Plant genetic variation and soil microorganisms are individually known to influence plant responses to climate change, but the interactive effects of these two factors are largely unknown. Using long-term observational studies in the field and common garden and greenhouse experiments of a foundation tree species () and its mutualistic ectomycorrhizal fungal (EMF) associates, we show that EMF community composition is under strong plant genetic control. Seedlings acquire the EMF community of their seed source trees (drought tolerant vs. drought intolerant), even when exposed to inoculum from the alternate tree type. Drought-tolerant trees had 25% higher growth and a third the mortality of drought-intolerant trees over the course of 10 y of drought in the wild, traits that were also observed in their seedlings in a common garden. Inoculation experiments show that EMF communities are critical to drought tolerance. Drought-tolerant and drought-intolerant seedlings grew similarly when provided sterile EMF inoculum, but drought-tolerant seedlings grew 25% larger than drought-intolerant seedlings under dry conditions when each seedling type developed its distinct EMF community. This demonstration that particular combinations of plant genotype and mutualistic EMF communities improve the survival and growth of trees with drought is especially important, given the vulnerability of forests around the world to the warming and drying conditions predicted for the future.

Sporadic patchy die-off of bush lupine, Lupinus arboreus, has long been known. We describe in detail a series of these incidents on the central California coast, based upon observational and comparative evidence. Stands of thousands of plants die, while nearby mature plants live on. In some sites, repeated die-off followed by regeneration from the seed bank has led to the cover and density of this woody, perennial plant fluctuating widely over the 40 year period for which records exist. Root damage by caterpillars of the ghost moth or "swift" Hepialus californicus (Lepidoptera, Hepialidae) is a major cause of individual bush death and a probable cause of die-off of stands of lupine. Hidden from view underground, a few of these insects readily kill a juvenile or young mature plant by girdling and reaming-out roots. The mass mortality of L. arboreus that we observed involved heavy root damage by these caterpillars in evenaged stands of plants in their first (1.5-year-old) or second (2.5-year-old) flowering season. The injured plants set seed before dying. Older, larger bush lupines better withstood root damage. In plants aged 3 or more years, damage and mortality were correlated with the intensity of ghost moth caterpillars in the roots. At the highest intensity (mean = 37.5, maximum = 62 caterpillars/root), a stand of large, old L. arboreus suffered 41% mortality; 45% of root cambium (median value) was destroyed by feeding caterpillars. Mass death of mature L. arboreus was not correlated with folivory, and leaf damage ranged from nil to moderate in instances of die-off. The western tussock moth, Orgyia vetusta, accounted for the highest levels of folivory, but this insect was rare when die-offs occurred. The lowest lupine mortality rates in our study occurred where tussock caterpillar intensities were high and where plants were repeatedly defoliated by this insect. However, experimental defoliation by high, but realistic, intensities of tussock moth caterpillars resulted in some mortality of mature bushes, and the combined effects of leaf and root herbivory have yet to be assessed. In its natural range on the California coast, bush lupine has several additional species of insect herbivores that can be locally abundant and injurious to the plant, although none is associated with die-off. Subterranean natural enemies of ghost moth caterpillars may play a role in the patchy waxing and waning of this shrub. Locally, a new species of entomophagous nematode (Heterorhabditis sp.) cause high mortality in the soil, before ghost moth caterpillars have entered the root. This natural enemy may thus afford lupines protection from heavy underground herbivory.

Indirect climate effects on tree fecundity that come through variation in size and growth (climate-condition interactions) are not currently part of models used to predict future forests. Trends in species abundances predicted from meta-analyses and species distribution models will be misleading if they depend on the conditions of individuals. Here we find from a synthesis of tree species in North America that climate-condition interactions dominate responses through two pathways, i) effects of growth that depend on climate, and ii) effects of climate that depend on tree size. Because tree fecundity first increases and then declines with size, climate change that stimulates growth promotes a shift of small trees to more fecund sizes, but the opposite can be true for large sizes. Change the depresses growth also affects fecundity. We find a biogeographic divide, with these interactions reducing fecundity in the West and increasing it in the East. Continental-scale responses of these forests are thus driven largely by indirect effects, recommending management for climate change that considers multiple demographic rates.

Although the importance of plant-associated microbes is increasingly recognized, little is known about the biotic and abiotic factors that determine the composition of that microbiome. We examined the influence of plant genetic variation, and two stressors, one biotic and one abiotic, on the ectomycorrhizal (EM) fungal community of a dominant tree species, Pinus edulis. During three periods across 16 years that varied in drought severity, we sampled the EM fungal communities of a wild stand of P. edulis in which genetically based resistance and susceptibility to insect herbivory was linked with drought tolerance and the abundance of competing shrubs. We found that the EM fungal communities of insect-susceptible trees remained relatively constant as climate dried, while those of insect-resistant trees shifted significantly, providing evidence of a genotype by environment interaction. Shrub removal altered the EM fungal communities of insect-resistant trees, but not insect-susceptible trees, also a genotype by environment interaction. The change in the EM fungal community of insect-resistant trees following shrub removal was associated with greater shoot growth, evidence of competitive release. However, shrub removal had a 7-fold greater positive effect on the shoot growth of insect-susceptible trees than insect-resistant trees when shrub density was taken into account. Insect-susceptible trees had higher growth than insect-resistant trees, consistent with the hypothesis that the EM fungi associated with susceptible trees were superior mutualists. These complex, genetic-based interactions among species (tree-shrub-herbivore-fungus) argue that the ultimate impacts of climate change are both ecological and evolutionary.

Interactions between extrinsic factors, such as disruptive selection and intrinsic factors, such as genetic incompatibilities among loci, often contribute to the maintenance of species boundaries. The relative roles of these factors in the establishment of reproductive isolation can be examined using species pairs characterized by gene flow throughout their divergence history. We investigated the process of speciation and the maintenance of species boundaries between Pinus strobiformis and Pinus flexilis. Utilizing ecological niche modelling, demographic modelling and genomic cline analyses, we illustrated a divergence history with continuous gene flow. Our results supported an abundance of advanced generation hybrids and a lack of loci exhibiting steep transition in allele frequency across the hybrid zone. Additionally, we found evidence for climate-associated variation in the hybrid index and niche divergence between parental species and the hybrid zone. These results are consistent with extrinsic factors, such as climate, being an important isolating mechanism. A build-up of intrinsic incompatibilities and of coadapted gene complexes is also apparent, although these appear to be in the earliest stages of development. This supports previous work in coniferous species demonstrating the importance of extrinsic factors in facilitating speciation. Overall, our findings lend support to the hypothesis that varying strength and direction of selection pressures across the long lifespans of conifers, in combination with their other life history traits, delays the evolution of strong intrinsic incompatibilities.