Abstract
Edaphic conditions have been documented as an important factor in the adaptive evolution of plant species. The soils in Mendocino County, California are heavily podzolized yet they sustain dwarf, endemic conifers such as Pinus contorta ssp. bolanderi. (Bolander pine) Interestingly, P. contorta ssp. contorta (shore pine), a sister taxon, occurs just off these soils and does not have the dwarf stature that Bolander pine displays. Because of the variation in environments that support each subspecies, these conifers provide an ideal system for examining the genetic polymorphisms associated with plants specialized for different edaphic conditions and the role of such conditions in adaptive divergence. This study characterizes patterns of DNA polymorphisms for 24 candidate genes related to growth and five different conditions of traits thought to be important for adaptation to harsh edaphic conditions. Candidate genes were defined using functional information from Arabidopsis thaliana and homology based searches of P. taeda (loblolly pine) unigene sets. Megagametophyte tissue from 46 and 47 individuals of shore pine and Bolander pine, respectively were sampled for these 24 candidate genes. As a null hypothesis, polymorphisms found within and between these two subspecies were assumed to be neutral and their patterns determined primarily by drift or historical demography. Rejection of the null hypothesis identified those loci that are putatively affected by natural selection. For each of these genes, summary statistics for diversity, estimates of neutrality, divergence and polymorphism (e.g. Hudson-Kreitman-Aguadé) based tests, and fixation indices (FST, GST, and NST) were calculated to determine if selection to different edaphic conditions has influenced divergence of Bolander pine from its common ancestor with shore pine. Three candidate genes, locus 0_15043 (is an ER type CA2+ transporting ATPase), locus UMN_4616 (which is involved in root and shoot growth in response to salt stress), and locus 2_1030 (involved in heavy metal tolerance of cadmium or lead, ion transporter activity) amplified as paralogous genes for which no analyses were performed. Fourteen candidate genes in these subspecies in trait categories for calcium, heavy metal and magnesium were found to likely be under strong purifying selection. Analysis found putative evidence of positive selection for two candidate genes: CL2494Contig1, involved in high aluminum tolerance and 0_16323, a gene involved in low phosphate tolerance. This finding suggests that there is genetic adaptation by Bolander pine to extremely acidic soils in the Mendocino pygmy forest ecosystem for gradients involving phosphate and aluminum.