title: Pinus ponderosa: A checkered past obscured four species.
abstract: OBJECTIVE
  Molecular genetic evidence can help delineate taxa in species complexes that lack diagnostic morphological characters. Pinus ponderosa (Pinaceae; subsection Ponderosae) is recognized as a problematic taxon: plastid phylogenies of exemplars were paraphyletic, and mitochondrial phylogeography suggested at least four subdivisions of P. ponderosa. These patterns have not been examined in the context of other Ponderosae species. We hypothesized that putative intraspecific subdivisions might each represent a separate taxon.
  
  
  METHODS
  We genotyped six highly variable plastid simple sequence repeats in 1903 individuals from 88 populations of P. ponderosa and related Ponderosae (P. arizonica, P. engelmannii, and P. jeffreyi). We used multilocus haplotype networks and discriminant analysis of principal components to test clustering of individuals into genetically and geographically meaningful taxonomic units.
  
  
  RESULTS
  There are at least four distinct plastid clusters within P. ponderosa that roughly correspond to the geographic distribution of mitochondrial haplotypes. Some geographic regions have intermixed plastid lineages, and some mitochondrial and plastid boundaries do not coincide. Based on relative distances to other species of Ponderosae, these clusters diagnose four distinct taxa.
  
  
  CONCLUSIONS
  Newly revealed geographic boundaries of four distinct taxa (P. benthamiana, P. brachyptera, P. scopulorum, and a narrowed concept of P. ponderosa) do not correspond completely with taxonomies. Further research is needed to understand their morphological and nuclear genetic makeup, but we suggest that resurrecting originally published species names would more appropriately reflect the taxonomy of this checkered classification than their current treatment as varieties of P. ponderosa.
authors.affiliation: Hendrix College, 1600 Washington Ave, Conway, Arkansas 72032 USA willyard@hendrix.edu.
authors.forename: Ann
authors.initials: A
authors.lastname: Willyard
authors.affiliation: Departmento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, A.P. 70-233, Mexico City 04510 México.
authors.forename: David S
authors.initials: DS
authors.lastname: Gernandt
authors.affiliation: Department of Forestry and Environmental Resources, North Carolina State University, Research Triangle Park, North Carolina 27709 USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Potter
authors.affiliation: National Forest Genetics Laboratory, USDA Forest Service, Placerville, California 95667 USA.
authors.forename: Valerie
authors.initials: V
authors.lastname: Hipkins
authors.affiliation: USDA Forest Service, Northern Research Station, Institute for Ecosystem Studies, 5985 Highway K, Rhinelander, Wisconsin 54501 USA.
authors.forename: Paula
authors.initials: P
authors.lastname: Marquardt
authors.affiliation: Genetic Resource Program, Northern, Rocky Mountain, Southwestern, and Intermountain Regions, USDA Forest Service, Moscow, Idaho 83843 USA.
authors.forename: Mary Frances
authors.initials: MF
authors.lastname: Mahalovich
authors.affiliation: 301 North Main #214, Layton, Utah 84041 USA.
authors.forename: Stephen K
authors.initials: SK
authors.lastname: Langer
authors.affiliation: W. J. Beal Botanical Garden, Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA.
authors.forename: Frank W
authors.initials: FW
authors.lastname: Telewski
authors.affiliation: Hendrix College, 1600 Washington Ave, Conway, Arkansas 72032 USA.
authors.forename: Blake
authors.initials: B
authors.lastname: Cooper
authors.affiliation: Hendrix College, 1600 Washington Ave, Conway, Arkansas 72032 USA.
authors.forename: Connor
authors.initials: C
authors.lastname: Douglas
authors.affiliation: Hendrix College, 1600 Washington Ave, Conway, Arkansas 72032 USA.
authors.forename: Kristen
authors.initials: K
authors.lastname: Finch
authors.affiliation: Hendrix College, 1600 Washington Ave, Conway, Arkansas 72032 USA.
authors.forename: Hassani H
authors.initials: HH
authors.lastname: Karemera
authors.affiliation: Hendrix College, 1600 Washington Ave, Conway, Arkansas 72032 USA.
authors.forename: Julia
authors.initials: J
authors.lastname: Lefler
authors.affiliation: Hendrix College, 1600 Washington Ave, Conway, Arkansas 72032 USA.
authors.forename: Payton
authors.initials: P
authors.lastname: Lea
authors.affiliation: Hendrix College, 1600 Washington Ave, Conway, Arkansas 72032 USA.
authors.forename: Austin
authors.initials: A
authors.lastname: Wofford
mesh_terms: D000483:Alleles; D016002:Discriminant Analysis; D005787:Gene Frequency; D014644:Genetic Variation; D005838:Genotype; D005843:Geography; D006239:Haplotypes; D018895:Microsatellite Repeats / Q000235:genetics; D010802:Phylogeny; D028223:Pinus / Q000145:classification / Q000235:genetics*; D041604:Pinus ponderosa / Q000235:genetics*; D018087:Plastids / Q000235:genetics; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014481:United States
keywords: Pinaceae; Pinus; Ponderosae; plastid microsatellites; ponderosa pine