Article: Fast production of large, time-calibrated, informal supertrees with tree.merger
Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, and Pasquale Raia
Abstract Assembling informal supertrees inclusive of extinct species is a useful but particularly long and complex procedure. We introduce a new, interactive, piece of software that allows the fast production of large, time-calibrated informal supertrees, single-handedly mixing multiple phylogenetic information from different sources. The software, embodied in the tree.merger function available as part of the RRphylo R package, allows the merging of different trees into one or adding individual species to a target phylogeny. Time calibration is implemented automatically within the function according to user-specified, optional age values that can be provided for nodes and/or tips. We applied tree.merger to two different case-studies. The first, hypothetical, case study pertains to the tree of odontocete cetaceans. The second case study regards the expansion of the new, higher-level phylogeny of dinosaurs proposing the sister clade relationship between Ornithoscelida and Sauropodomorpha from c. 50 to a 357 species tree. The two case studies took less than five seconds each to complete, on a regular personal computer.