DOI: 10.5061/dryad.5mkkwh7j8
title: Data from: The shoulder girdle of early chondrichthyans grew by skeletal remodelling

description: A distinct shoulder region, defined by endoskeletal and dermal girdles and
 associated pectoral musculature, is a major evolutionary adaptation of
 jawed vertebrates. In teleost model species the large (macromeric)
 pectoral dermal bones can be derived from multiple embryonic tissues,
 identifying the shoulder of osteichthyans as a developmentally complex
 area at the head-trunk boundary. The absence of bone in living
 chondrichthyans makes Palaeozoic stem groups capable of dermal
 ossification key to understanding the underpinnings of skeletal growth in
 the shoulder of crown gnathostomes (osteichthyans and chondrichthyans).
 Here, using synchrotron X-ray tomography we demonstrate that individual
 pectoral plates in the oldest unequivocal jawed vertebrate, the Silurian
 (c. 439 Mya) chondrichthyan Fanjingshania renovata, develop from five
 separate growth centres. These centres correspond to pectoral bony spines
 that fuse neighbouring dermal scales into a pinnal plate and their
 expansion is accompanied by cyclical resorption and remodelling of bone
 and dentine. Our phylogenetic analyses support an interpretation of these
 processes as crown and stem gnathostome characters that co-occur only in
 the shoulder girdle of stem chondrichthyans. The systematic hard tissue
 remodelling in Fanjingshania reveals an unexpected growth dynamic within
 chondrichthyans that relates to the formation of a macromeric skeleton
 through integration of modular elements.
description: (a) Material The studied skeletal elements of
 <em>Fanjingshania renovata</em> are part of a larger fossil
 collection (more than 1000 fin spines, spines, tesserae, scales and dermal
 plates belonging to the species) recovered from the lower Silurian
 (Aeronian) beds of the Rongxi Formation, exposed near the village of
 Leijiatun, Shiqian county, Guizhou province, China. They are represented
 by a pinnal plate fragment (IVPP V27433.8) and other incomplete pinnal
 plates fused to prepectoral (IVPP V27433.9) and admedian (IVPP V27434.2)
 spines and pectoral fin spine fragments (IVPP V27433.10, IVPP V27433.11,
 IVPP V27433.12, IVPP V27433.4). All specimens were deposited at the
 Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), Chinese
 Academy of Sciences. (b) Synchrotron radiation X-ray
 tomographic microscopy The fossil material was analysed
 with synchrotron radiation X-ray tomographic microscopy at the
 TOMCAT-X02DA beamline of the Swiss Light Source, Paul Scherrer Institute,
 Villigen, Switzerland. The scans were performed with a 10X and a 4X
 objectives, producing 1501 and 1201 projections respectively, acquired
 over a 180-degree rotation arc. The beam energy was set to either 25keV or
 28keV and the beam was attenuated with 100μm Al, 10μm Cu and 10μm Fe
 filters. The projections were processed with tomographic reconstruction
 algorithms developed by Marone et al. 2017 which produced tomographic
 slices with pixel size of 1.625μm (4X objective) and 0.65μm (10X
 objective). Analysis, segmentation and 3D visualisation
 of the tomographic slices was performed in Dragonfly software, Version
 2022.2 (www.theobjects.com/dragonfly). (c) Phylogeny We performed a phylogenetic analysis under parsimony criteria based on a data matrix modified from Brazeau et al. 2023. The matrix was analysed in TNT version 1.6 employing the traditional search function. Search parameters were set to random seed value of 2, number of addition-sequence replicates to 1,000, a tree bisection reconnection (TBR) swapping algorithm limited to 100 trees per replication and a tree buffer of 10,000. The analysis was constrained by designating the** galeaspid <em>Hanyangaspis guodingshanensis</em> as an outgroup taxon and the Osteostraci as monophyletic according to the current phylogenetic framework of early vertebrates. This produced 1800 most parsimonious trees (MPTs) with a length of 1198 steps. Bayesian analysis was also conducted for the same data matrix in MrBayes version 3.2.7. We ran a Markov chain Monte Carlo (MCMC) simulation for 10 million generations with <em>Hanyangaspis guodingshanensis</em> set as an outgroup** and jawed vertebrates constrained as monophyletic. Burn-in fraction was set to 25%, the sampling frequency of the chain to 1000 generations and the number of simultaneous MCMC chains to four. Ancestral states for the parsimony and Bayesian trees were reconstructed with the MBASR toolkit in R version 4.4.2 running in RStudio (version 2024.09.0) integrated development environment. A random sample of 50 Run 1 and 50 run 2 tree outputs with posterior estimates (last 75% trees, burnin fraction 25%) were converted to nwk format in FigTree v.1.4.4. Similarly, 100 random most parsimonious trees containing branch lengths were exported to a nwk in FigTree version 1.4.4. Ancestral states estimates for the subsets of parsimony and Bayesian trees were generated by running in loop the MBASR toolkit with a custom script (see electronic supplementary material). Finally, we calculated the geometric mean of the ancestral state values in each subset of trees.
description: # Data from: The shoulder girdle of early chondrichthyans grew by skeletal
 remodelling Dataset DOI:
 [10.5061/dryad.5mkkwh7j8](10.5061/dryad.5mkkwh7j8) ## Description of the
 data and file structure **Description of the data files:** File:
 3D_model_of_IVPP_V27433.11.stl Description: 3D surface geometry file of a
 pinnal plate fragment fused to an incomplete pectoral fin spine (IVPP
 V27433.11) belonging to *Fanjingshania renovata*. File generated from a
 synchrotron tomography dataset acquired at the TOMCAT beamline at the
 Swiss Light Source. File: 3D_model_of_IVPP_V27433.8.stl Description: 3D
 surface geometry file of a pinnal plate fragment (IVPP V27433.8) belonging
 to *Fanjingshania renovata*. File generated from a synchrotron tomography
 dataset acquired at the TOMCAT beamline at the Swiss Light Source. File:
 3D_model_of_IVPP_V27434.2.stl Description: Description: 3D surface
 geometry file of a pinnal plate fragment fused to admedian spines (IVPP
 V27434.2) belonging to *Fanjingshania renovata*. File generated from a
 synchrotron tomography dataset acquired at the TOMCAT beamline at the
 Swiss Light Source. **Folder:** Bayesian_analysis_data.zip Description:
 Input and output files and code for Bayesian phylogenetic analysis
 performed in MrBayes version 3.2.7. File: Bayesian_run1\_ branch\_
 lengths.tre Description: FanjV2matrix.nex.run1.t file converted to a ‘tre’
 format. File: Bayesian_run2\_ branch\_ lengths.tre Description:
 FanjV2matrix.nex.run2.t file converted to a ‘tre’ format. File:
 FanjV2matrix.nex Description: The data matrix for the Bayesian
 phylogenetic analysis. File: Bayesian_analysis_script.rtf Description: The
 script used to set the parameters, run and summarise the results of the
 Bayesian analysis. File: FanjV2matrix.nex.run1.t Sampled phylogenetic
 trees from run 1 of the Bayesian analysis. File: FanjV2matrix.nex.run2.t
 Description: Sampled phylogenetic trees from run 2 of the Bayesian
 analysis. File: FanjV2matrix.nex.run1.p Description: Log file of parameter
 values for the first MCMC run of the Bayesian analysis. File:
 FanjV2matrix.nex.run2.p Description: Log file of parameter values for the
 second MCMC run of the Bayesian analysis. File: FanjV2matrix.nex.ckp
 Description: Checkpoint file for the Bayesian analysis. File:
 FanjV2matrix.nex.ckp~ Description: Checkpoint file for the Bayesian
 analysis. File: FanjV2matrix.nex.mcmc Description: command script
 generated by MrBayes that stores the settings for the Markov chain Monte
 Carlo (MCMC) runs. File: FanjV2matrix.nex.parts Description: A file
 listing clade statistics for post burn-in trees. File:
 FanjV2matrix.nex.con.tre Description: Majority-rule consensus tree
 generated from trees sampled in both MCMC runs. File:
 FanjV2matrix.nex.trprobs Description: File containing all post burn-in
 tree topologies. File: FanjV2matrix.nex.tstat Description: File containing
 statistics for trees sampled by the MCMC runs. File:
 FanjV2matrix.nex.vstat Description: File containing statistics about the
 variation between the two MCMC runs. **Folder:**
 Parsimony_analysis_data.zip Description: Input and output files and code
 for parsimony phylogenetic analysis performed in TNT version 1.6. File:
 Fanjingshania_matrix (tnt).nex Description: Data matrix used in the
 parsimony phylogenetic analysis. File: Parsimony (TNT)_50majority rule
 tree.nex Description: 50 percent majority-rule tree calculated from the
 most parsimonious trees. File: Parsimony analysis (TNT) most parsimonious
 trees.nex Description: File containing the most parsimonious trees. File:
 MBASR script for single tree and single character.R Description: Script
 for running the MBASR toolkit in R used to reconstruct ancestral character
 states. File: Parsimony (TNT) analysis output log.out Description: TNT log
 file for the parsimonious analysis. **Folder:**
 Synchrotron_tomography_dataset_for_IVPP_V27434.2_Part1_.zip Description:
 First part of a X-ray synchrotron tomography dataset for *Fanjingshania
 renovata* specimen IVPP V27434.2. Data acquired at the TOMCAT beamline at
 the Swiss Light Source. Files: 1548 tomography slices in tif format.
 **Folder:** Synchrotron_tomography_dataset_for_IVPP_V27434.2_Part2_.zip
 Description: Second part of a X-ray synchrotron tomography dataset for
 *Fanjingshania renovata* specimen IVPP V27434.2. Data acquired at the
 TOMCAT beamline at the Swiss Light Source. Files: 1562 tomography slices
 in tif format. ## Access information Other publicly accessible locations
 of the data: * n/a Data was derived from the following sources: * n/a