Exceptionally preserved shark fossils from Mexico elucidate the long-standing enigma of the Cretaceous elasmobranch Ptychodus
Data files
Mar 20, 2024 version files 12.36 MB
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All_trees_Ptychodus.nex
3 MB
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All_trees_Ptychodus.tre
7.63 MB
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Ptychodus_bremer_script.tnt
930 B
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Ptychodus_bremer.log
27.60 KB
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Ptychodus_matrix.nex
60 KB
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Ptychodus_matrix.tnt
27.65 KB
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Ptychodus_Pars_script.tnt
1.38 KB
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Ptychodus.log
1.58 MB
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README.md
3.61 KB
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STATS.RUN
529 B
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Step_mat.nex
28.75 KB
Abstract
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.
README: 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
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
procedurefollowed by the location in your computer of the file name in this case, Ptychodus_matrix.tnt. This file also will produce a:logfile that can be used to trace the results of the analysis (Ptychodus.log), atrefile containing all the trees revered in the analysis (All_trees_Ptychodus.tre and All_trees_Ptychodus.nex) and anexcontaining 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:
logfile. - STATS.RUN: is a script provided along with TNT and is executed as one of the commands of Ptychodus_Pars_script.tnt. This
runfile 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:
logfile of the phylogenetic analysis carried out in our paper. - Ptychodus_bremer.log:
logfile 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.
Methods
We explored the phylogenetic relationships of the genus Ptychodus Agassiz, 1834 within the elasmobranchs using a modified version of Jambura et al.’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 Pucapampella and Doliodus 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 et al.’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.