Nuclear genetic variation across the range of ponderosa pine (Pinus ponderosa): Phylogeographic, taxonomic and conservation implications

  • Kevin M. PotterEmail author
  • Valerie D. Hipkins
  • Mary F. Mahalovich
  • Robert E. Means
Original Paper
Part of the following topical collections:
  1. Gene Conservation


Ponderosa pine (Pinus ponderosa) is among the most broadly distributed conifer species of western North America, where it possesses considerable ecological, esthetic, and commercial value. It exhibits complicated patterns of morphological and genetic variation, suggesting that it may be in the process of differentiating into distinct regional lineages. A robust analysis of genetic variation across the ponderosa pine complex is necessary to ensure the effectiveness of management and conservation efforts given the species’ large distribution, the existence of many isolated disjunct populations, and the potential susceptibility of some populations to climate change and other threats. We used highly polymorphic nuclear microsatellite markers and isozyme markers from 3113 trees in 104 populations to assess genetic variation and structure across the geographic range of ponderosa pine. The results reveal pervasive inbreeding and patterns of genetic diversity consistent with the hypothesis that ponderosa existed in small, as-yet-undetected Pleistocene glacial refugia north of southern Arizona and New Mexico. The substructuring of genetic variation within the species complex was consistent with its division into two varieties, with genetic clusters within varieties generally associated with latitudinal zones. The analyses indicate widespread gene flow and/or recent common ancestry among genetic clusters within varieties, but not between varieties. Isolated disjunct populations had lower genetic variation by some measures and greater genetic differentiation than main-range populations. These results should be useful for decision-making and conservation planning related to this widespread and important species.


Biogeography Gene conservation Inbreeding Isozymes Microevolution Microsatellites 



The authors thank the natural resource specialists from government agencies who assisted with the identification and collection of samples. The authors thank Doug Page, Connie Millar, and David Charlet for multiple collections; Jody Mello, Rosanna Hanson, Ricardo Hernandez, Pat Guge, Suellen Carroll, Kristin Motz, Courtney Owens, and Sara Trujillo for laboratory analyses; Mark Lesser for sharing the Pinus contorta primer sequences; and Julie Canavin for manuscript preparation assistance. This project was a cooperative effort between the Bureau of Land Management Wyoming and the National Forest Genetics Laboratory of the United States Department of Agriculture (USDA) Forest Service, Forest Management Staff. It was supported in part through Research Joint Venture Agreement 10-JV-11330146-049 between the Southern Research Station of the USDA Forest Service and North Carolina State University. Mention of a trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by the USDA and does not imply its approval to the exclusion or other products or vendors that also may be suitable.

Data Archiving Statement

Microsatellite and isozyme genotypes at all loci for all samples, as well as population names and coordinates, are archived at TreeGenes ( as TGDR035.

Supplementary material

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Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2015

Authors and Affiliations

  • Kevin M. Potter
    • 1
    Email author
  • Valerie D. Hipkins
    • 2
  • Mary F. Mahalovich
    • 3
  • Robert E. Means
    • 4
  1. 1.Department of Forestry and Environmental ResourcesNorth Carolina State UniversityResearch Triangle ParkUSA
  2. 2.National Forest Genetics LaboratoryUSDA Forest ServicePlacervilleUSA
  3. 3.Genetic Resource Program, Northern, Rocky Mountain, Southwestern and Intermountain RegionsUSDA Forest ServiceMoscowUSA
  4. 4.Bureau of Land Management WyomingCheyenneUSA

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