title: Resolving deep relationships of PACMAD grasses: a phylogenomic approach.
abstract: BACKGROUND
  Plastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation sequencing methods were used to provide complete plastome sequences for 12 species. Sanger sequencing was performed to determine the plastome of one species, Hakonechloa macra, to provide a reference for annotation. These analyses were conducted to resolve deep subfamilial relationships within the clade. Divergence estimates were assessed to determine potential factors that led to the rapid radiation of this lineage and its dominance of warmer open habitats.
  
  
  RESULTS
  New plastomes were completely sequenced and characterized for 13 PACMAD species. An autapomorphic ~1140 bp deletion was found in Hakonechloa macra putatively pseudogenizing rpl14 and eliminating rpl16 from this plastome. Phylogenomic analyses support Panicoideae as the sister group to the ACMAD clade. Complete plastome sequences provide greater support at deep nodes within the PACMAD clade. The initial diversification of PACMAD subfamilies was estimated to occur at 32.4 mya.
  
  
  CONCLUSIONS
  Phylogenomic analyses of complete plastomes provides resolution for deep relationships of PACMAD grasses. The divergence estimate of 32.4 mya at the crown node of the PACMAD clade coincides with the Eocene-Oligocene Transition (EOT). The Eocene was a period of global cooling and drying, which led to forest fragmentation and the expansion of open habitats now dominated by these grasses. Understanding how these grasses are related and determining a cause for their rapid radiation allows for future predictions of grassland distribution in the face of a changing global climate.
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, Illinois, 60115-2861, U.S.A. joebtcotton@gmail.com.
authors.forename: Joseph L
authors.initials: JL
authors.lastname: Cotton
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, Illinois, 60115-2861, U.S.A. wwysoc2@gmail.com.
authors.forename: William P
authors.initials: WP
authors.lastname: Wysocki
authors.affiliation: Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, Iowa, 50011-1020, U.S.A. lgclark@iastate.edu.
authors.forename: Lynn G
authors.initials: LG
authors.lastname: Clark
authors.affiliation: Biological Sciences, Idaho State University, 921 S. 8th Ave, Pocatello, Idaho, 83209, U.S.A. kelchner@isu.edu.
authors.forename: Scot A
authors.initials: SA
authors.lastname: Kelchner
authors.affiliation: Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211-7310, U.S.A. piresjc@missouri.edu.
authors.forename: J Chris
authors.initials: JC
authors.lastname: Pires
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, U.S.A. pedger@gmail.com.
authors.forename: Patrick P
authors.initials: PP
authors.lastname: Edger
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Rd, St. Louis, Missouri, 63132, U.S.A. dmayfield-jones@danforthcenter.org.
authors.forename: Dustin
authors.initials: D
authors.lastname: Mayfield-Jones
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, Illinois, 60115-2861, U.S.A. mel-duvall@niu.edu.
authors.forename: Melvin R
authors.initials: MR
authors.lastname: Duvall
mesh_terms: D005075:Biological Evolution; D017753:Ecosystem; D019143:Evolution, Molecular; D054628:Genome, Chloroplast; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D006109:Poaceae / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins