Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Most of Australia's sclerophyllous Rutaceae belong to a clade informally known as the 'Eriostemon group' (including 16 genera, similar to 209 species). We investigated generic relationships in this group using analyses of complete plastome sequence data for 60 species and analyses of a supermatrix including sequences of four plastome spacer regions for 22 additional species. Maximum likelihood, Bayesian inference, and shortcut coalescent phylogenetic analyses produced congruent phylogenies that were highly supported, except for a series of short unsupported branches in the backbone of the Eriostemon group. We found high support for four major clades branching from this polytomy and discuss evolutionary inferences of generic relationships in each lineage. In an effort to resolve the polytomy, we analysed gene tree topologies in tree space, phylogenetic informativeness with likelihood mapping, and conducted topology tests to assess support for all possible topological resolutions of the polytomy. These approaches did not clarify the polytomy, which may be caused by insufficient data, features of plastome evolution, or rapid radiation. Results from analyses of the combined supermatrix dataset suggest that Philotheca section Philotheca is paraphyletic with regards to Drummondita and Geleznowia. In all phylogenies, Philotheca sections Corynonema and Cyanochlamys were not placed with other members of Philotheca.

Automated summary

This study investigated the relationships within the 'Eriostemon group' of sclerophyllous Rutaceae in Australia. The researchers used complete plastome sequence data for 60 species and a supermatrix including sequences of four plastome spacer regions for 22 additional species. The results revealed four major clades branching from a polytomy, with discussions on the evolutionary inferences of each lineage. However, the polytomy could not be resolved due to insufficient data or rapid radiation.