J. Bradley St. Clair

Association Genetics of Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-Hardiness Related Traits

Adaptation to cold is one of the greatest challenges to forest trees. This process is highly synchronized with environmental cues relating to photoperiod and temperature. Here, we use a candidate gene-based approach to search for genetic associations between 384 single-nucleotide polymorphism (SNP) markers from 117 candidate genes and 21 cold-hardiness related traits. A general linear model approach, including population structure estimates as covariates, was implemented for each marker–trait pair. We discovered 30 highly significant genetic associations [false discovery rate (FDR) Q < 0.10] across 12 candidate genes and 10 of the 21 traits. We also detected a set of 7 markers that had elevated levels of differentiation between sampling sites situated across the Cascade crest in northeastern Washington. Marker effects were small (r2 < 0.05) and within the range of those published previously for forest trees. The derived SNP allele, as measured by a comparison to a recently diverged sister species, typically affected the phenotype in a way consistent with cold hardiness. The majority of markers were characterized as having largely nonadditive modes of gene action, especially underdominance in the case of cold-tolerance related phenotypes. We place these results in the context of trade-offs between the abilities to grow longer and to avoid fall cold damage, as well as putative epigenetic effects. These associations provide insight into the genetic components of complex traits in coastal Douglas fir, as well as highlight the need for landscape genetic approaches to the detection of adaptive genetic diversity.

Pacific Northwest Forest Tree Seed Zones: A Template for Native Plants?

Seed movement guidelines for restoration activities are lacking for most native grasses, forbs, and shrubs. The forestry community has decades of experience in establishing seed zones and seed movement guidelines that may be of value to restoration managers. We review the history of seed zone development in forest trees, with emphasis on the Pacific Northwest, and make some suggestions concerning seed transfer guidelines for other native plants.

Generalized provisional seed zones for native plants

Deploying well-adapted and ecologically appropriate plant materials is a core component of successful restoration projects. We have developed generalized provisional seed zones that can be applied to any plant species in the United States to help guide seed movement. These seed zones are based on the intersection of high-resolution climatic data for winter minimum temperature and aridity (as measured by annual heat : moisture index), each classified into discrete bands. This results in the delineation of 64 provisional seed zones for the continental United States. These zones represent areas of relative climatic similarity, and movement of seed within these zones should help to minimize maladaptation. Superimposing Omerniks level III ecoregions over these seed zones distinguishes areas that are similar climatically yet different ecologically. A quantitative comparison of provisional seed zones with level III ecoregions and provisional seed zones within ecoregions for three species showed that provisional seed zone within ecoregion often explained the greatest proportion of variation in a suite of traits potentially related to plant fitness. These provisional seed zones can be considered a starting point for guidelines for seed transfer, and should be utilized in conjunction with appropriate species-specific information as well as local knowledge of microsite differences.

Considerations for restoring temperate forests of tomorrow: Forest restoration, assisted migration, and bioengineering

Tomorrow’s forests face extreme pressures from contemporary climate change, invasive pests, and anthropogenic demands for other land uses. These pressures, collectively, demand land managers to reassess current and potential forest management practices. We discuss three considerations, functional restoration, assisted migration, and bioengineering, which are currently being debated in the literature and have the potential to be applied independently or concurrently across a variety of scales. The emphasis of functional restoration is to reestablish or maintain functions provided by the forest ecosystem, such as water quality, wildlife habitat, or carbon sequestration. Maintaining function may call upon actions such as assisted migration—moving tree populations within a species current range to aid adaptation to climate change or moving a species far outside its current range to avoid extinction—and we attempt to synthesize an array of assisted migration terminology. In addition, maintenance of species and the functions they provide may also require new technologies, such as genetic engineering, which, compared with traditional approaches to breeding for pest resistance, may be accomplished more rapidly to meet and overcome the challenges of invasive insect and disease pests. As managers develop holistic adaptive strategies to current and future anthropogenic stresses, functional restoration, assisted migration, and bioengineering, either separately or in combinations, deserve consideration, but must be addressed within the context of the restoration goal.

Mapping genetic variation and seed zones for Bromus carinatus in the Blue Mountains of eastern Oregon, USA

Seed transfer zones ensure that germplasm selected for restoration is suitable and sustainable in diverse environments. In this study, seed zones were developed for mountain brome (Bromus carinatus...

Growth phenology of coast Douglas-fir seed sources planted in diverse environments

The timing of periodic life cycle events in plants (phenology) is an important factor determining how species and populations will react to climate change. We evaluated annual patterns of basal-area and height growth of coast Douglas-fir (Pseudotusga menziesii var. menziesii (Mirb.) Franco) seedlings from four seed sources that were planted in four diverse environments as part of the Douglas-fir Seed-Source Movement Trial. Stem diameters and heights were measured periodically during the 2010 growing season on 16 open-pollinated families at each study installation. Stem diameters were measured on a subset of trees with electronic dendrometers during the 2010 and 2011 growing seasons. Trees from the four seed sources differed in phenology metrics that described the timing of basal-area and height-growth initiation, growth cessation and growth rates. Differences in the height-growth metrics were generally larger than differences in the basal-area growth metrics and differences among installations were larger than differences among seed sources, highlighting the importance of environmental signals on growth phenology. Variations in the height- and basal-area growth metrics were correlated with different aspects of the seed-source environments: precipitation in the case of height growth and minimum temperature in the case of basal-area growth. The detailed dendrometer measurements revealed differences in growth patterns between seed sources during distinct periods in the growing season. Our results indicate that multiple aspects of growth phenology should be considered along with other traits when evaluating adaptation of populations to future climates.

Incorporating genetic variation into a model of budburst phenology of coast Douglas-fir (Pseudotsuga menziesii var. menziesii)

Models to predict budburst and other phenological events in plants are needed to forecast how climate change may impact ecosystems and for the development of mitigation strategies. Differences among genotypes are important to predicting phenological events in species that show strong clinal variation in adaptive traits. We present a model that incorporates the effects of temperature and differences among genotypes to predict the timing of budburst of coast Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco). The main components of the model are (i) functions to calculate the accumulation of chilling units (CU) and forcing units (FU) during dormancy and (ii) a function defining the combinations of CU and FU needed for budburst (the possibility line). The possibility line was fit to data from 59 populations subjected to eight different winter environments. Differences among populations were incorporated into the possibility line using population coefficients that vary the FU required for budbu...

Risk of genetic maladaptation due to climate change in three major European tree species

Tree populations usually show adaptations to their local environments as a result of natural selection. As climates change, populations can become locally maladapted and decline in fitness. Evaluating the expected degree of genetic maladaptation due to climate change will allow forest managers to assess forest vulnerability, and develop strategies to preserve forest health and productivity. We studied potential genetic maladaptation to future climates in three major European tree species, Norway spruce (Picea abies), silver fir (Abies alba), and European beech (Fagus sylvatica). A common garden experiment was conducted to evaluate the quantitative genetic variation in growth and phenology of seedlings from 77 to 92 native populations of each species from across Switzerland. We used multivariate genecological models to associate population variation with past seed source climates, and to estimate relative risk of maladaptation to current and future climates based on key phenotypic traits and three regional climate projections within the A1B scenario. Current risks from climate change were similar to average risks from current seed transfer practices. For all three climate models, future risks increased in spruce and beech until the end of the century, but remained low in fir. Largest average risks associated with climate projections for the period 2061-2090 were found for spruce seedling height (0.64), and for beech bud break and leaf senescence (0.52 and 0.46). Future risks for spruce were high across Switzerland. However, areas of high risk were also found in drought-prone regions for beech and in the southern Alps for fir. Genetic maladaptation to future climates is likely to become a problem for spruce and beech by the end of this century, but probably not for fir. Consequently, forest management strategies should be adjusted in the study area for spruce and beech to maintain productive and healthy forests in the future.

Photoperiod cues and patterns of genetic variation limit phenological responses to climate change in warm parts of species’ range: Modeling diameter-growth cessation in coast Douglas-fir

Abstract The phenology of diameter‐growth cessation in trees will likely play a key role in mediating species and ecosystem responses to climate change. A common expectation is that warming will delay cessation, but the environmental and genetic influences on this process are poorly understood. We modeled the effects of temperature, photoperiod, and seed‐source climate on diameter‐growth‐cessation timing in coast Douglas‐fir (an ecologically and economically vital tree) using high‐frequency growth measurements across broad environmental gradients for a range of genotypes from different seed sources. Our model suggests that cool temperatures or short photoperiods can induce cessation in autumn. At cool locations (high latitude and elevation), cessation seems to be induced primarily by low temperatures in early autumn (under relatively long photoperiods), so warming will likely delay cessation and extend the growing season. But at warm locations (low latitude or elevation), cessation seems to be induced primarily by short photoperiods later in autumn, so warming will likely lead to only slight extensions of the growing season, reflecting photoperiod limitations on phenological shifts. Trees from seed sources experiencing frequent frosts in autumn or early winter tended to cease growth earlier in the autumn, potentially as an adaptation to avoid frost. Thus, gene flow into populations in warm locations with little frost will likely have limited potential to delay mean cessation dates because these populations already cease growth relatively late. In addition, data from an abnormal heat wave suggested that very high temperatures during long photoperiods in early summer might also induce cessation. Climate change could make these conditions more common in warm locations, leading to much earlier cessation. Thus, photoperiod cues, patterns of genetic variation, and summer heat waves could limit the capacity of coast Douglas‐fir to extend its growing season in response to climate change in the warm parts of its range. &NA; The phenology of tree diameter‐growth cessation in autumn is an important process that strongly impacts organism and ecosystem function, but its environmental and genetic drivers are poorly understood, impeding predictions of climate change impacts. As favorable growing conditions shift later into autumn with warming, trees would likely need to delay the timing of growth cessation to track favorable climate. We studied diameter‐growth cessation in coast Douglas‐fir (a foundation species) and found that cool temperatures or short photoperiods can induce cessation, implying that in cool parts of the range low temperatures primarily trigger cessation, while in warm parts short photoperiods are the primary cue. In addition, we found that trees from seed sources with higher frost frequencies tended to cease growth earlier. Thus, climate change will likely lead to strong shifts to later cessation in cool locations, but weak shifts in warm locations, reflecting photoperiod and genetic limitations on phenological responses. Figure. No caption available.

Linking phenotype, genotype and environment to unravel genetic components underlying cold hardiness in coastal Douglas-fir ( Pseudotsuga menziesii var. menziesii )

Global climate change may detrimentally affect future generations of numerous forest tree species, hampering their long-term sustainability if appropriate evolutionary responses remain lacking. To face these novel threats, conservation biologists are in need of a thorough understanding and identification of adaptive variation in key fitness traits. We here provide an elaborate synthesis of pre-existing and novel analyses of an association mapping, genecological and landscape genomic study integrating genotypic, environmental and phenotypic data to gain insights into the genetic basis of cold-hardiness adaptation in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii). Data were collected across part of the natural range for a total of 643 individuals. A landscape genomic approach revealed 28 putative non-neutral genes, although a variance partitioning analysis indicated only moderate power of this gene set in explaining cold-hardiness-related phenotypic variation, and suggests many important genes await discovery. Integrating these results within the entire phenotype-genotype-environment spectrum allowed us to delineate the six most promising candidate genes under selection. By combining genomic, phenotypic and environmental data, this study attempts to gain insights in the genetic basis of key adaptations, which may ultimately aid forestry managers to establish resilient ecosystems in face of future climate change.