Saarela, Jeffery M., Wysocki, William P., Barrett, Craig F., Soreng, Robert J., Davis, Jerrold I., Clark, Lynn G., Kelchner, Scot A., Pires, J. C., Edger, Patrick P., Mayfield, Dustin R., and Duvall, Melvin R. 2015. "Plastid phylogenomics of the cool-season grass subfamily: Clarification of relationships among early-diverging tribes." AoB Plants 7:1-72. https://doi.org/10.1093/aobpla/plv046
Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some "early-diverging" tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent nine tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood, maximum parsimony and Bayesian inference robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared to protein coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae–Meliceae and Ampelodesmeae–Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae–Triticeae clade and Poeae. Within Poeae, a novel sister-group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae–Brizinae clade, are discordant between maximum parsimony and maximum likelihood/Bayesian inference trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae–Loliinae clade.