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A peer-reviewed article of this Preprint also exists.
With respect to the cladogram, the allodaposuchid Allodaposuchus subjuniperus has been re-assigned to the new genus Agaresuchus by Narváez et al. (2016), while Theriosuchus symplesiodon has been re-assigned to Sabresuchus by Tennant et al. (2016), and T. guimarotae has been re-assigned to Knoetschkesuchus by Schwarz et al. (2017). Pristichampsus is no longer valid, and Boverisuchus used for eusuchians previously assigned to Pristichampsus (Brochu 2013), and Paralligator is distinct from Shamosuchus, so Pristichampsus vorax, Shamosuchus major, and S. gradilifrons should be changed to in the cladogram to Boverisuchus vorax, Paralligator major, and P. gradilifrons respectively. You might also want to test the relationship of Wahasuchus (Saber et al. 2018) to other derived neosuchians because that genus is the youngest African mesoeucrocodylian from outside Madagascar.
Brochu, C. A. (2013). "Phylogenetic relationships of Palaeogene ziphodont eusuchians and the status of Pristichampsus Gervais, 1853". Earth and Environmental Science Transactions of the Royal Society of Edinburgh: 1. doi:10.1017/S1755691013000200.
I. Narváez; C.A. Brochu; F. Escaso; A. Pérez-García; F. Ortega (2016). "New Spanish Late Cretaceous eusuchian reveals the synchronic and sympatric presence of two allodaposuchids". Cretaceous Research. 65: 112–125. doi:10.1016/j.cretres.2016.04.018.
Daniela Schwarz; Maik Raddatz; Oliver Wings (2017). "Knoetschkesuchus langenbergensis gen. nov. sp. nov., a new atoposaurid crocodyliform from the Upper Jurassic Langenberg Quarry (Lower Saxony, northwestern Germany), and its relationships to Theriosuchus". PLoS ONE. 12 (2): e0160617. doi:10.1371/journal.pone.0160617.
Sara Saber; Joseph J.W. Sertich; Hesham M. Sallam; Khaled A. Ouda; Patrick M. O'Connor; Erik R. Seiffert (2018). "An enigmatic crocodyliform from the Upper Cretaceous Quseir Formation, central Egypt". Cretaceous Research. 90: 174–184. doi:10.1016/j.cretres.2018.04.004.
Jonathan P. Tennant; Philip D. Mannion; Paul Upchurch (2016). "Evolutionary relationships and systematics of Atoposauridae (Crocodylomorpha: Neosuchia): implications for the rise of Eusuchia". Zoological Journal of the Linnean Society. 177 (4): 854–936. doi:10.1111/zoj.12400.
Just a quick one. We provide a lot of discussion about choanal evolution in atoposaurids and related taxa here (https://onlinelibrary.wiley.com/doi/abs/10.1111/zoj.12400), especially in the context of the rise of eusuchians. I see this paper has been noted above too, but there is a specific section on the choana that might come in handy here! This is a great looking study, nice work.