Climate suitability is projected to decline for many subalpine species, raising questions about managing species under a deteriorating climate. Whitebark pine (WBP) (Pinus albicaulis) in the Greater Yellowstone Ecosystem (GYE) crystalizes the challenges that natural resource managers of many high mountain ecosystems will likely face in the coming decades. We review the system of interactions among climate, competitors, fire, bark beetles, white pine blister rust (Cronartium ribicola), and seed dispersers that make WBP especially vulnerable to climate change. A well-formulated interagency management strategy has been developed for WBP, but it has only been implemented across <1% of the species GYE range. The challenges of complex climate effects and land allocation constraints on WBP management raises questions regarding the efficacy of restoration efforts for WBP in GYE. We evaluate six ecological mechanisms by which WBP may remain viable under climate change: climate microrefugia, climate tolerances, release from competition, favorable fire regimes, seed production prior to beetle-induced mortality, and blister-rust resistant trees. These mechanisms suggest that WBP viability may be higher than previously expected under climate change. Additional research is warranted on these mechanisms, which may provide a basis for increased management effectiveness. This review is used as a basis for deriving recommendations for other subalpine species threatened by climate change.

Whitebark pine is difficult to distinguish from limber pine when seed cones are not present. This is often the case because of young stand age, growth at environmental extremes, or harvesting by vertebrate species. Developing an economical genetic identification tool that distinguishes non-cone-bearing limber from whitebark pine, therefore, could aid many kinds of research on these species. Phylogenetic studies involving limber and whitebark pine suggest that chloroplast DNA sequences differ between these species. We therefore wanted to identify chloroplast loci that could differentiate limber from whitebark pine trees by taking an economical approach involving restriction-site analysis. We generated chloroplast DNA barcode sequences sampled from limber and whitebark pine trees that we identified using attached seed cones. We searched for nucleotide differences associated with restriction endonuclease recognition sites. Our analyses revealed that matK and the psbA-trnH spacer each readily amplified and harbored multiple DNA-sequence differences between limber and whitebark pine. The matK coding sequence of whitebark pine has a BsmAI restriction site not found in limber pine. The psbA-trnH spacer of limber pine has two PsiI restriction sites, neither of which is found in whitebark pine. DNA-sequence and restriction-site analysis of the psbA-trnH spacer from 111 trees showed complete congruence between visually and genetically identified limber (n = 68) and whitebark (n = 43) pine trees. We conclude that restriction site analysis of the chloroplast psbA-trnH spacer and matK involves both minimal technical expertize and research funds. These findings should be of value to foresters interested in species identification and distribution modeling, as well as the analysis of fossil pine pollen, given that gymnosperms transmit chloroplast DNA paternally.