correlated with fluctuations in
 taphonomic grades. Our results highlight that the factors controlling the
 animal macrofossil record are varied, and that the interplay between these
 variables, taphonomic grade, and taxonomic precision impacts our ability
 to use the fossil record to understand macroevolution.
description: This dataset includes the specimen dataset used for analysis, as
 well as custom R scripts for generating results and figures. 
 The specimen dataset was collected from 33 museums by the lead
 author (Jeffrey R. Thompson) and bolstered by additional specimens found
 in the available literature. The associated lithology and grain size were
 recorded for each specimen, alongside data on taxonomy (including
 most-specific taxonomic rank possible), stratigraphic provenance and
 locality of collection, and an estimate was made of the associated
 Taphonomic Grade (see manuscript for full details). All data were
 collected by one individual (J.R. Thompson), who also vetted all the
 taxonomic designations of all specimens. Specimens without precise
 geographic coordinates were georeferenced by locating text-based locality
 descriptions on Google Maps (available from http://google.com/maps); we
 additionally included the likely precision of this estimate in the
 degrees-minutes-seconds format. Palaeo-coordinates for these locations
 were obtained using the ‘PALAEOMAP’ rotation model through the GPlates
 API, using the ‘palaeorotate' function of the ‘palaeoverse’ package
 (Jones et al., 2023). Data were additionally assigned to stage, series,
 and period level time bins using the ‘majority’ method of the ‘bin_time’
 function from the ‘palaeoverse’ package (Jones et al., 2023).
description: # Data from: Taphonomic controls on a multi-element skeletal fossil record
 [https://doi.org/10.5061/dryad.3j9kd51vw](https://doi.org/10.5061/dryad.3j9kd51vw) ## Description of the data and file structure This dataset includes the specimen dataset used for analysis, as well as additional datasets and custom R scripts for generating results and figures.  The main specimen dataset was collected from 33 museums by the lead author (Jeffrey R. Thompson), and bolstered by additional specimens found in the available literature. The associated lithology and grain size were recorded for each specimen, alongside data on taxonomy (including most-specific taxonomic rank possible), stratigraphic provenance and locality of collection, and an estimate was made of the associated Taphonomic Grade (see manuscript for full details). All data were collected by one individual (J.R. Thompson), who also vetted all the taxonomic designation of all specimens. Specimens without precise geographic co-ordinates were georeferenced by locating text-based locality descriptions on Google Maps (available from [http://google.com/maps](http://google.com/maps)); we additionally included the likely precision of this estimate in the degrees-minutes-seconds format. Palaeo-coordinates for these locations were obtained using the ‘PALAEOMAP’ rotation model through the GPlates API, using the ‘palaeorotate' function of the ‘palaeoverse’ package (Jones et al., 2023). Data were additionally assigned to stage, series and period level time bins using the ‘majority’ method of the ‘bin_time’ function from the ‘palaeoverse’ package (Jones et al., 2023). ### Files and variables #### File: Data.zip **Description:** This .zip file contains two folders: 1. Additional_data: This contains additional files containing timescales and covariates used for analyses. Files include: 1. series.csv: A .csv file containing information on geological series through time for time binning. Variables include: * bin: Bin name, at stage level (e.g. Devonian) * max_ma: Maximum age of bin in millions of years * min_ma: Minimum age of bin in millions of years * abbr: Bin name abbreviation * color: Colour associated with bin 2. Specimen_data: This contains the main dataset, as well as additional datasets of PBDB downloads used for correlations. Files include: 1. Final_Database*_*for_analysis.csv: A .csv file containing the finalised dataset. Variables include: * ID: Unique specimen ID number * Original_taxon_description: Taxonomic description as written on museum label * Rank: Taxonomic rank of specimen  * Family: Family of specimen * Genus: Genus of specimen * Species: Species of specimen * Museum_Number: Museum number of specimen * Museum: Museum at which the specimen is accessioned * Museum_country: County of museum in which the specimen is accessioned * Museum_code: Code of museum in which the specimen is accessioned * Publication: Publication(s) in which the specimen is reported * Museum_only: Is the specimen only present in museum collections and is not published? (0: published; 1: only in museum) * In_PBDB: Is the specimen present as an occurrence in the Paleobiology Database? * Preservation_score: Taphonomic grade assigned to the specimen (described in detail in main manuscript) * Description: Notes on preserved anatomical details of the specimen * Locality: Character based description of the site of collection * Continent: Continent in which the specimen was found * Country: Country in which the specimen was found * lat: Latitudinal position of specimen, in degrees (°) * lng: Longitudinal position of specimen, in degrees (°) * latlngPrecision: Precision/accuracy of lat/lng coordinates * Group: Geological group in which the specimen was found * Formation: Geological formation in which the specimen was found * Member: Geological member in which the specimen was found * Formation_Notes: Original description of stratigraphic/geologic context * Strat Citation: Citation related to the geological context * Age_resolution: Resolution of the age of the specimen (e.g. Stage, Period etc.) * Age: Original text description of age of specimen * Max_period: Maximum age of Period of specimen * Min_period: Minimum age of Period of specimen * max_stage: Maximum age of Stage of specimen * min_stage: Minimum age of Stage of specimen * Finalised_lith: Formatted lithology associated with specimen * Lithology: Original description of lithology associated with specimen * Finalised_grainsize: Formatted grain size associated with specimen * Grain size: Original description of grain size associated with specimen * Notes: Additional notes (generally distinguishing whether specimen is a holotype) * Preservation state/notes: Notes on the preservational state of the specimen * More notes: Other notes not covered by other columns * Subperiod: Subperiod of specimen ## Code/software There are 4 R scripts included with this dataset: 1. Taph_Functions.R: An R file containing all the custom functions necessary to run analyses. 2. Taph_Setup.R: An R file containing the processing and cleaning necessary prior to running analyses. 3. Taph_Main_Script.R: An R file containing the main script for running all analyses carried out in the paper. 4. Taph_Figures.R: An R file containing the necessary code to produce the figures for the manuscript. ### ESM (electronic supplementary materials) There are three electronic supplementary materials files included with this dataset available via Zenodo: 1. ESM 1: A Word document providing the additional supplementary figures: * SI Figs. 1-10 2. ESM 2: An Excel file containing the additional supplementary tables: * SI Tables 1-9.  3. Specimen_data: A folder containing .csv files of the PBDB downloads used in this research. Further info on these files can be found on the Index page of both ESM files. ## Access information Other publicly accessible locations of the data: * [https://github.com/ChristopherDavidDean/Echino_taph](https://github.com/ChristopherDavidDean/Echino_taph) Data was derived from the following sources: * [http://palaeobiob.org](http://palaeobiob.org)