Summary1 Phytophthora ramorum (causal agent of sudden oak death) is an emerging generalist pathogen in coastal forests of California and Oregon, USA, that causes lethal stem infections on oaks ( Quercus spp.) and tanoak ( Lithocarpus densiflorus ) as well as nonlethal foliar infections on a broad range of trees and shrubs. 2 We studied P. ramorum over its known range in coastal redwood forests to determine forest compositional variables that are important to its epidemiology within the geographical area that it has already invaded. Redwood forests are dominated by coast redwood ( Sequoia sempervirens ), tanoak and California bay laurel ( Umbellularia californica ). 3 A total of 120 permanent plots (500 m 2 each) were established in redwood forests at 12 sites within the main epidemic area in California. Over 5000 trees were mapped and examined for the presence of P. ramorum during spring 2002 and resampled in spring 2003. 4 Mean incidence of P. ramorum across all plots was 0.17 ± 0.01 in 2002 and 0.24 ± 0.02 in 2003. The highest infection levels by P. ramorum were found on California bay laurel (range 0.42-0.69) and tanoak (0.32-0.45). The highest levels of mortality were associated with tanoak and ranged from 0 to 66%, with 62.5% of that mortality associated with P. ramorum infection. 5 Disease incidence above 30% was most often associated with bay laurel importance value. In plots with few bay laurel stems, high disease levels were associated with the presence of understorey tanoaks. Bay laurel and small tanoaks are thought to represent the main source of inoculum for further spread of P. ramorum . 6 Differential host mortality due to this emerging generalist pathogen will exert considerable influence on redwood forest dynamics, with potentially dramatic shifts in forest composition and structure and subsequent cascading ecological and evolutionary effects.

Substantial genetic variation in development time is known to exist among mountain pine beetle (Dendroctonus ponderosae Hopkins) populations across the western United States. The effect of this variation on geographic patterns in voltinism (generation time) and thermal requirements to produce specific voltinism pathways have not been investigated. The influence of voltinism on fitness traits, body size, and sex ratio is also unclear. We monitored mountain pine beetle voltinism, adult body size, sex ratio, and air temperatures at sites across latitudinal and elevational gradients in the western United States. With the exception of two sites at the coolest and warmest locations, the number of days required to complete a generation was similar. Thermal units required to achieve a generation, however, were significantly less for individuals at the coolest sites. Evolved adaptations explain this pattern, including developmental rates and thresholds that serve to synchronize cohorts and minimize cold-sensitive life stages in winter. These same adaptations reduce the capacity of mountain pine beetle at the warmest sites to take full advantage of increased thermal units, limiting the capacity for bivoltinism within the current realized distribution. Temperature was not correlated with adult size and sex ratio, and size was greatest in host trees other than lodgepole pine (Pinus contorta Dougl.). Our results provide baseline information for evaluating population responses in a changing climate.

The finding of Phytophthora ramorum -the pathogen that causes sudden oak death in four California native trees -on rhododendron in Europe led us to hypothesize that its host range in California's natural forests was much greater than previously suspected. In addition to the affected oak species, we have now identified an additional 13 species from 10 plant families that act as hosts for P. ramorum in California. Our data indicates that nearly all of the state's main tree species in mixedevergreen and redwood-tanoak forests -including the coniferous timber species coast redwood and Douglas fir -may be hosts for P. ramorum. The broad host range of P. ramorum, the variability of symptoms among different hosts and the ability of the pathogen to disperse by air suggests that it may have the potential to cause long-term, landscape-level changes in California forests.

We described 38 relictual old-growth stands -with data on the mortality, regeneration, floristic richness, fuel load and disease incidence in our study area in the Tahoe Basin of California and Nevada. The stands are within the lower and upper montane zones (1900-2400 m a.s.l.) and they are rare, occupying < 2% of the land in the Basin's watershed. Correlation matrices and ANOVAs of forest types and conifer species with environmental gradients revealed significant relationships with elevation, distance east of the Sierran crest, slope aspect, annual precipitation, date of complete snow melt, litter depth and degree of soil profile development. Pathogens, parasites and wood-boring insects were present on 23% of living trees; 16% of all trees were dead. We compared these stands to a reconstruction of pre-contact Basin forests and to ecologically analogous old-growth forests of Baja California that have never experienced fire suppression management. Currently, overstorey trees (> 180 yr old) in the Basin stands have ca. 33% cover, 54 m 2 .ha -1 basal area and 107 individuals.ha -1 , values very similar to reconstructions of pre-contact Basin forests and to modern Baja California forests. Understorey trees (60-180 yr old), however, are several times more dense than historic levels and species composition is strongly dominated by A. concolor, regardless of the overstorey composition. The ratio of Pinus : Abies has increased -and the age structure of extant stands predicts that it will continue to increase -from approximately 1:1 in pre-contact time to 1:7 within the next century. Disease incidence and mortality in Baja forests were lower. Although we quantitatively defined current Basin oldgrowth forests -in terms of stand structure -we realize that our definition will differ from that of both past and future oldgrowth forests unless management protocols are changed.

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Patterns of local adaptation at fine spatial scales are central to understanding how evolution proceeds, and are essential to the effective management of economically and ecologically important forest tree species. Here, we employ single and multilocus analyses of genetic data (n = 116 231 SNPs) to describe signatures of fine‐scale adaptation within eight whitebark pine (Pinus albicaulis Engelm.) populations across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation (FST = 0.0069), there is strong evidence for adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we build upon evidence from a common garden study and find that allele frequencies of loci associated with four phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit significantly higher signals of selection (covariance of allele frequencies) than could be expected to arise, given the data. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results replicate empirical support for theoretical expectations of local adaptation for populations exhibiting strong gene flow and high selective pressures and suggest that ongoing adaptation of many P. albicaulis populations within the Lake Tahoe Basin will not be constrained by the lack of genetic variation. Even so, some populations exhibit low levels of heritability for the traits presumed to be related to fitness. These instances could be used to prioritize management to maintain adaptive potential. Overall, we suggest that established practices regarding whitebark pine conservation be maintained, with the additional context of fine‐scale adaptation.

lis ia 69 of 80 Lind et al: Local adaptation of P. albicaulis 2 Running Title: Local adaptation of P. albicaulis 19 20 ABSTRACT 38 For populations exhibiting high levels of gene flow, the genetic architecture of fitness-related 39 traits is expected to be polygenic and underlain by many small-effect loci that covary across a 40 network of linked genomic regions. For most coniferous taxa, studies describing this 41 architecture have been limited to single-locus approaches, possibly leaving the vast majority of 42 the underlying genetic architecture undescribed. Even so, molecular investigations rarely search 43 for patterns indicative of an underlying polygenic basis, despite prior expectations for this signal.44 Here, using a polygenic perspective, we employ single and multilocus analyses of genome-wide 45 data (n = 116,231 SNPs) to describe the genetic architecture of adaptation within whitebark pine 46 (Pinus albicaulis Engelm.) across the local extent of the environmentally heterogeneous Lake ୗ = 0.0069) there is 48 strong evidence for polygenic adaptation to the rain shadow experienced across the eastern 49 Sierra Nevada. Specifically, we find little evidence for large-effect loci and that the frequencies 50 of loci associated with 4/5 phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 51 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit 52 significantly higher covariance than random SNPs. We also provide evidence that this 53 covariance tracks environmental measures related to soil water availability through subtle allele 54 frequency shifts across populations. Our results provide replicative support for theoretical 55 expectations and highlight advantages of a polygenic perspective, as unremarkable loci when 56 viewed from a single-locus perspective are noteworthy when viewed through a polygenic lens, 57 particularly when considering protective measures such as conservation guidelines and 58 restoration strategies. Lind et al: Local adaptation of P. albicaulis 5 empirical (Hall et al. 2007; Luquez et al. 2007) investigations exploring the relationship between 86 phenotypic differentiation (e.g., Q ST ) and that of the underlying loci (e.g, G ST or F ST ) have shown 87 that discordance between these two structural indices can occur under adaptive evolution. 88Moreover, as the number of underlying loci increases, the divergence between these indices 89 increases as well, and the contribution of F ST to any individual underlying locus decreases. In 90 cases that exhibit strong diversifying selection and high gene flow, this adaptive divergence 91 results from selection on segregating genetic variation (Hermisson and Pennings 2005; Barret 92 and Schluter 2008) and is attributable to the between-population component of linkage 93 disequilibrium (Ohta 1982, Latta 1998). In the short term, local adaptation will be realized 94 through subtle coordinated shifts of allele frequencies across populations causing covariance 95