Phylogenomic analysis confirms polyphyly of Leptospermum and delineates five major clades that warrant generic recognition

Leptospermum is an ecologically and economically important genus with a long unresolved taxonomic issue concerning polyphyly, as indicated from early molecular analysis on two chloroplast regions. To resolve this, we used genome skimming to obtain high-copy chloroplast and nuclear ribosomal DNA for a comprehensive phylogenomic analysis of 110 accessions comprising of 38 Leptospermum taxa, 6 closely allied genera and 5 outgroup genera. Maximum likelihood and Bayesian analyses resolved congruent clades for the chloroplast (132,143 bp: 80 CDSs, 4 rRNA genes, 29 tRNA genes, 17 introns and 97 IGSs) and nuclear (1219 bp: ITS1, ITS2, ETS, 5.8S) alignments to provide a robust interpretation of evolutionary relationships. Together, these data confirmed extensive polyphyly of Leptospermum that separated the genus into five monophyletic clades spread amongst clades representing six closely allied genera: Agonis, Asteromyrtus, Homalospermum, Kunzea, Neofabricia and Pericalymma. These five Leptospermum clades share some similarities with morphological and genetic groupings identified previously but provide greater resolution to inform a clear pathway to taxonomic revision. The evidence presented here provides support for resolution of the current polyphyly of Leptospermum through the recognition of five genera, while retaining all other genera of Leptospermeae in their current circumscription.