DOI: 10.5061/dryad.s7h44j1g8
title: Data from: The Paleozoic assembly of the holocephalan body plan far preceded post-Cretaceous radiations into the ocean depths

description: Among cartilaginous fishes, Holocephali represents the
 species-depauperate, morphologically conservative sister to sharks, rays,
 and skates and the last survivor of a once far greater Paleozoic and
 Mesozoic diversity. Currently, holocephalan diversity is concentrated in
 deep-sea species, suggesting that this lineage might contain relictual
 diversity that persists in the ocean depths. Yet, the relationships of
 living holocephalans to their extinct relatives and the timescale of
 diversification of living species remain unclear. Here, we reconstruct the
 evolutionary history of holocephalans using comprehensive morphological
 and DNA sequence datasets. Our results suggest that crown holocephalans
 entered and diversified in deep (&gt;1000 m) ocean waters after the
 Cretaceous-Paleogene mass extinction, contrasting with the hypothesis that
 this ecosystem has acted as a refugium of ancient cartilaginous fishes.
 These invasions were decoupled from the evolution of key features of the
 holocephalan body plan, including crushing dentition, a single frontal
 clasper, and holostylic jaw suspension, during the Paleozoic Era. Yet,
 they considerably postdated the appearance of extant holocephalan families
 by 150 million years ago during a major period of biotic turnover in
 oceans termed the Mesozoic Marine Revolution. These results clarify the
 origins of living holocephalans as the recent diversification of a single
 surviving clade among numerous Paleozoic lineages.
description: <em>Morphological Dataset Construction. </em>In order
 to test the phylogenetic position of living holocephalans and Mesozoic
 species among the larger Paleozoic diversity of the total clade, we
 constructed a new taxon-character matrix by expanding the dataset of Frey
 et al. [8] using characters from Didier [17] and Patterson [46]. We also
 edited character states and added 14 living and extinct holocephalan taxa
 to thoroughly sample holocephalan diversity within and proximal to the
 crown clade. Newly added data include genus-level scorings for all five
 living holocephalan genera, as well as for species in the genera
 †<em>Acanthorhina</em>, †<em>Chimaeropsis</em>,
 †<em>Elasmodectes</em>, †<em>Ischyodus</em>,
 †<em>Metopacanthus</em>, †<em>Myriacanthus</em>,
 and †<em>Squaloraja</em>. Due to the lack of available
 information on their morphology and our focus on incorporating
 post-Palaeozoic taxa into the analysis, we did not include any
 representatives of the Paleozoic pan-holocephalan clades
 †<em>Eugenodontia </em>and
 †<em>Petalodontiformes</em>, which mostly include tooth taxa
 and for which only a handful of holomorphic specimens [10,11,47] of
 limited phylogenetic informativeness are known. Future discoveries,
 including the description of unpublished specimens [4], will be needed to
 resolve the relationships of these Carboniferous and Permian
 pan-holocephalans; we expect that the phylogenetic matrix employed in this
 study will contribute to this pursuit. The final matrix included 36
 operational taxonomic units coded for 236 characters. Details of sources
 for character scorings, character additions, removals, state
 modifications, and taxon inclusion are included in the Supplementary
 Information. <em>DNA Sequence Dataset
 Assembly. </em>In order to sample the species diversity of living
 holocephalans most fully, we targeted sequences for the
 <em>cytb</em>, <em>COXI</em>,
 <em>ND2</em>, and <em>16s</em> mitochondrial loci
 on the NCBI repository Genbank. Using this approach, we were able to
 sample 100% of all living holocephalan genera and species complexes,
 including all three species in <em>Callorhinchus</em>, seven
 of the nine recognized species in <em>Rhinochimaeridae</em>,
 and 35 of 47 described species of <em>Chimaeridae </em>[40],
 plus two specimens of <em>Chimaera </em>sp. with mitogenomes
 that appear to diverge considerably from other species [48,49]. We
 concatenated these data into a single set of aligned sequences for
 subsequent phylogenetic analyses.
description: # Data from: The Paleozoic assembly of the holocephalan body plan far
 preceded post-Cretaceous radiations into the ocean depths
 [https://doi.org/10.5061/dryad.s7h44j1g8](https://doi.org/10.5061/dryad.s7h44j1g8) ## Description of the data and file structure Sequence data were taken from Genbank, and morphological data were collected from CT scans and the literature. ### Files and variables #### File: runs.zip Output analyses for the three independent tip dating run in BEAST2, including log and tree files. #### File: input.zip Input for the three independent tip dating runs in BEAST2, including XML files and input sequence fasta. #### File: holocephali.R R code. #### File: output\_trees.zip Output posterior tree set (combined from runs) and maximum clade credibility tree from analyses of the molecular sequence dataset under a tip-dating Bayesian protocol in BEAST2. #### File: PAUP\_runs.zip Output trees from parsimony analyses of the morphological dataset in PAUP. #### File: Mr\_*Bayes\_*runs.zip Output trees from Bayesian analyses of the morphological dataset in MrBayes. #### File: BEAST\_Morph.zip Input and output from Bayesian tip-dating analyses of the morphological dataset in BEAST2, including input XML files and output log and tree files. #### File: Maximum\_Likelihood.zip Output for the analyses of the molecular sequence dataset in IQ-TREE. ## Code/software All code is attached in the R file. ## Access information Other publicly accessible locations of the data: * Genbank Data was derived from the following sources: * Genbank