Phylogenetic systematics of Juncaceae, alignments associated with phylogenetic trees

Juncaceae has needed a taxonomic revision for some time. Specifically, the genus Juncus s.l. is known to be paraphyletic, as five small southern hemisphere genera have been shown repeatedly to be nested within it. In 2022, a new classification was proposed, based on phylogenies built from one nuclear and three chloroplast regions sequenced across much of Juncaceae, meant to resolve the paraphyletic nature of Juncus s.l. It created six new genera and was criticized on the basis that the genera proposed are not necessarily monophyletic, given the limited nature of the phylogenetic analyses available and the fact that the generic circumscriptions draw heavily on the morphology-based classifications found in the latest monograph of Juncaceae from 2002. We assembled a dataset consisting of hundreds of chloroplast and nuclear loci, using the Angiosperms 353 target capture probe set, to assess the monophyly of the newly proposed genera of Juncaceae. We found that the proposed genera mostly represent monophyletic groups, but that the proposed genus Juncinella is nested within the proposed genus Boreojuncus. We additionally found that Juncinella capitata was placed as sister to either Luzula or Oreojuncus and should be recognized as a monotypic genus. Finally, Australojuncus cyperoides and Verojuncus chlorocephalus were recovered outside of their morphologically assigned genera and require further investigation to be placed confidently. Here, we propose taxonomic revisions to rectify the issues stated above, but also find that further research is necessary, particularly to correctly place the South African annual taxa in Juncus s.l.