DOI: 10.5061/dryad.v7m05
title: Data from: Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn

description: 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.
description: 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.txt