Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.
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 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with 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 MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.
Botany Section, Research and Collections, Canadian Museum of Nature, PO Box 3443 Stn. D, Ottawa, ON, Canada K1P 3P4 jsaarela@mus-nature.ca mel-duvall@niu.edu.
Jeffery M
JM
Saarela
Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA.
William P
WP
Wysocki
Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, CA 90032-8201, USA.
Craig F
CF
Barrett
Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Robert J
RJ
Soreng
Section of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NY 14853, USA.
Jerrold I
JI
Davis
Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011-1020, USA.
Lynn G
LG
Clark
Biological Sciences, Idaho State University, 921 S. 8th Ave, Pocatello, ID 83209, USA.
Scot A
SA
Kelchner
Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA.
J Chris
JC
Pires
Department of Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA 94720, USA.
Patrick P
PP
Edger
Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA.
Dustin R
DR
Mayfield
Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA jsaarela@mus-nature.ca mel-duvall@niu.edu.
Melvin R
MR
Duvall
Chloroplast genome; Poeae; Schedonorus arundinaceus; core Pooideae; phylogenetics; phylogenomics; plastome