DOI: 10.5061/dryad.zpc866tfn
title: Data from: Rise and diversification of chondrichthyans in the Paleozoic

description: 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.
description: 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. 
description: # Data from: Rise and diversification of chondrichthyans in the Paleozoic
 **Authors:** Lisa Schnetz;
 Emma Dunne; Iris Feichtinger; Richard J. Butler; Michael I. Coates; Ivan
 J. Sansom. Corresponding author email:
 [lisa.schnetz@gmail.com](mailto:lisa.schnetz@gmail.c) 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
 (). 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:
 
 ## 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 1. Number of
 variables: 33 2. Number of rows: 2539 3. 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. 4. Missing data codes: NA (data not available), ? (not certain) #####
 DATA-SPECIFIC INFORMATION FOR:
 Chondrichthyan\_diversity\_data\_Schnetz\_et\_al.xlsx 1. Number of tabs: 3
 2. 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. 3. 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.
 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.