Phylogenetics and character evolution in the grass family (Poaceae): Simultaneous analysis of morphological and Chloroplast DNA restriction site character sets

A phylogenetic analysis of the grass family (Poaceae) was conducted using two character sets, one representing variation in 364 mapped and cladistically informative restriction sites from all regions of the chloroplast genome, the other representing variation in 42 informative “structural characters.” The structural character set includes morphological, anatomical, chromosomal, and biochemical features, plus structural features of the chloroplast genome. The taxon sample comprises 75 exemplar taxa, including 72 representatives of Poaceae and one representative of each of three related families (Flagellariaceae, Restionaceae, and Join-villeaceae);Flagellaria served as the outgroup for the purpose of cladogram rooting. Among the grasses, 24 tribes and all 16 subfamilies of grasses recognized by various modern authors were sampled. Transformations of structural characters are mapped onto the phylogenetic hypotheses generated by the analysis, and interpreted with respect to biogeography and the evolution of wind pollination in the grass family. A major goal of the study was to test the monophyly of several putatively natural groups, including Bambusoideae, Pooideae, Arundinoideae, and the “PACC clade” (the latter comprising subfamilies Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae), as well as to analyze the phylogenetic structure within these groups and others. Several genera of controversial placement (Amphipogon, Anisopogon, Anomochloa, Brachyelytrum, Diarrhena, Eremitis, Ehrharta, Lithachne, Lygeum, Nardus, Olyra, Pharus, andStreptochaeta) also were included, with the goal of determining their phylogenetic affinities. The two character sets were analyzed separately, and a simultaneous analysis of the combined matrices also was conducted. The combined data set also was analyzed using homoplasy-implied weights. Among major results of the combined unweighted analysis were resolution of a sister-group relationship betweenJoinvillea and Poaceae; resolution of a clade comprisingAnomochloa andStreptochaeta as the sister of all other grasses, withPharus the next group to diverge from the lineage that includes all remaining grasses; and resolution of other taxa often assigned to Bambusoideae s.l. (includingEhrharta and Oryzeae, and excluding a few other taxa as noted) as a paraphyletic assemblage, within which is nested a clade that consists ofBrachyelytrum, the PACC clade (includingAmphipogon), and Pooideae (including Brachypodieae, Stipeae,Anisopogon, Diarrhena, Lygeum, andNardus). Within the PACC clade,Aristida is identified as the sister of all other elements of the group; Chloridoideae, Centothecoideae, and Panicoideae are each resolved as monophyletic, the latter two being sister-groups; and the remaining Arundinoid elements constitute a paraphyletic group within which are nested these three subfamilies. Within the Pooideae, four “core tribes” (Bromeae, Hordeeae [i.e., Triticeae], Agrostideae [i.e., Aveneae], andPoeae, the latter includingSesleria) are resolved as a monophyletic group that is nested among the remaining elements of the subfamily (Brachypodieae, Meliceae, Stipeae,Anisopogon, Diarrhena, Lygeum, andNardus). A second principal goal of the analysis was to identify structural synapomorphies of clades. Among the synapomorphies identified for some of the major clades are the following: gain of a 6.4 kb inversion in the chloroplast genome inJoinvillea and the grasses; reduction to 1 ovule per pistil, gain of a lateral “grass-type” embryo, and gain of an inversion around the gene trnT in the chloroplast genome in the grasses; loss of arm cells in the clade that consists ofBrachyelytrum, Pooideae, and the PACC clade; loss of the epiblast and gain of an elongate mesocotyl internode in the PACC clade; gain of proximal female-sterile florets in female-fertile spikelets, gain of overlapping embryonic leaf margins, and gain ofPanicum- type endosperm starch grains in the clade that comprises Centothecoideae and Panicoideae; and loss of the scutellar tail of the embryo in Pooideae (in one of two alternative placements of Pooideae among other groups). These findings are consistent with an origin and early diversification of grasses as forest understory herbs, followed by one or more radiations into open habitats, concomitant with multiple origins of C4 photosynthesis and specialization for wind pollination.