Recent climate change should result in expansion of species to northern or high elevation range margins, and contraction at southern and low elevation margins in the northern hemisphere, because of local extirpations or range shifts or both. We combined museum occurrence records from both the continental U.S. and Mexico with a new eco-physiological model of extinction developed for lizard families of the world to predict the distributions of 30 desert -endemic reptile and amphibian species under climate change scenarios. The model predicts that 38 % of local populations will go extinct in the next 50 years, across all 30 species. However, extinctions may be attenuated in forested sites and by the presence of montane environments in contemporary ranges. Of the 30 species, three were at very high risk of extinction as a result of their thermal limits being exceeded, which illustrates the predictive value of ecophysiological modeling approaches for conservation studies. In tandem with global strategies of limiting CO2 emissions, we propose urgent regional management strategies for existing and new reserves that are targeted at three species: Barred Tiger Salamander (Ambystomatidae: Ambystoma mavortium stebbinsi), Desert Short -horned Lizard (Phrynosomatidae: Phrynosoma ornatissimum), and Morafka's Desert Tortoise (Testudinidae: Gopherus morafkai), which face a high risk of extinction by 2070. These strategies focus on assisted migration and preservation within climatic refugia, such as high -elevation and forested habitats. We forecast where new reserves should be established by merging our model of extinction risk with gap analysis. We also highlight that acclimation (i.e., phenotypic plasticity) could ameliorate risk of extinction but is rarely included in ecophysiological models. We use Ambystoma salamanders to show how acclimation can be incorporated into such models of extinction risk.

The fundamental trade-off between current and future reproduction has long been considered to result in a tendency for species that can grow large to begin reproduction at a larger size. Due to the prolonged time required to reach maturity, estimates of tree maturation size remain very rare and we lack a global view on the generality and the shape of this trade-off. Using seed production from five continents, we estimate tree maturation sizes for 486 tree species spanning tropical to boreal climates. Results show that a species' maturation size increases with maximum size, but in a non-proportional way: the largest species begin reproduction at smaller sizes than would be expected if maturation were simply proportional to maximum size. Furthermore, the decrease in relative maturation size is steepest in cold climates. These findings on maturation size drivers are key to accurately represent forests' responses to disturbance and climate change.

Multispecies interbreeding networks, or syngameons, have been increasingly reported in natural systems. However, the formation, structure, and maintenance of syngameons have received little attention. Through gene flow, syngameons can increase genetic diversity, facilitate the colonization of new environments, and contribute to hybrid speciation. In this study, we evaluated the history, patterns, and consequences of hybridization in a pinyon pine syngameon using morphological and genomic data to assess genetic structure, demographic history, and geographic and climatic data to determine niche differentiation. We demonstrated that Pinus edulis, a dominant species in the Southwestern US and a barometer of climate change, is a core participant in the syngameon, involved in the formation of two drought-adapted hybrid lineages including the parapatric and taxonomically controversial fallax-type. We found that species remain morphologically and genetically distinct at range cores, maintaining species boundaries while undergoing extensive gene flow in areas of sympatry at range peripheries. Our study shows that sequential hybridization may have caused relatively rapid speciation and facilitated the colonization of different niches, resulting in the rapid formation of two new lineages. Participation in the syngameon may allow adaptive traits to be introgressed across species barriers and provide the changes needed to survive future climate scenarios.

The benefits of masting (volatile, quasi-synchronous seed production at lagged intervals) include satiation of seed predators, but these benefits come with a cost to mutualist pollen and seed dispersers. If the evolution of masting represents a balance between these benefits and costs, we expect mast avoidance in species that are heavily reliant on mutualist dispersers. These effects play out in the context of variable climate and site fertility among species that vary widely in nutrient demand. Meta-analyses of published data have focused on variation at the population scale, thus omitting periodicity within trees and synchronicity between trees. From raw data on 12 million tree-years worldwide, we quantified three components of masting that have not previously been analysed together: (i) volatility, defined as the frequency-weighted year-to-year variation; (ii) periodicity, representing the lag between high-seed years; and (iii) synchronicity, indicating the tree-to-tree correlation. Results show that mast avoidance (low volatility and low synchronicity) by species dependent on mutualist dispersers explains more variation than any other effect. Nutrient-demanding species have low volatility, and species that are most common on nutrient-rich and warm/wet sites exhibit short periods. The prevalence of masting in cold/dry sites coincides with climatic conditions where dependence on vertebrate dispersers is less common than in the wet tropics. Mutualist dispersers neutralize the benefits of masting for predator satiation, further balancing the effects of climate, site fertility and nutrient demands. A new method to quantify three masting components from individual tree-years has revealed that globally, masting is uncommon in tree species that depend on mutualist dispersers, with its distribution further mediated by climate and nutrient availability.

Natural plant populations often exhibit marked differences in gene expression patterns that can reflect heterogeneity in selective pressures. Analyzing gene expression as a quantitative trait provides a unique opportunity to evaluate the underlying genomic basis of a plethora of traits and their interactions in driving adaptive evolution. We investigated patterns and processes driving expression differentiation under conditions mimicking future climates by combining common garden experiments with transcriptome-wide datasets obtained from hybrid populations of Pinus strobiformis and P. flexilis. We found strong signals of genotype-environment interactions (GEI) at the individual transcript and the co-expression module levels suggesting a marked influence of drought related variables on adaptive evolution. Overall, survival was positively associated with P. flexilis ancestry, but it exhibited an environment-specific pattern. Co-expression modules exhibiting strong associations with survival and genomic ancestry were representative of similar functional categories across both gardens. Using network topology measures, putatively adaptive garden-specific expression traits were pleiotropic and belonged to modules exhibiting high population differentiation yet low preservation across gardens. Overall, our study suggests the presence of substantial genetic variation underlying univariate and multivariate traits in novel climates that may enable populations of long-lived forest trees to respond to rapid shifts in climatic conditions in early seedling stages when mortality tends to be the highest. Our finding of pleiotropic trait architectures underlying adaptive traits, however, implies rapid adaptive responses to changing selection pressures depend on whether trait covariances align with the direction of change in selection pressures.

Tree fecundity and recruitment have not yet been quantified at scales needed to anticipate biogeographic shifts in response to climate change. By separating their responses, this study shows coherence across species and communities, offering the strongest support to date that migration is in progress with regional limitations on rates. The southeastern continent emerges as a fecundity hotspot, but it is situated south of population centers where high seed production could contribute to poleward population spread. By contrast, seedling success is highest in the West and North, serving to partially offset limited seed production near poleward frontiers. The evidence of fecundity and recruitment control on tree migration can inform conservation planning for the expected long-term disequilibrium between climate and forest distribution.

The relationships that control seed production in trees are fundamental to understanding the evolution of forest species and their capacity to recover from increasing losses to drought, fire, and harvest. A synthesis of fecundity data from 714 species worldwide allowed us to examine hypotheses that are central to quantifying reproduction, a foundation for assessing fitness in forest trees. Four major findings emerged. First, seed production is not constrained by a strict trade-off between seed size and numbers. Instead, seed numbers vary over ten orders of magnitude, with species that invest in large seeds producing more seeds than expected from the 1:1 trade-off. Second, gymnosperms have lower seed production than angiosperms, potentially due to their extra investments in protective woody cones. Third, nutrient-demanding species, indicated by high foliar phosphorus concentrations, have low seed production. Finally, sensitivity of individual species to soil fertility varies widely, limiting the response of community seed production to fertility gradients. In combination, these findings can inform models of forest response that need to incorporate reproductive potential.

Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our study unravelled the genetic architecture of adaptive evolution in a conifer hybrid zone formed between Pinus strobiformis and P. flexilis. Using a multifaceted approach emphasising the spatial and environmental patterns of linkage disequilibrium and ancestry enrichment, we identified recently introgressed and background genetic variants to be driving adaptive evolution along different environmental gradients. Specifically, recently introgressed variants from P. flexilis were favoured along freeze-related environmental gradients, while background variants were favoured along water availability-related gradients. We posit that such mosaics of allelic variants within conifer hybrid zones will confer upon them greater resilience to ongoing and future environmental change and can be a key resource for conservation efforts.

Despite its importance for forest regeneration, food webs, and human economies, changes in tree fecundity with tree size and age remain largely unknown. The allometric increase with tree diameter assumed in ecological models would substantially overestimate seed contributions from large trees if fecundity eventually declines with size. Current estimates are dominated by overrepresentation of small trees in regression models. We combined global fecundity data, including a substantial representation of large trees. We compared size-fecundity relationships against traditional allometric scaling with diameter and two models based on crown architecture. All allometric models fail to describe the declining rate of increase in fecundity with diameter found for 80% of 597 species in our analysis. The strong evidence of declining fecundity, beyond what can be explained by crown architectural change, is consistent with physiological decline. A downward revision of projected fecundity of large trees can improve the next generation of forest dynamic models.

Abstract Seedling emergence, survival, morphological and physiological traits, and oxidative stress resistance of southwestern white pine (Pinus strobiformis Engelm.) were studied in response to warming treatments applied during embryogenesis, germination, and early seedling growth. Daytime air temperature surrounding cones in tree canopies was warmed by +2.1°C during embryo development. Resulting seeds and seedlings were assigned to three thermal regimes in growth chambers, with each regime separated by 4°C to encompass the wide range of temperatures observed over space and time across the species’ range, plus the effect of heat waves coupled with a high carbon emissions scenario of climate warming. The embryo warming treatment reduced percent seedling emergence in all germination and growth environments and reduced mortality of seedlings grown in the warmest environment. Warm thermal regimes during early seedling growth increased subsequent seedling resistance to oxidative stress and transpirational water use. Experimental warming during seed development, germination, and seedling growth affected seedling emergence and survival. Oxidative stress resistance, morphology, and water relations were affected only by warming imposed during germination and seedling growth. This work explores potential outcomes of climate warming on multiple dimensions of seedling performance and uniquely illustrates that plant responses to heat vary with plant developmental stage in addition to the magnitude of temperature change.

SummaryVariation in gene expression among natural populations are key contributors to adaptive evolution. Understanding the architecture underlying adaptive trait evolution provides insights into the adaptive potential of populations exposed to novel selective pressures.We investigated patterns and processes driving trait differentiation under novel climatic conditions by combining common garden experiments with transcriptome-wide datasets obtained from Pinus strobiformis - Pinus flexilis hybrid zone populations.We found strong signals of genotype-environment interactions at the individual transcript and the co-expression module level, a marked influence of drought related variables on adaptive evolution and an environment dependent influence of P. flexilis ancestry on survival. Using co-expression network connectivity as a proxy for pleiotropy we highlight that adaptive transcripts were pleiotropic across both gardens and modules with strong population differentiation exhibited lower preservation across gardens.Our work highlights the utility of integrating transcriptomics with space-for-time substitution studies to evaluate the adaptive potential of long-lived species. We conclude by suggesting that the combination of pleiotropic trait architectures and substantial genetic variation may enable long-lived forest tree species to respond to rapid shift in climatic conditions.

Background Forest dieback driven by rapid climate warming threatens ecosystems worldwide. The health of forested ecosystems depends on how tree species respond to warming during all life history stages. While it is known that seed development is temperature-sensitive, little is known about possible effects of climate warming on seed development and subsequent seedling performance. Exposure of seeds to high air temperatures may influence subsequent seedling performance negatively, though conversely, warming during seed development may aid acclimation of seedlings to subsequent thermal stress. Technical challenges associated with in-situ warming of developing tree seeds limit understanding of how tree species may respond to seed development in a warmer climate. Results We developed and validated a simple method for passively warming seeds as they develop in tree canopies to enable controlled study of climate warming on seedling performance. We quantified thermal effects of the cone-warming method across individual pine trees and stands by measuring the air temperature surrounding seed cones using thermal loggers and the temperature of seed cone tissue using thermocouples. We then investigated seedling phenotypes in relation to the warming method through a common garden study. We assessed seedling morphology, physiology, and mycorrhizal nodulation in response to experimental cone-warming in 20 seed-source-tree canopies on the San Francisco Peaks in northern Arizona, USA. The warming method increased air temperature surrounding developing seed cones by 2.1 °C, a plausible increase in mean air temperature by 2050 under current climate projections. Notable effect sizes of cone-warming were detected for seedling root length, shoot length, and diameter at root collar using Cohen’s Local f 2 . Root length was affected most by cone-warming, but effect sizes of cone-warming on root length and diameter at root collar became negligible after the first year of growth. Cone-warming had small but significant effects on mycorrhizal fungal richness and seedling multispectral near-infrared indices indicative of plant health. Conclusions The method was shown to reliably elevate the temperature surrounding seed cones and thereby facilitate experimental in-situ climate warming research on forest trees. The method was furthermore shown to influence plant traits that may affect seedling performance under climate warming.

We subjected southwestern white pine (Pinus strobiformis Engelm.) seeds to controlled warming treatments to study responses of seed and seedling demographics, and morphological and physiological traits following warming during embryogenesis, germination, and early seedling growth. Daytime air temperature surrounding cones in tree canopies was warmed by +2.1 ◦C during embryo development. Resulting seeds and seedlings were assigned to three thermal regimes in growth chambers, with each regime separated by 4 ◦C. The embryo-warming treatment reduced percent seedling emergence in all germination and growth environments and reduced mortality of seedlings grown in the warmest environment. Warm thermal regimes during early seedling growth increased seedling resistance to oxidative stress and seedling transpirational water use even after applying cooler temperatures and experimental drought. Experimental warming imposed during seed development affected seedling demographic processes, and warming imposed during germination and seedling growth affected stress resistance and water relations. This work illustrates that the study of numerous ecophysiological and functional trait responses to various types of stress across multiple plant developmental stages is essential for understanding the effects of climate warming on forest regeneration processes.

We are studying the ecological and evolutionary processes affecting the geographical distribution of southwestern white pine (SWWP; Pinus strobiformis), an important tree species of the Southwestern USA and Mexico. Southwestern white pine viability is threatened by changing climate and an invasive tree disease, white pine blister rust (caused by the fungal pathogen, Cronartium ribicola). Rapid climate change is negatively affecting SWWP by increasing heat and drought stress, and thus challenging its ability to adapt. White pine blister rust causes extensive tree decline and mortality, including in SWWP. The dual threats of climate change and invasive species make forecasting future tree distributions at continental scales an urgent challenge. The goal of our project is to determine how gene movement among populations, adaptation to disease and drought, heritable changes beyond DNA mutations, and a changing environment interact to govern the success of SWWP. We are utilizing and developing tools to help forecast and manage the future of the species, including those from genomics, common gardens, tree disease resistance testing, engineering, and technology innovation to measure drought tolerance and physiological response. Results will be synthesized and included in cutting-edge landscape genomics models to meet our overarching goal. We will present our framework and current project status, including results. Completed products include development of landscape genomic models, a species distribution model incorporating climate change, and adaptive trait, phenotype plasticity, and genomic variation analyses. Continuing work incorporates these aspects in addition to transgenerational plasticity research and a genome-wide association study.

In forestry, common garden experiments traditionally require manual measurements and visual inspections. Unmanned aircraft systems (UAS) are a newer method of monitoring plants that is potentially more efficient than traditional techniques. This study had two objectives: to assess the size and mortality of Pinus strobiformis Engelm. seedlings using UAS and to predict the second-year seedling size using manual measurements from the first year and from UAS size estimates. Raised boxes containing 150 seedlings were surveyed twice, one year apart, using multispectral UAS. Seedling heights and diameters at root collar (DRC) were measured manually in both years. We found that size estimates made using a vegetation mask were suitable predictors for size, while spectral indices were not. Furthermore, we provided evidence that inclusion of UAS size estimates as predictors improves the fit of the models. Our study suggests that common variables used in forest monitoring are not necessarily best suited for seedlings. Therefore, we created a new variable, called the longitudinal area (height × DRC), which proved to be a significant predictor for both height and DRC. Finally, we demonstrate that seedling mortality can be effectively measured from remotely sensed data, which is useful for common garden and regeneration studies.

Southwestern white pine (Pinus strobiformis Engelm.) faces dual threats of climate change shifting its environmental niche and mortality due to a nonnative, invasive fungal pathogen. To inform efforts to sustain this species, we established experimental field trials in three common gardens along an elevational gradient with drought treatments to assess trait responses in southwestern white pine. We measured predawn and midday water potential on 44 maternal families from 10 populations at each garden. We used regression between predawn and midday water potentials to estimate hydroscape area, an index of stomatal regulation of transpiration. We measured leaf carbon isotope ratio and estimated carbon isotope discrimination and leaf mass per area to understand the effects of gardens and treatments on stomatal aperture and leaf structure. Water stress caused by experimental drought and temperature decreased leaf carbon isotope discrimination and leaf mass per area, indicating formation of thin leaves with low stomatal conductance in response to heat and drought. The hydroscape area of southwestern white pine suggests tight control of transpiration via stomatal closure, similar to other isohydric pines. Families with greater stomatal closure (inferred from carbon isotope ratio) at the warm, dry garden had higher survival than other families, suggesting an important role of isohydry in acclimation of southwestern white pine to expected habitat drying and warming.

We implemented multilocus selection in a spatially-explicit, individual-based framework that enables multivariate environmental gradients to drive selection in many loci as a new module for the landscape genetics programs, CDPOP and CDMetaPOP. Our module simulates multilocus selection using a linear additive model, providing a flexible platform to evaluate a wide range of genotype-environment associations. Importantly, the module allows simulation of selection in any number of loci under the influence of any number of environmental variables. We validated the module with individual-based selection simulations under Wright-Fisher assumptions. We then evaluated results for simulations under a simple landscape selection model. Next, we simulated individual-based multilocus selection across a complex selection landscape with three loci linked to three different environmental variables. Finally, we demonstrated how the program can be used to simulate multilocus selection under varying selection strengths across different levels of gene flow in a landscape genetics framework. This new module provides a valuable addition to the study of landscape genetics, allowing for explicit evaluation of the contributions and interactions between gene flow and selection-driven processes across complex, multivariate environmental and landscape conditions.

Worldwide, trees are confronting increased temperature and aridity, exacerbating susceptibility to herbivory. Long-term studies comparing patterns of plant performance through drought can help identify variation among and within populations in vulnerability to climate change and herbivory. We use long-term monitoring data to examine our overarching hypothesis that the negative impacts of poor soil and herbivore susceptibility would be compounded by severe drought. We studied pinyon pine, Pinus edulis, a widespread southwestern tree species that has suffered extensive climate-change related mortality. We analyzed data on mortality, growth, male reproduction, and herbivory collected for 14-32 years in three areas with distinct soil-types. We used standardized precipitation-evapotranspiration index (SPEI) as a climate proxy that summarizes the impacts of drought due to precipitation and temperature variation on semi-arid forests. Several key findings emerged: (1) Plant performance measurements did not support our hypothesis that trees growing in stressful, coarse-textured soils would suffer more than trees growing in finer-textured soils. Stem growth at the area with coarse, young cinder soils (area one) responded only weakly to drought, while stem growth on more developed soils with sedimentary (area two) and volcanic (area three) substrates, was strongly negatively affected by drought. Male reproduction declined less with drought at area one and more at areas two and three. Overall mortality was 30% on coarse cinder soils (area one) and averaged 55% on finer soil types (areas two and three). (2) Although moth herbivore susceptible trees were hypothesized to suffer more with drought than moth resistant trees, the opposite occurred. Annual stem growth was negatively affected by drought for moth resistant trees, but much less strongly for moth susceptible trees. (3) In contrast to our hypothesis, moths declined with drought. Overall, chronically water-stressed and herbivore-susceptible trees had smaller declines in performance relative to less-stressed trees during drought years. These long-term findings support the idea that stressed trees might be more resistant to drought since they may have adapted or acclimated to resist drought-related mortality.