title: Chloroplast heterogeneity and historical admixture within the genus Malus.
abstract: •
  
  
  OBJECTIVE
  The genus Malus represents a unique and complex evolutionary context in which to study domestication. Several Malus species have provided novel alleles and traits to the cultivars. The extent of admixture among wild Malus species has not been well described, due in part to limited sampling of individuals within a taxon.•
  
  
  METHODS
  Four chloroplast regions (1681 bp total) were sequenced and aligned for 412 Malus individuals from 30 species. Phylogenetic relationships were reconstructed using maximum parsimony. The distribution of chloroplast haplotypes among species was examined using statistical parsimony, phylogenetic trees, and a median-joining network.•
  
  
  RESULTS
  Chloroplast haplotypes are shared among species within Malus. Three major haplotype-sharing networks were identified. One includes species native to China, Western North America, as well as Malus domestica Borkh, and its four primary progenitor species: M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., M. sylvestris (L.) Mill., and M. prunifolia (Willd.) Borkh; another includes five Chinese Malus species, and a third includes the three Malus species native to Eastern North America.•
  
  
  CONCLUSIONS
  Chloroplast haplotypes found in M. domestica belong to a single, highly admixed network. Haplotypes shared between the domesticated apple and its progenitors may reflect historical introgression or the retention of ancestral polymorphisms. Multiple individuals should be sampled within Malus species to reveal haplotype heterogeneity, if complex maternal contributions to named species are to be recognized.
authors.affiliation: USDA-ARS National Center for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, Colorado 80521.
authors.forename: Gayle M
authors.initials: GM
authors.lastname: Volk
authors.affiliation: USDA-ARS National Center for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, Colorado 80521.
authors.forename: Adam D
authors.initials: AD
authors.lastname: Henk
authors.affiliation: USDA-ARS Dale Bumpers National Rice Research Center, 2890 Hwy. 130 E., Stuttgart, Arkansas 72160.
authors.forename: Angela
authors.initials: A
authors.lastname: Baldo
authors.affiliation: USDA-ARS Plant Genetic Resources Unit, 630 West North Street, Geneva, New York 14456-0462.
authors.forename: Gennaro
authors.initials: G
authors.lastname: Fazio
authors.affiliation: USDA-ARS Plant Genetic Resources Unit, 630 West North Street, Geneva, New York 14456-0462.
authors.forename: C Thomas
authors.initials: CT
authors.lastname: Chao
authors.affiliation: USDA-ARS National Center for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, Colorado 80521.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Richards
mesh_terms: D000483:Alleles; D005075:Biological Evolution; D002736:Chloroplasts / Q000235:genetics*; D018742:DNA, Chloroplast / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D006239:Haplotypes; D027845:Malus / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D011003:Ploidies; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast
keywords: apple; chloroplast sequence diversity; crop wild relatives; domestication; phylogenetic relationships; ploidy