Data from: Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn

Background and Aims: Subfamily Arundinoideae represents one of the last unsolved taxonomic mysteries in the grass family (Poaceae) due to the narrow and remote distributions of many of its 19 morphologically and ecologically heterogeneous genera. Resolving the phylogenetic relationships of these genera could have substantial implications for understanding character evolution in the grasses, for example the twisted geniculate awn – a hygroscopic awn that has been shown to be important in seed germination for some grass species. In this study, the phylogenetic positions of most arundinoid genera were determined using DNA from herbarium specimens, and their placement affects interpretation of this ecologically important trait. Methods: A phylogenetic analysis was conducted on a matrix of full-plastome sequences from 123 species in 107 genera representing all grass subfamilies, with 15 of the 19 genera in subfamily Arundinoideae. Parsimony and maximum likelihood mapping approaches were used to estimate ancestral states for presence of a geniculate lemma awn with a twisted column across Poaceae. Lastly, anatomical characters were examined for former arundinoid taxa using light microscopy and scanning electron microscopy. Key Results: Four genera traditionally included in Arundinoideae fell outside the subfamily in the plastome phylogeny, with the remaining 11 genera forming Arundinoideae sensu stricto. The twisted geniculate awn has originated independently at least five times in the PACMAD grasses, in the subfamilies Panicoideae, Danthonioideae/Chloridoideae and Arundinoideae. Morphological and anatomical characters support the new positions of the misplaced arundinoid genera in the phylogeny, but also highlight convergent and parallel evolution in the grasses. Conclusions: In placing the majority of arundinoid genera in a phylogenetic framework, our study answers one of the last remaining big questions in grass taxonomy while highlighting examples of convergent evolution in an ecologically important trait, the hygroscopic, twisted geniculate awn.Unedited plastome alignment from MAFFT131 plastomes aligned using MAFFT by major region (LSC, SSC, IR) and then concatenated. No further modifications to alignment made.plastomes_aligned2.fsaAll Gaps Plastome Alignment131 plastomes aligned using MAFFT by major region and then trimmed using the 'All Gaps' option in Gblocks.allgaps_alignment.fsaHalf Gaps Plastome Alignment131 plastomes aligned using MAFFT by major regions and then trimmed using the 'Half Gaps' option in Gblocks.halfgaps_alignment.fsaNo Gaps Plastome Alignment131 plastomes aligned using MAFFT by major regions and then trimmed using the 'No Gaps' option in Gblocks.nogaps_alignment.fsaUnedited ML PhylogenyRAxML phylogeny of plastome alignment not trimmed with Gblocks.RAxML_bipartitions.plastomes_aligned2.fsa.raxml.outAll Gaps ML PhylogenyRAxML phylogeny of plastome alignment trimmed with the 'All Gaps' option in GblocksRAxML_bipartitions.allgaps_alignment.fsa.raxml.outHalf Gaps ML PhylogenyRAxML phylogeny of plastome alignment trimmed with 'Half Gaps' option in GblocksRAxML_bipartitions.halfgaps_alignment.fsa.raxml.outNo Gaps ML PhylogenyRAxML phylogeny of plastome alignment trimmed with 'No Gaps' option in GblocksRAxML_bipartitions.nogaps_alignment.fsa.raxml.outBEAST Input FileInput XML file for each of 5 BEAST runs 100 million generations each.BEAST_infile.xmlBayesian All Gaps PhylogenyMrBayes phylogeny of plastome alignment trimmed with the 'All Gaps' option in GblocksMrBayesTree.treBEAST Run LogsCombined logs from 5 runs of 100 million generations each in BEAST.allgaps_mltree_combined.log.txtBEAST TreesTrees from 5 combined runs of 100 million generations each in BEASTallgaps_mltree_combined.trees.txtFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-145774