title: Understanding diploid diversity: A first step in unraveling polyploid, apomictic complexity in Amelanchier.
abstract: OBJECTIVE
  Delimitation of Amelanchier species is difficult because of polyploidy and gametophytic apomixis. A first step in unraveling this species problem is understanding the diversity of the diploids that contributed genomes to polyploid apomicts. This research helps clarify challenging species-delimitation problems attending polyploid, apomictic complexity.
  
  
  METHODS
  We sampled 431 diploid accessions from 13 species, of which 10 are North American and three are Old World. Quantitative morphological analyses tested the null hypothesis of no discrete groups. Using three to nine diploid accessions per species, we constructed phylogenies with DNA sequences from ETS, ITS, the second intron of LEAFY, and chloroplast regions rpoB-trnC, rpl16, trnD-trnT, and ycf6-psbM.
  
  
  RESULTS
  Most Amelanchier diploid taxa are morphologically and ecogeographically distinct and genetically exclusive lineages. They rarely hybridize with one another. Nuclear and chloroplast DNA sequences almost completely resolve the Amelanchier phylogeny. The backbone is the mostly western North American clade A, eastern North American clade B, and Old World clade O. DNA sequences and morphology support clades A and O as sister taxa. Despite extensive paralogy, our LEAFY data are phylogenetically informative and identify a clade (T) of three arborescent taxa within clade B.
  
  
  CONCLUSIONS
  Amelanchier diploids differ strikingly from polyploid apomicts, in that hybridization among them is rare, and they form taxa that would qualify as species by most species concepts. Knowledge of diploid morphology, phylogeny, and ecogeography provides a foundation for understanding the evolutionary history of polyploid apomicts, their patterns of diversification, and their species status.
authors.affiliation: Department of Biological Sciences, State University of New York Plattsburgh, Plattsburgh, New York 12901, USA michael.b.burgess@plattsburgh.edu.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Burgess
authors.affiliation: School of Biology and Ecology, University of Maine, Orono, Maine 04469, USA.
authors.forename: Kevin R
authors.initials: KR
authors.lastname: Cushman
authors.affiliation: School of Biology and Ecology, University of Maine, Orono, Maine 04469, USA.
authors.forename: Eric T
authors.initials: ET
authors.lastname: Doucette
authors.affiliation: Maryland Department of Natural Resources, Natural Heritage Program, 909 Wye Mills Road, Wye Mills, Maryland 21679, USA.
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Frye
authors.affiliation: School of Biology and Ecology, University of Maine, Orono, Maine 04469, USA.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Campbell
mesh_terms: D060832:Apomixis; D005075:Biological Evolution; D060365:Chloroplast Proteins / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D004171:Diploidy; D014644:Genetic Variation; D007438:Introns; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D027824:Rosaceae / Q000235:genetics / Q000502:physiology*
chemical_list: D060365:Chloroplast Proteins; D021901:DNA, Intergenic; D010940:Plant Proteins
keywords: ETS; ITS; LEAFY; apomixis; cpDNA; microspecies; paralogy; polyploidy; semicryptic ploidy variation