Computational protocol: A Devonian predatory fish provides insights into the early evolution of modern sarcopterygians

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Protocol publication

[…] To explore the phylogenetic position of Qingmenodus, we conducted phylogenetic analyses using a modified data set with 242 characters and 37 taxa (see Supplementary Materials and Methods). This data set is based on the work of Cloutier and Ahlberg (), Zhu and Yu (), Friedman (), Lu and Zhu (), Zhu et al. (), Forey (), and Zhu and Schultze (). Thirteen new cranial characters (11 of them based on CT data) were added in the character data (characters 65, 66, and 232 to 242 based on HRCT). The actinopterygians (Dialipina, Howqualepis, Cheirolepis, Mimipiscis, and Moythomasia) plus Ligulalepis were designated as the outgroup.Character data entry and formatting were performed in Mesquite (version 3.04) (). The data matrix was subjected to parsimony analysis in PAUP* (version 4.0b10) () using the heuristic algorithm. All characters were treated as unordered and weighted equally. The synapomorphies listed (fig. S12) were obtained under DELTRAN (delayed transformation) optimization. MacClade 4.0 () was used to trace the character transformation in the selected cladogram. Bremer decay indices were obtained using command files composed by TreeRot () in conjunction with the heuristic search algorithm in PAUP*.The strict consensus tree of 845 shortest trees (fig. S11) places the onychodonts, excluding Bukkanodus, as the sister group of coelacanths, within the crown sarcopterygians. Bukkanodus is placed as the sister clade of onychodonts plus coelacanths. The 50% majority consensus tree resolves Strunius as the most basal onychodont. The crownward Qingmenodus, Grossius, and Onychodus form a trichotomy (fig. S12). The interrelationship of coelacanths is not fully resolved in the current analysis. [...] The three-dimensional reconstructions were created with the software Mimics (version 16.1). The images of the reconstructions were exported from Mimics and finalized in Adobe Photoshop and Adobe Illustrator, and the restorations were carried out in Adobe Photoshop and Adobe Illustrator. In addition to neurocranial structures that were modeled as preserved, the final three-dimensional model included one area of reconstruction produced by application of a prosthetic. This was the floor of the anterior part of the brain cavity of the otoccipital portion, which was not bounded by skeleton because it lay within the basicranial fenestra. The level of this floor was reconstructed from preserved correlates, such as the level of the brain cavity floor of the ethmosphenoid portion. The retrodeformation of the posterior part of the ethmosphenoid was based on the perimeter of the notochordal facet as a parameter, working on the assumption that the facet would have been approximately circular in life. […]

Pipeline specifications

Software tools Mesquite, PAUP*, MacClade, Adobe Illustrator
Applications Miscellaneous, Phylogenetics
Organisms Latimeria chalumnae