Data from: Rise and diversification of chondrichthyans in the Paleozoic
Cite this dataset
Schnetz, Lisa et al. (2024). Data from: Rise and diversification of chondrichthyans in the Paleozoic [Dataset]. Dryad. https://doi.org/10.5061/dryad.zpc866tfn
Abstract
The Paleozoic represents a key time interval in the origins and early diversification of chondrichthyans (cartilaginous fishes), but their diversity and macroevolution are largely obscured by heterogenous spatial and temporal sampling. The predominantly cartilaginous skeletons of chondrichthyans pose an additional limitation on their preservation potential and hence on the quality of their fossil record. Here, we use a newly compiled genus-level dataset and the application of sampling standardization methods to analyze global total-chondrichthyan diversity dynamics through time from their first appearance in the Ordovician through to the end of the Permian. Subsampled estimates of chondrichthyan genus richness were initially low in the Ordovician and Silurian but increased substantially in the early Devonian. Richness reached its maximum in the middle Carboniferous before dropping across the Carboniferous/Permian boundary and gradually decreasing throughout the Permian. Sampling is higher in both the Devonian and Carboniferous compared with the Silurian and most of the Permian stages. Shark-like scales from the Ordovician are too limited to allow for some of the subsampling techniques. Our results detect two Paleozoic radiations in chondrichthyan diversity: the first in the earliest Devonian, led by acanthodians (stem-group chondrichthyans), which then decline rapidly by the late Devonian, and the second in the earliest Carboniferous, led by holocephalans, which increase greatly in richness across the Devonian-Carboniferous boundary. Dispersal of chondrichthyans, specifically holocephalans, into deeper water environments may reflect a niche expansion following the faunal displacement in the aftermath of the Hangenberg extinction event at the end of the Devonian.
README: Data from: Rise and diversification of chondrichthyans in the Paleozoic
https://doi.org/10.5061/dryad.zpc866tfn
Authors: Lisa Schnetz; Emma Dunne; Iris Feichtinger; Richard J. Butler; Michael I. Coates; Ivan J. Sansom. Corresponding author email: lisa.schnetz@gmail.com
This repository contains the input dataset and additional data information to perform the analyses presented in the paper entitled 'Rise and diversification of chondrichthyans in the Paleozoic.
Description of the data and file structure
These data were generated to quantify the rise and diversification of the total group chondrichthyans in the Paleozoic using standard and subsampling techniques. A dataset of ~1318 occurrences, representing 443 Paleozoic chondrichthyan genera, from the Late Ordovician (Darriwilian) to the end of the Permian (Changhsingian) was compiled from museum visits and augmented with peer-reviewed literature.
The input data tab in the Chondrichthyan_diversity_data_Schnetz_et_al.xlsx file can be loaded into R to start analysing (recommended to convert to csv before loading into R). This file does not contain the acanthodian occurrences which can be retrieved from the Schnetz et al. 2022 Dryad repository (doi linked below).
The Chondrichthyan_groups_Schnetz_et_al.xlsx can also be loaded into R by converting into a .csv file and can be used to run all of the analyses (it includes the acanthodian input data). This file also includes the chondrichthyan group divisions, hence we modified and added the acanthodian data from Schnetz et al. 2022.
Sharing/Access information
The acanthodian data was taken from Schnetz et al. 2022 (https://doi.org/10.5061/dryad.j0zpc86ff). Additional information regarding the acanthodian occurrence data can also be found there.
Links to other publicly accessible locations of the data:
- This data and additional code will also be made available via github: https://github.com/LisaSchnetz/Palaeozoic_chondrichthyan_diversity
DATA & FILE OVERVIEW
1. File List:
A) Chondrichthyan_groups_Schnetz_et_al.xlsx
B) Chondrichthyan_diversity_data_Schnetz_et_al.xlsx
DATA-SPECIFIC INFORMATION FOR: Chondrichthyan_groups_Schnetz_et_al.xlsx
- Number of variables: 33
- Number of rows: 2539
Variable list:
*GENUS: taxon genus
*SPECIES: taxon species
*ORDER: taxon order
*FAMILY: taxon family
*SUBCLASS: taxon subclass
*GROUP_GINTER: systematic grouping of taxa according to Ginter et al. (2010). Divisions based on major superorders and cohorts.
*GROUP_GINTER2: systematic grouping of taxa according to Ginter et al. (2010). Divisions based on subclasses.
*ACANTHODIAN_GROUP: whether taxa were considered to be part of the acanthodian group. N for no and Y for yes. Please refer to the methods section in the manuscript for further details.
*TOOTH_PLATE: subset including all taxa with tooth plates (specific dentition morphology). N for no and Y for yes.
*DUPLICATE: whether taxon includes multiple occurrences. N equals to a single occurrence (hence no duplicates), Y equals multiple.
*PERIOD: major division of geological time.
*EARLIEST: earliest time interval of occurrence (geological stage time-level).
*MAX_DATE: earliest time in Ma (million years ago) of occurrence.
*LATEST: latest time interval of occurrence (geological stage time-level).
*MIN_DATE: latest time in Ma (million years ago) of occurrence.
*MID POINT: mid time point of occurrence in Ma (million years ago) of occurrence, calculated by MAX_DATE - ((MAX_DATE-MIN_DATE)/2)
*LAZARUS: whether taxon is a Lazarus taxon or not. A Lazarus taxon disappears for one or more time intervals from the fossil record but appears again later in time.
*COLLECTION: collection here is equivalent to an individual occurrence fossil locality (e.g., a quarry or road cutting).
*FORMATION: geological formation the taxon occurrence was found in
*Latitude: modern day latitude coordinate of taxon locality
*Longitude: modern day longitude coordinate of taxon locality
*CONTINENT: which continent the taxon occurrence was found in
*HEMISPHERE: which hemisphere the taxon occurrence was found in
*BA_0: whether the taxon occurrence was found in depositional setting BA 0 (BA = benthic assemblage zone). 0 = not found and 1 = found. Please refer to the methods section in the manuscript for further details.
*BA_1: whether the taxon occurrence was found in depositional setting BA 1 (BA = benthic assemblage zone). 0 = not found and 1 = found. Please refer to the methods section in the manuscript for further details.
*BA_2: whether the taxon occurrence was found in depositional setting BA 2 (BA = benthic assemblage zone). 0 = not found and 1 = found. Please refer to the methods section in the manuscript for further details.
*BA_3: whether the taxon occurrence was found in depositional setting BA 3 (BA = benthic assemblage zone). 0 = not found and 1 = found. Please refer to the methods section in the manuscript for further details.
*BA_4: whether the taxon occurrence was found in depositional setting BA 4 (BA = benthic assemblage zone). 0 = not found and 1 = found. Please refer to the methods section in the manuscript for further details.
*BA_5: whether the taxon occurrence was found in depositional setting BA 5 (BA = benthic assemblage zone). 0 = not found and 1 = found. Please refer to the methods section in the manuscript for further details.
*BA_6: whether the taxon occurrence was found in depositional setting BA 6 (BA = benthic assemblage zone). 0 = not found and 1 = found. Please refer to the methods section in the manuscript for further details.
*SCALE_ONLY: whether the taxon is known from isolated scales only. N for now and Y for yes.
*FINSPINE_ONLY: whether the taxon is known from isolated fin spines only. N for now and Y for yes.
*TOOTH_ONLY: whether the taxon is known from isolated teeth only. N for now and Y for yes.
Missing data codes: NA (data not available), ? (not certain)
DATA-SPECIFIC INFORMATION FOR: Chondrichthyan_diversity_data_Schnetz_et_al.xlsx
- Number of tabs: 3
Tab list:
-Contents: content list for the file
-Input data: input data list to be used for analyses (this list does not contain chondrichthyan group information, please refer to Chondrichthyan_groups_Schnetz_et_al.xlsx for this). Explanations of variables are given above and are identical to those in file Chondrichthyan_groups_Schnetz_et_al.xlsx .
-Specimen information: Additional information for each specimen collected. Empty cells in this tab are either for aesthetic purposes to make it more readable or denote that there is no information available for the variable for the specific occurrence. It is not recommended to use this file for analyses but to look up additional information. The information includes:
*Genus: taxon genus
*Species: taxon species
*Order: taxon order
*Family: taxon family
*Inventory number: museum/collection inventory number of taxon.
*Notes: notes on the fossil occurrence (e.g., morphological features, etc.).
*Taxon notes: notes regarding taxon validity, e.g., where systematics were taken from.
*System: chronostratigraphic division of geologic time.
*Series: chronostratigraphic division of geologic time.
*Stage: chronostratigraphic division of geologic time.
*Regional Stage: chronostratigraphic division that is not applied globally.
*Group: geological lithostratigraphic group the taxon was found in
*Formation: geological lithostratigraphic formation the taxon occurrence was found in
*Member: geological lithostratigraphic member the taxon occurrence was found in
*Locality: individual occurrence fossil locality (e.g., a quarry or road cutting).
*Continent: which continent the taxon occurrence was found in.
*Environmental notes: notes regarding the environment/ depositional setting of the locality/formation the occurrence was found in. This is then used to assign benthic assemblage zones (see methods section in the manuscript for more details).
*Benthic Assemblage Zone: benthic assemblage zone assignment of occurrence (see methods section in the manuscript for more details).
*Max Age: earliest time in Ma (million years ago) of occurrence.
*Min Age: latest time in Ma (million years ago) of occurrence.
*Collection: which museum/collection the occurrence was studied/retrieved from.
*Reference: published literature references for occurrence. This was mainly recorded for occurrences that were only retrieved from literature searches.
Missing data codes: NA (data not available), ? (not certain)
Code/Software
All data was analysed using the programming environment R v. 4.2.0 (R Core Team 2019). Packages used include rgplates (v.0.3.2, Kocsis et al. 2023), divDyn (v. 0.8.1, Kocsis et al. 2019), iNEXT (v. 3.0.0, Hsieh et al. 2016), nlme (Pinheiro et al. 2018), MuMIn (v. 3.1-157, Barton 2018) and divvy (version 0.2.0.9000, Antell 2023).
References
Antell, G. 2023. divvy: Spatial Subsampling of Biodiversity Occurrence Data. R package version 0.2.0.9000.
Barton, K. 2018. MuMIn: multi-model inference. R package v. 1.43.17. https://CRAN.Rproject.org/package=MuMIn
Ginter, M., Hampe, O., and C. Duffin. 2010. Chondrichthyes. Paleozoic Elasmobranchii: Teeth. In H.-P. Schultze, ed. Handbook of palaeoichthyology, volume 3D. Verlag Dr. Friedrich Pfeil, München. Hsieh, T. C., Ma, K. H., and A. Chao. 2016. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods in Ecology and Evolution 7: 1451–1456.
Kocsis, Á. T., Reddin, C. J., Alroy, J., and W. Kiessling. 2019. The r package divDyn for quantifying diversity dynamics using fossil sampling data. Methods in Ecology & Evolution 10: 735–743.
Kocsis, Á.T., Raja, N.B. and S. Williams. 2023. rgplates: R interface for the GPlates Web Service and Desktop Application.
Pinheiro, J., Bates, D., DeBroy, S., Sarkar, D., and R Core Team. 2018. nlme: linear and nonlinear mixed effects models. R package v. 3.1-137.
R Core Team 2019. R: a language and environment for statistical computing. v. 4.2.0. R Foundation for Statistical Computing. https://www.r-project.org
Methods
All information on data collection as well as specific details can be found in the Methods section of the manuscript. Please also see the README file for additional data & method information.
Funding
Natural Environment Research Council, Award: NE/L002493/1, CENTA
SYNTHESYS project