title: Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing.
abstract: OBJECTIVE
  Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous-particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny.
  
  
  METHODS
  Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were used to enrich for chloroplast targets. Ten taxa were enriched using both methods for comparison. Chloroplast sequence data were generated for 31 representatives of the 14 Arecoideae tribes and five outgroup taxa. The phylogeny was reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses.
  
  
  RESULTS
  Long range PCR and hybrid gene capture both enriched the plastid genome and provided similar sequencing coverage. Subfamily Arecoideae was resolved as monophyletic with tribe Chamaedoreeae as the earliest-diverging lineage, implying that the development of flowers in triads defines a synapomorphy for the Arecoideae clade excluding Chamaedoreeae. Three major clades within this group were recovered: Roystoneeae/Reinhardtieae/Cocoseae (RRC), Areceae/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae (core arecoids), and Podococceae/Oranieae/Sclerospermeae (POS). An Areceae + Euterpeae clade was resolved within the core arecoids. The POS clade was sister to a RRC + core arecoids clade, implying a shared ancestral area in South America for these three clades.
  
  
  CONCLUSIONS
  The plastome phylogeny recovered here provides robust resolution of previously ambiguous studies and new insights into palm evolution.
authors.affiliation: University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Comer
authors.affiliation: University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA.
authors.forename: Wendy B
authors.initials: WB
authors.lastname: Zomlefer
authors.affiliation: California State University, Los Angeles, Department of Biological Sciences, Los Angeles, California 90032-8201 USA.
authors.forename: Craig F
authors.initials: CF
authors.lastname: Barrett
authors.affiliation: Cornell University, Department of Plant Biology, Ithaca, New York 14853-4301 USA.
authors.forename: Jerrold I
authors.initials: JI
authors.lastname: Davis
authors.affiliation: New York Botanical Garden, Bronx, New York 10458-5126 USA.
authors.forename: Dennis Wm
authors.initials: DW
authors.lastname: Stevenson
authors.affiliation: University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA.
authors.forename: Karolina
authors.initials: K
authors.lastname: Heyduk
authors.affiliation: University of Georgia, Department of Plant Biology, Athens, Georgia 30602-7271 USA.
authors.forename: James H
authors.initials: JH
authors.lastname: Leebens-Mack
mesh_terms: D028023:Arecaceae / Q000235:genetics*; D001483:Base Sequence; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016013:Likelihood Functions; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D016133:Polymerase Chain Reaction; D013045:Species Specificity
keywords: Arecaceae; Arecoideae; gene capture; next-generation sequencing; oil palm; phylogenetics