Data for: Is there synchronicity between brachiopod diversity changes and palaeobiogeographical shifts across the Late Ordovician mass extinction?
Data files
Nov 04, 2024 version files 4.53 MB
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Brachiopoda_data.csv
4.35 MB
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GTS2020.csv
177.81 KB
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README.md
3.38 KB
Abstract
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.
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
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.
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).