DOI: 10.5061/dryad.db4dt3t
title: Data from: Molecular and morphological data reveal three new tribes within the Scirpo-Caricoid Clade (Cyperoideae, Cyperaceae)

description: The circumscription of the circumboreal tribe Scirpeae has been
 contentious since the earliest infrafamilial classifications of the
 Cyperaceae (&gt;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.
description: Suppl. Fig. 1. matK
 treeMaximum likelihood
 topology based on matK sequence data alone, with parsimony/likelihood
 bootstrap percentages for every branch with &gt;50% parsimony or ML
 bootstrap. Branches with &gt;85% parsimony bootstrap support are
 emphasized with bold lines. A dash (-) indicates &lt;50%
 bootstrap.SuppFig01-matk.pdfSuppl. Fig. 2. matK indels treeMaximum likelihood topology based on matK indels alone, with parsimony/likelihood bootstrap percentages for every branch with &gt;50% parsimony or ML bootstrap. Branches with &gt;85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates &lt;50% bootstrap.SuppFig02-matk_indels.pdfSuppl. Fig. 3. ndhF treeMaximum likelihood topology based on ndhF sequence data alone, with parsimony/likelihood bootstrap percentages for every branch with &gt;50% parsimony or ML bootstrap. Branches with &gt;85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates &lt;50% bootstrap.SuppFig03-ndhf.pdfSuppl. Fig. 4. ndhF indels treeMaximum likelihood topology based on ndhF indels alone, with parsimony/likelihood bootstrap percentages for every branch with &gt;50% parsimony or ML bootstrap. Branches with &gt;85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates &lt;50% bootstrap.SuppFig04-ndhf_indels.pdfSuppl. Fig. 5. rps16 treeMaximum likelihood topology based on rps16 sequence data alone, with parsimony/likelihood bootstrap percentages for every branch with &gt;50% parsimony or ML bootstrap. Branches with &gt;85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates &lt;50% bootstrap.SuppFig05-rps16.pdfSuppl. Fig. 6. rps16 indels treeMaximum likelihood topology based on rps16 indels alone, with parsimony/likelihood bootstrap percentages for every branch with &gt;50% parsimony or ML bootstrap. Branches with &gt;85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates &lt;50% bootstrap.SuppFig06-rps16_indels.pdfSuppl. Fig. 7. ETS treeMaximum likelihood topology based on ETS-1f sequence data alone, with parsimony/likelihood bootstrap percentages for every branch with &gt;50% parsimony or ML bootstrap. Branches with &gt;85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates &lt;50% bootstrap.SuppFig07-ets.pdfSuppl. Fig. 8. ETS indels treeMaximum likelihood topology based on ETS-1f indels alone, with parsimony/likelihood bootstrap percentages for every branch with &gt;50% parsimony or ML bootstrap. Branches with &gt;85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates &lt;50% bootstrap.SuppFig08-ets_indels.pdfSuppl. Fig. 9. ITS treeMaximum likelihood topology based on ITS sequence data alone, with parsimony/likelihood bootstrap percentages for every branch with &gt;50% parsimony or ML bootstrap. Branches with &gt;85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates &lt;50% bootstrap.SuppFig09-its.pdfSuppl. Fig. 10. ITS indels treeMaximum likelihood topology based ITS indels alone, with parsimony/likelihood bootstrap percentages for every branch with &gt;50% parsimony or ML bootstrap. Branches with &gt;85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates &lt;50% bootstrap.SuppFig10-its_indels.pdfSuppl. Fig. 11. morphology treeMaximum likelihood topology based on morphology alone, with parsimony/likelihood bootstrap percentages for every branch with &gt;50% parsimony or ML bootstrap. Branches with &gt;85% parsimony bootstrap support are emphasized with bold lines. A dash (-) indicates &lt;50% bootstrap.SuppFig11-morph.pdfSuppl. data: alignmentsNEXUS concatenated data matrix including DNA sequence, indel and morphological partitions, and relaxed PHYLIP alignments of each individual partition.Leveille-Bourret_Starr_newTribes_datasets.zip