Case studies: species delimitation
To test the performance of species delimitation algorithms applied on different USCO datasets, we delineated species with tr2 (Fujisawa et al., 2016) and SODA v. 1.0.2 (Rabiee et al., 2020) based on the results of the three different extraction approaches in all four case studies, using the programs’ default parameters and not providing a guide tree. Tr2 conducts species delimitation based on the topological variation between rooted gene trees using the distribution of triplets (i.e., topologies with three individuals). As input, we used the gene trees generated by IQ-TREE, with the gene trees being re-rooted with nw_reroot (part of Newick Utilities 1.6.0; Junier & Zdobnov, 2010) on the outgroup of the respective study case. We included only trees that contained all specimens, as gene trees lacking specimens cannot be handled by the program. SODA uses the distribution of topologies of quartets of individuals in unrooted gene trees to infer species boundaries (Rabiee et al., 2020). We used all gene trees as input for SODA.