The circumscription of the circumboreal tribe Scirpeae has been contentious since the earliest infrafamilial classifications of the Cyperaceae (>100 genera, ~5,500 species). Molecular phylogenetic studies place Scirpeae in a strongly supported clade with the enigmatic genus Khaosokia and tribes Cariceae, Dulichieae, and Sumatroscirpeae, a lineage comprising more than 40% of all Cyperaceae species. This lineage was previously known as the Cariceae-Dulicheae-Scirpeae (“CDS”) clade. Here we informally characterise it as the “Scirpo-Caricoid Clade”. Previous phylogenetic and phylogenomic studies of the Scirpo-Caricoid Clade have shown Scirpeae to be paraphyletic, forming four distinct lineages that are successive sisters to a Cariceae + Sumatroscirpeae clade, thus confirming decade old suspicions that the modern circumscription of Scirpeae is unnatural. Using a total-evidence phylogenetic analysis incorporating three plastid markers (matK, ndhF, rps16), two nuclear ribosomal markers (ETS-1f, ITS), and 64 morphological characters, this study confirms the paraphyly of Scirpeae, the isolated phylogenetic position of Khaosokia, and identifies morphological synapomorphies for seven monophyletic lineages that are here recognized as tribes. Our new classification places for the first time all genera of the Scirpo-Caricoid Clade into natural tribes that are identifiable using morphological and embryological characters. Three new tribes are proposed: Calliscirpeae trib. nov., Khaosokieae trib. nov. and Trichophoreae trib. nov. Diagnoses for all tribes of the Scirpo-Caricoid Clade, an identification key to all currently recognized Cyperaceae tribes, and identification keys for all genera of the Scirpo-Caricoid Clade are provided.
Suppl. Fig. 1. matK tree
Maximum likelihood topology based on matK sequence data alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig01-matk.pdf
Suppl. Fig. 2. matK indels tree
Maximum likelihood topology based on matK indels alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig02-matk_indels.pdf
Suppl. Fig. 3. ndhF tree
Maximum likelihood topology based on ndhF sequence data alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig03-ndhf.pdf
Suppl. Fig. 4. ndhF indels tree
Maximum likelihood topology based on ndhF indels alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig04-ndhf_indels.pdf
Suppl. Fig. 5. rps16 tree
Maximum likelihood topology based on rps16 sequence data alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig05-rps16.pdf
Suppl. Fig. 6. rps16 indels tree
Maximum likelihood topology based on rps16 indels alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig06-rps16_indels.pdf
Suppl. Fig. 7. ETS tree
Maximum likelihood topology based on ETS-1f sequence data alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig07-ets.pdf
Suppl. Fig. 8. ETS indels tree
Maximum likelihood topology based on ETS-1f indels alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig08-ets_indels.pdf
Suppl. Fig. 9. ITS tree
Maximum likelihood topology based on ITS sequence data alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig09-its.pdf
Suppl. Fig. 10. ITS indels tree
Maximum likelihood topology based ITS indels alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig10-its_indels.pdf
Suppl. Fig. 11. morphology tree
Maximum likelihood topology based on morphology alone, with parsimony/likelihood bootstrap percentages for every branch with >50% parsimony or ML bootstrap. Branches with >85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates <50% bootstrap.
SuppFig11-morph.pdf
Suppl. data: alignments
NEXUS concatenated data matrix including DNA sequence, indel and morphological partitions, and relaxed PHYLIP alignments of each individual partition.
Leveille-Bourret_Starr_newTribes_datasets.zip