title: Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (Pinaceae): range-wide evolutionary history and implications for conservation.
abstract: OBJECTIVE
  Ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic mitochondrial DNA marker, with results offering insights into how geographical and climatological processes drove the modern evolutionary structure of tree species in the region.
  
  
  METHODS
  We amplified the mtDNA nad1 second intron minisatellite region for 3,100 trees representing 104 populations, and sequenced all length variants. We estimated population-level haplotypic diversity and determined diversity partitioning among varieties, races and populations. After aligning sequences of minisatellite repeat motifs, we evaluated evolutionary relationships among haplotypes.
  
  
  RESULTS
  The geographical structuring of the 10 haplotypes corresponded with division between Pacific and Rocky Mountain varieties. Pacific haplotypes clustered with high bootstrap support, and appear to have descended from Rocky Mountain haplotypes. A greater proportion of diversity was partitioned between Rocky Mountain races than between Pacific races. Areas of highest haplotypic diversity were the southern Sierra Nevada mountain range in California, northwestern California, and southern Nevada.
  
  
  CONCLUSIONS
  Pinus ponderosa haplotype distribution patterns suggest a complex phylogeographic history not revealed by other genetic and morphological data, or by the sparse paleoecological record. The results appear consistent with long-term divergence between the Pacific and Rocky Mountain varieties, along with more recent divergences not well-associated with race. Pleistocene refugia may have existed in areas of high haplotypic diversity, as well as the Great Basin, Southwestern United States/northern Mexico, and the High Plains.
authors.affiliation: Department of Forestry and Environmental Resources, North Carolina State University, Research Triangle Park, North Carolina 27709, USA. kpotter@ncsu.edu
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Potter
authors.forename: Valerie D
authors.initials: VD
authors.lastname: Hipkins
authors.forename: Mary F
authors.initials: MF
authors.lastname: Mahalovich
authors.forename: Robert E
authors.initials: RE
authors.lastname: Means
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D003247:Conservation of Natural Resources; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D006239:Haplotypes; D018598:Minisatellite Repeats / Q000235:genetics; D015205:Northwestern United States; D059372:Nucleotide Motifs; D058974:Phylogeography; D028223:Pinus / Q000235:genetics*; D041604:Pinus ponderosa / Q000235:genetics*; D011110:Polymorphism, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA; D015206:Southwestern United States; D014197:Trees
chemical_list: D004272:DNA, Mitochondrial; D018744:DNA, Plant
keywords: Migration; Pinus ponderosa; Pinus washoensis; Pleistocene; minisatellite; mitochondrial DNA; phylogeography; polymorphism