DOI: 10.5061/dryad.12jm63z5n
title: Exceptionally preserved shark fossils from Mexico elucidate the long-standing enigma of the Cretaceous elasmobranch Ptychodus

description: The fossil fish Ptychodus Agassiz, 1834, characterized by a highly
 distinctive grinding dentition and an estimated gigantic body size, has
 remained one of the most enigmatic extinct elasmobranchs (i.e. sharks,
 skates, and rays) for nearly two centuries. This widespread Cretaceous
 taxon is common in Albian to Campanian deposits from almost all
 continents. However, specimens mostly consist of isolated teeth or more or
 less complete dentitions, whereas cranial and post-cranial skeletal
 elements are very rare. Here we describe newly discovered material from
 the early Late Cretaceous of Mexico, including complete articulated
 specimens with preserved body outline, which reveals crucial information
 on the anatomy and systematic position of Ptychodus. Our phylogenetic and
 ecomorphological analyses indicate that ptychodontids were high-speed
 (tachypelagic) durophagous lamniforms (mackerel sharks), occupying a
 specialized predatory niche previously unreported among both extant and
 extinct elasmobranchs. Our results support the view that lamniforms were
 ecomorphologically highly diverse and represented the dominant group of
 sharks in Cretaceous marine ecosystems. Ptychodus may have fed
 predominantly on nektonic hard-shelled prey items such as ammonites and
 sea turtles rather than on benthic invertebrates, and its extinction
 during the Campanian, well before the end-Cretaceous crisis, might have
 been related to competition with emerging blunt-toothed globidensine and
 prognathodontine mosasaurs.
description: We explored the phylogenetic relationships of the genus
 <em>Ptychodus </em>Agassiz, 1834 within the
 elasmobranchs<em> </em>using a modified version of Jambura
 <em>et al.</em>’s (2023) data matrix. In order to provide a
 broader context of these relations, several Palaeozoic, Mesozoic,
 Cenozoic, and Recent chondrichthyan taxa were additionally included as
 outgroups, with <em>Pucapampella </em>and
 <em>Doliodus</em> serving as the root. To accommodate the
 inclusion of these groups, several modifications and additional characters
 from previous works were added to the present data matrix (e.g., Allis
 1923; Holmgren 1940, 1941; Patterson 1965; Schaeffer 1981; Maisey 1980,
 1984, 1985, 2001; Compagno 1990a; Nishida 1990; Shirai 1996;  Goto 2001).
 The resulting data matrix was assembled in Mesquite 3.81 (Madisson and
 Madisson 2023) and includes 221 characters. Analysis was carried out in
 TNT v.1.6 (Goloboff and Morales 2023), under Goloboff <em>et
 al.</em>’s (2021) protocol, considering the inclusion of
 inapplicable characters. A traditional parsimony search with step matrices
 (smatrix &) was conducted with the command (mult) using TBR (tree
 bisection and reconnection) as the algorithm for branch permutations for
 10000 iterations holding ten trees for each iteration. This protocol was
 repeated ten times using the command loop with different random seeds to
 evaluate if the tree space was adequately explored by the
 parameters.
description: # Exceptionally preserved shark fossils from Mexico elucidate the
 long-standing enigma of the Cretaceous elasmobranch *Ptychodus*
 (Phylogenetic analyses)
 [https://doi.org/10.5061/dryad.12jm63z5n](https://doi.org/10.5061/dryad.12jm63z5n) This dataset contains all the information needed to perform the phylogenetic analysis carried out in our paper "Exceptionally preserved shark fossils from Mexico elucidate the long-standing enigma of the Cretaceous elasmobranch *Ptychodus*." In this study, our objective was to determine the phylogenetic relations of the Cretaceous extinct shark *Ptychodus* based on the newly described holomorphic specimens described in our paper. A Parsimony analysis was carried out to determine these relations, which involved a traditional search under the TBR algorithm for branch swapping and the use of step matrices. ## Description of the data and file structure This dataset contains an extensive sampling of morphological characters that includes crown elasmobranchs but presents a comprehensive sample of other chondrichthyan groups. In this repository, you will find 10 files. Here, we shortly explain the relation between these files and what they contain: * The character matrix **Ptychodus_matrix.nex** was assembled using Mesquite 3.81 (Madisson and Madisson 2023) containing 221 characters and 91 taxa, which can be opened using Mesquite or any text editor (e.g., Sublime text or Note pad). * **Ptychodus_matrix.tnt:** is the character matrix in a readable format for the phylogenetic software TNT v.1.6 (Goloboff and Morales, 2023). Software in which the analyses were carried out using the command-driven version. * **Ptychodus_Pars_script.tnt:** contains the series of commands used in our phylogenetic analysis; this file can be executed directly in TNT by using the command `procedure` followed by the location in your computer of the file name in this case, **Ptychodus_matrix.tnt**. This file also will produce a: `log` file that can be used to trace the results of the analysis (**Ptychodus.log)**, a `tre` file containing all the trees revered in the analysis (**All_trees_Ptychodus.tre** and **All_trees_Ptychodus.nex**) and a `nex` containing the phylogenetic trees (trees) and the step matrices estimated by the program during the analysis in a nexus format (**Step_mat.nex**), all of which will be located in the same locations as the file **Ptychodus_matrix.tnt**. * **Ptychodus_bremer_script.tnt:** contains the series of commands to carry out a Bremer support analysis for the clades (groups of taxa) found in the phylogenetic trees; this file can be executed directly in TNT by using the command procedure followed by the location in your computer of the file name in this case, **Ptychodus_matrix.tnt**. This file also will produce a: `log` file. * **STATS.RUN:** is a script provided along with TNT and is executed as one of the commands of **Ptychodus_Pars_script.tnt**. This `run` file is used to estimate the values of the Consistency and Retention Indexes, for phylogenies. We provided a copy of this script on this repository so the user would have everything in the same location, facilitating the process of analysis. * **Ptychodus.log**: `log` file of the phylogenetic analysis carried out in our paper. * **Ptychodus_bremer.log**: `log` file of the Bremer support analysis carried out in our paper. * **All_trees_Ptychodus.tre:** file containing all of the trees recovered in our analysis in a Newick format. * **All_trees_Ptychodus.nex:** file containing all of the trees recovered in our analysis in a Nexus format.