DOI: 10.5061/dryad.wdbrv15xw
title: Data for: Is there synchronicity between brachiopod diversity changes and palaeobiogeographical shifts across the Late Ordovician mass extinction?

description: As the first major biotic event in the Phanerozoic, the two‐phased Late
 Ordovician mass extinction (LOME) resulted in a substantial decline in
 marine benthic biodiversity and heralding shifts in palaeobiogeography.
 However, the interplay between palaeobiogeographical distribution and
 biodiversity dynamics during this event remains unknown. Drawing upon
 brachiopod occurrence data from five intervals pre‐ and post‐LOME,
 extracted from the Paleobiology Database, we conducted a comprehensive
 analysis of palaeogeographic units across the extinction event. Through
 examination of generic diversity, origination and extinction rates, and
 biogeographic connectedness, we elucidate the evolutionary trajectories of
 both endemic and cosmopolitan taxa throughout the extinction. Our findings
 indicate increased vulnerability of endemic taxa to biotic events and
 their aftermath relative to their cosmopolitan counterparts. Notably, we
 observe a concordance between shifts in the palaeogeographic distribution
 of brachiopods and fluctuations in their diversity during and after the
 LOME. Moreover, the extinction and subsequent recovery dynamics of
 brachiopods during this event demonstrate temporal symmetry concerning
 biodiversity change and palaeobiogeographic structural shifts. Shortly
 after the extinction event, within a timeframe similar to the decline in
 diversity and contraction of palaeogeographic distribution, both aspects
 revert to pre‐extinction levels, suggesting the limited intensity of the
 LOME event.
description: This study used the most recent global brachiopod occurrence data
 downloaded from the Paleontological Database (PBDB) for September 2023
 (http://paleobiodb.org). The dataset contains 20,501 items. To pre-process
 the data, the fossil brush tool (Flannery-Sutherland et al., 2022) was
 used to eliminate records of brachiopods with unknown ages, missing
 paleogeographic coordinates, and single taxonomic location errors. Thus,
 the final dataset includes 19,937 records of the emergence of brachiopods
 from the Late Ordovician Mass Extinction (LOME), spanning five successive
 epochs from Katian (Late Ordovician) to Telychian (early
 Silurian).
description: # **Data for:** **Is there synchronicity between brachiopod diversity
 changes and palaeobiogeographical shifts across the Late Ordovician mass
 extinction?**
 [https://doi.org/10.5061/dryad.wdbrv15xw](https://doi.org/10.5061/dryad.wdbrv15xw) This dataset provides the data used for the analysis along with the R code which enables a comprehensive analysis of brachiopod trends before, during, and after the Late Ordovician Mass Extinction, providing insights into biodiversity changes, origination and extinction rates, biogeographic connectedness, and paleogeographic distributions during this critical period. ## **Description of the data and file structure** The database contains several key components: Two CSV files containing the primary data: **"Brachiopoda_data"**: This file includes the latest global brachiopod occurrence data from 453 ma to 432 ma, downloaded from the Paleobiology Database (PBDB) in September 2023. This data is processed data. The raw data was downloaded from the PBDB and then processed with  "data_clean". This data can be published under CC0. Download parameters are as follows: time intervals = Late Ordovician and early Silurian (453 Ma–432 Ma), region = all, 402 paleoenvironment = marine, Order = Brachiopoda. Some columns in the document contain missing values but do not affect the analysis. The complete data for the PBDB contains approximately 187 variables, of which we used 24, partly for analysis and partly to identify the data to avoid confusion. There is not enough space to list them all. A detailed description of each variable can be found at [https://paleobiodb.org/data1.2/occs/list#RESPONSE]() which is the official website of PBDB.  **"GTS2020"**: This file contains the most recent geological time scale information, correlating geological ages to stages. This allows for mapping the 453-432 Ma data to the corresponding stages from Katian to Telychian. GTS2020 is an abbreviation of GEOLOGIC TIME SCALE 2020. Order from old to new, starting from order=75 is the number of each stage. FAD is the start time, FAD is the end time, and they're measured in millions of years. Several R code files for data analysis and visualization of brachiopod trends across the Late Ordovician Mass Extinction (LOME): data_clean: For cleaning and preprocessing the brachiopod occurrence data background: Creates aesthetically pleasing backgrounds for diversity, origination, and extinction plots. BC_calculate: Calculates biogeographic connectedness to reflect palaeobiogeographic structure paleogeography: For analyzing or visualizing paleogeographic data of brachiopods across the LOME. rarefaction: Performs rarefaction analysis on brachiopod data frequency: Generates frequency histograms and pie diagrams depicting global palaeobiogeographic analysis units of brachiopods. diversity_oe_rate: Analyzes biodiversity, origination, and extinction patterns of brachiopods across the LOME. ## **Sharing/Access information** Links to other publicly accessible locations of the data: [https://paleobiodb.org/classic/displayDownloadGenerator](https://paleobiodb.org/classic/displayDownloadGenerator) ## **Code/Software** •   R version 4.4.1 •   RStudio version 2024 •   Main packages used: divDyn, scales, lmodel2, tidyr, fossilbrush, bootstrap, ggplot2, sf, readxl, tmap, spData, vegan, rgplates.