title: Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment.
abstract: OBJECTIVE
  The sunflower genus Helianthus has long been recognized as economically significant, containing species of agricultural and horticultural importance. Additionally, this genus displays a large range of phenotypic and genetic variation, making Helianthus a useful system for studying evolutionary and ecological processes. Here we present the most robust Helianthus phylogeny to date, laying the foundation for future studies of this genus.
  
  
  METHODS
  We used a target enrichment approach across 37 diploid Helianthus species/subspecies with a total of 103 accessions. This technique garnered 170 genes used for both coalescent and concatenation analyses. The resulting phylogeny was additionally used to examine the evolution of life history and growth form across the genus.
  
  
  RESULTS
  Coalescent and concatenation approaches were largely congruent, resolving a large annual clade and two large perennial clades. However, several relationships deeper within the phylogeny were more weakly supported and incongruent among analyses including the placement of H. agrestis, H. cusickii, H. gracilentus, H. mollis, and H. occidentalis.
  
  
  CONCLUSIONS
  The current phylogeny supports three major clades including a large annual clade, a southeastern perennial clade, and another clade of primarily large-statured perennials. Relationships among taxa are more consistent with early phylogenies of the genus using morphological and crossing data than recent efforts using single genes, which highlight the difficulties of phylogenetic estimation in genera known for reticulate evolution. Additionally, conflict and low support at the base of the perennial clades may suggest a rapid radiation and/or ancient introgression within the genus.
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602 United States.
authors.forename: Jessica D
authors.initials: JD
authors.lastname: Stephens
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602 United States.
authors.forename: Willie L
authors.initials: WL
authors.lastname: Rogers
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602 United States.
authors.forename: Chase M
authors.initials: CM
authors.lastname: Mason
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602 United States.
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Donovan
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602 United States.
authors.forename: Russell L
authors.initials: RL
authors.lastname: Malmberg
mesh_terms: D002736:Chloroplasts / Q000235:genetics; D004171:Diploidy; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D006368:Helianthus / Q000145:classification* / Q000235:genetics*; D016013:Likelihood Functions; D010802:Phylogeny; D013045:Species Specificity
keywords: coalescent; gene capture; phylogenomics; phylogeny; sunflower