The biogeography and ecology of P. balfouriana, a subalpine conifer endemic to California, were studied. Direct gradient-analysis, classification, and ordination were combined to identify the primary factors controlling the tree community in the southern Sierra Nevada. Competition, disturbance, and temperature were inferred as the most important factors regulating the tree community. Pinus balfouriana responded strongly to variation in soil drainage, distrubance, and temperature. Wildfire was the most important chronic disturbance agent in southwestern Inyo National Forest. Stochastic models of wildfire probability in space and time were developed. Evidence of thunderstorm genesis zones in the vicinity of Overlook Mountain and Ball Mountain in the Golden Trout Wilderness was found. A gradient in wildfire ignition probability was identified. Wildfire ignition is most likely at 2700 m elevation on submesic sites. Wildfire return interval is long enough to permit the coexistence of P. balfouriana and P. murrayana; and, short enough that it has important fitness consequences for P. balfouriana. Wildfire disturbance may limit the geographic range of the species in the southern Sierra Nevada. There was a close negative correlation between the abundance of P. balfouriana near the lower-forest-border and the wildfire disturbance gradient. However, the northern range boundary is probably not determined solely by wildfire disturbance. The canopies of mature P. balfouriana were found to be highly elliptic (when viewed from above) with the major axis of the ellipse oriented exactly north-to-south. This trait permits maximum photosynthesis in the early morning and late afternoon. It simultaneously minimizes evaporative demands during midday. Elliptic canopies minimize solar interception during winter and maximize it during summer. This is important for carbon-balance since the photosynthetic apparatus is only active for a brief period during mid-summer. The lower-forest-border was accurately predicted with a carbon-balance model strongly suggesting carbon-balance limitations. The dispersal potential of P. balfouriana, in the absence of vertebrate seed dispersers, was studied. Anemochory under modern climatic conditions would permit closure of the disjunction in P. balfouriana within a single (120,000 year) glacial cycle.

Foxtail pine (Pinus balfouriana) is a subalpine conifer endemic to California, notably separated into two disjunct subspecies. Previous studies have described the northern subspecies,Pinus balfouriana subsp. balfouriana,as having an uncommonly high level of genetic differentiation and no discernible spatial patterns in phenotypic variation. This study seeks to characterize the spatial genetic structure and patterns of selection of the northern subspecies (Pinus balfouriana subsp. balfouriana) using genome-wide data and to identify the influence of ecology and environment on the unique genetic patterns. I show that genetic differentiation among populations is much less than previously estimated (FST= 0.000644) and there is weak isolation-by-distance structure, but ongoing gene flow is unlikely. Within populations, stand density and competitor effects contribute to inbreeding. I also show that previously measured traits are predominantly determined by genetics. Analyzing by sliding window in the genome, I show that connectivity patterns vary widely throughout the genome and identify several areas that are important to the genetic architecture of the phenotypic traits and plasticity (GxE). Overall, there is high connectivity, genetic similarity, and genetically based trait variation among and within populations of the northern subspecies of foxtail pine due to historical processes, despite biotic interactions driving inbreeding. Persistent genetic isolation, however, may make adaptation to future climate a challenge for the subspecies.

The goal of this project was to determine the genetic architecture of water-use efficiency (WUE) for foxtail pine, which included genomic loci, and effect sizes of this trait. Foxtail pine is a subalpine endemic conifer that inhabits two distinct regional populations separated by 500 km in the mountains of California. In order to achieve this goal, a robust linkage map containing thousands of genetic markers was created using four megagametophyte arrays ranging in size from approximately 70 to 95 megagametophytes. Quantitative trait loci (QTL) discovered for WUE were mapped along the linkage map using linear mixed models and five half-sibling families grown in a common garden. Effect sizes of these QTL were tested for differences between the two regional populations of foxtail pine.