Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1).

Circumscriptions of and relationships among many genera and suprageneric taxa of the diverse grass tribe Poeae remain controversial. In an attempt to clarify these, we conducted phylogenetic analyses of >2400 new DNA sequences from two nuclear ribosomal regions (ITS, including internal transcribed spacers 1 and 2 and the 5.8S gene, and the 3'-end of the external transcribed spacer (ETS)) and five plastid regions (, , , , ), and of more than 1000 new and previously published ITS sequences, focused particularly on Poeae chloroplast group 1 and including broad and increased species sampling compared to previous studies. Deep branches in the combined plastid and combined ITS+ETS trees are generally well resolved, the trees are congruent in most aspects, branch support across the trees is stronger than in trees based on only ITS and fewer plastid regions, and there is evidence of conflict between data partitions in some taxa. In plastid trees, a strongly supported clade corresponds to Poeae chloroplast group 1 and includes Agrostidinae p.p., Anthoxanthinae, Aveninae s.str., Brizinae, Koeleriinae (sometimes included in Aveninae s.l.), Phalaridinae and Torreyochloinae. In the ITS+ETS tree, a supported clade includes these same tribes as well as Sesleriinae and Scolochloinae. Aveninae s.str. and Sesleriinae are sister taxa and form a clade with Koeleriinae in the ITS+ETS tree whereas Aveninae s.str. and Koeleriinae form a clade and Sesleriinae is part of Poeae chloroplast group 2 in the plastid tree. All species of are part of Koeleriinae, but the genus is polyphyletic. Koeleriinae is divided into two major subclades: one comprises , , , , and subg. Trisetum, and the other / p.p. (multiple species from Mexico to South America), , , , and subg. , , and fall in different clades of Koeleriinae in plastid vs. nuclear ribosomal trees, and are likely of hybrid origin. ITS and trees identify a third lineage of Koeleriinae corresponding to Trisetum subsect. Sibirica, and affinities of with respect to Aveninae s.str. and Koeleriinae are incongruent in nuclear ribosomal and plastid trees, supporting recognition of in its own subtribe. A large clade comprises taxa of Agrostidinae, Brizinae and Calothecinae, but neither Agrostidinae nor Calothecinae are monophyletic as currently circumscribed and affinities of Brizinae differ in plastid and nuclear ribosomal trees. Within this clade, one newly identified lineage comprises , , (Agrostidinae p.p.) and (Calothecinae p.p.), and another comprises (Calothecinae p.p.) and (Agrostidinae p.p.). Within Agrostidinae p.p., the type species of and s.str. are closely related, supporting classification of as a synonym of s.str. Furthermore, the two species of are not sister taxa and are nested among different groups of s.str., supporting their classification in . , and form a clade and species of each are variously intermixed in plastid and nuclear ribosomal trees. Additionally, all but one species from South America classified in Deyeuxia sect. Stylagrostis resolve in Holcinae p.p. (). The current phylogenetic results support recognition of the latter species in , and we also demonstrate is part of this clade. Moreover, Holcinae is not monophyletic in its current circumscription because does not form a clade with and , which are sister taxa. The results support recognition of in its own subtribe Aristaveninae. Substantial further changes to the classification of these grasses will be needed to produce generic circumscriptions consistent with phylogenetic evidence. The following 15 new combinations are made: Calamagrostis × calammophila, , C. breviligulata subsp. champlainensis, C. × don-hensonii, , , , D. chrysantha var. phalaroides, , D. eminens var. fulva, D. eminens var. inclusa, , , and var. ; the new name is proposed; the new subtribe Lagurinae is described; and a second-step lectotype is designated for the name .