Lodgepole pine (Pinus contorta Dougl.) is an important component of forest ecosystems in western North America. Its current range extends from the Yukon through British Columbia and western Alberta, south to California and southeast along the Rocky Mountains into Idaho, Utah and Colorado. The population structure, genetic diversity, gene flow and relationships among the subspecies of lodgepole pine were investigated using RAPD markers and sequencing data.

Fifteen populations of lodgepole pine were surveyed for diversity across 52 Random Amplified Polymorphic DNAs (RAPDs). The objective was to compare single-locus and multilocus structures in four marginal, three intermediate and eight central populations. Single-locus estimates indicated average observed and expected heterozygosity to be 0.19 and 0.17, respectively. When these estimates were split into population categories, a clear trend of increasing diversity was detected in the direction of marginal to central populations. F -statistics indicated an excess of heterozygotes, with FIS ranging from -0.08 for marginal populations to -0.13 for central populations. The estimates of FST decreased towards the margins of the species range, indicating increased population differentiation. Multilocus analysis showed significant two-locus and high order gametic disequilibria in all 15 populations. The most prominent components of the two-locus analysis were the variance of disequilibrium (46.2%) and the multilocus Wahlund's effect (31.9%).

To explore the relationship among the subspecies of lodgepole pine and the possibility of northern glacial refugia for subsp. latifolia and coastal refugia for subsp. contorta , 31 populations were analysed using RAPD markers, to determine whether a pattern of isolation by distance exists. Heterozygosity estimates ranged from 0.15 for subsp. latifolia to 0.08 for subspecies bolanderi . Estimates of GST for subspecies latifolia, murrayana and contorta were 0.067, 0.036 and 0.079 respectively. A significant pattern of isolation by distance was detected when all 31 populations were analysed together, and for the 19 populations of subsp. latifolia .

Sequence data from two chloroplast and one mitochondrial loci were used to evaluate the relationships between the four subspecies of lodgepole pine. At these loci however, nucleotide variation was confined to a small number of individuals and differentiation between subspecies was not detectable. Estimates of mean diversity were 0.000,178 and 0.000,186 for the two chloroplast loci.