Fast production of large, time-calibrated, informal supertrees with tree.merger

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.

Automated summary

This article introduces a new interactive software for the fast production of large, time-calibrated informal supertrees, which allows the merging of different phylogenetic information from various sources. The software automatically implements time calibration and has been applied to two case studies with efficient results.