Towards a time-tree solution for Branchiopoda diversification: a jackknife assessment of fossil age priors

An understanding of Branchiopoda’s evolutionary history is crucial for a comprehensive knowledge of the Pancrustacea tree of life, given their close evolutionary relationship with Hexapoda. Despite significant advances in molecular and morphological phylogenetics that have resolved much of the branchiopod backbone topology, a reliable temporal framework remains elusive. Key challenges include a sparse fossil record, long-term morphological stasis, and past topological inconsistencies. Leveraging a Bayesian Inference approach and the most extensive phylogenomic dataset for branchiopod to date, encompassing 46 species and over 130 genes, we inferred a time-calibrated phylogenetic tree. Furthermore, to strengthen the confidence in our divergence times estimation, we assessed the impact of age priors, topological uncertainties, and gene trees which are discordant from the species trees. Our results are largely consistent with the fossil record and with previous studies, indicating that Branchiopoda originated between 400 and 500 million years ago, and the orders of large branchiopods diversified during the Mesozoic. Concerning Cladocera, results remain problematic, with a sharper uncertainty in the diversification time with respect to the fossil record. Though, the jackknife resampling of fossils and the other sensitivity analyses proved our calibration method to be robust, suggesting that the difficulties in obtaining a paleontological-consistent time tree may be hindered by the variability in branchiopod substitution rates and topological instability within certain clades.