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Despite an increased focus on multiscale relationships and interdisciplinary integration, few macroecological studies consider the contribution of genetic-based processes to landscape-scale patterns. We test the hypothesis that tree genetics, climate, and geography jointly drive continental-scale patterns of community structure, using genome-wide SNP data from a broadly distributed foundation tree species (Populus fremontii S. Watson) and two dependent communities (leaf-modifying arthropods and fungal endophytes) spanning southwestern North America. Four key findings emerged: (1) Tree genetic structure was a significant predictor for both communities; however, the strength of influence was both scale- and community-dependent. (2) Tree genetics was the primary driver for endophytes, explaining 17% of variation in continental-scale community structure, whereas (3) climate was the strongest predictor of arthropod structure (24%). (4) Power to detect tree genotype—community phenotype associations changed with scale of genetic organization, increasing from individuals to populations to ecotypes, emphasizing the need to consider nonstationarity (i.e., changes in the effects of factors on ecological processes across scales) when inferring macrosystem properties. Our findings highlight the role of foundation tree species as drivers of macroscale community structure and provide macrosystems ecology with a theoretical framework for linking fine- and intermediate-scale genetic processes to landscape-scale patterns. Management of the genetic diversity harbored within foundation species is a critical consideration for conserving and sustaining regional biodiversity. 

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 betweenPinus strobiformisandP. 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 fromP. flexiliswere 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.

 

An assumption of correlative landscape genetic methods is that genetic differentiation at neutral markers arises solely from the degree to which the intervening landscape between individuals or populations resists gene flow. However, this assumption is violated when gene flow occurs into the sampled population from an unsampled, differentiated deme. This may happen when sampling within only a portion of a population's extent or when closely related species hybridize with the sampled population. In both cases, violation of the modelling assumptions has the potential to reduce landscape genetic model selection accuracy and result in poor inferences. We used individual‐based population genetic simulations in complex landscapes within a model selection framework to explore the potential confounding effect of gene flow from unsampled demes. We hypothesized that as gene flow from outside the sampling extent increased, model selection accuracy would decrease due to the formation of a hybrid zone where allele frequencies were perturbed in a way that was not correlated with effective distances between sampled individuals. Surprisingly, we found this expectation was unfounded, because the reduced accuracy due to admixture was counteracted by an increase in allelic diversity as alleles spread from the unsampled deme into the sampled population. These new alleles increased the power to detect landscape genetic relationships and even slightly improving model selection accuracy overall. This is a reassuring result, suggesting that sampling the full extent of a population or related species that may hybridize may be unnecessary, as long as other well‐established sampling requirements are met.

 

The coordination of traits from individual organs to whole plants is under strong selection because of environmental constraints on resource acquisition and use. However, the tight coordination of traits may provide underlying mechanisms of how locally adapted plant populations can become maladapted because of climate change.

To better understand local adaptation in intraspecific trait coordination, we studied trait variability in the widely distributed foundation tree species,Populus fremontiiusing a common garden near the mid‐elevational point of this species distribution. We examined 28 traits encompassing four spectra: phenology, leaf economic spectrum (LES), whole‐tree architecture (Corner's Rule) and wood economic spectrum (WES).

Based on adaptive syndrome theory, we hypothesized that trait expression would be coordinated among and within trait spectra, reflecting local adaptation to either exposure to freeze‐thaw conditions in genotypes sourced from high‐elevation populations or exposure to extreme thermal stress in genotypes sourced from low‐elevation populations.

High‐elevation genotypes expressed traits within the phenology and WES that limit frost exposure and tissue damage. Specifically, genotypes sourced from high elevations had later mean budburst, earlier mean budset, higher wood densities, higher bark fractions and smaller xylem vessels than their low‐elevation counterparts. Conversely, genotypes sourced from low elevations expressed traits within the LES that prioritized hydraulic efficiency and canopy thermal regulation to cope with extreme heat exposure, including 40% smaller leaf areas, 67% higher stomatal densities and 34% higher mean theoretical maximum stomatal conductance. Low‐elevation genotypes also expressed a lower stomatal control over leaf water potentials that subsequently dropped to pressures that could induce hydraulic failure.

Synthesis. Our results suggest thatPopulus fremontiiexpresses a high degree of coordination across multiple trait spectra to adapt to local climate constraints on photosynthetic gas exchange, growth and survival. These results, therefore, increase our mechanistic understanding of local adaptation and the potential effects of climate change that in turn, improves our capacity to identify genotypes that are best suited for future restoration efforts.

 

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.

 

A lack of optimal gene combinations, as well as low levels of genetic diversity, is often associated with the formation of species range margins. Conservation efforts rely on predictive modelling using abiotic variables and assessments of genetic diversity to determine target species and populations for controlled breeding, germplasm conservation and assisted migration. Biotic factors such as interspecific competition and hybridization, however, are largely ignored, despite their prevalence across diverse taxa and their role as key evolutionary forces. Hybridization between species with well‐developed barriers to reproductive isolation often results in the production of offspring with lower fitness. Generation of novel allelic combinations through hybridization, however, can also generate positive fitness consequences. Despite this possibility, hybridization‐mediated introgression is often considered a threat to biodiversity as it can blur species boundaries. The contribution of hybridization towards increasing genetic diversity of populations at range margins has only recently gathered attention in conservation studies. We assessed the extent to which hybridization contributes towards range dynamics by tracking spatio‐temporal changes in the central location of a hybrid zone between two recently diverged species of pines:Pinus strobiformisandP. flexilis. By comparing geographic cline centre estimates for global admixture coefficient with morphological traits associated with reproductive output, we demonstrate a northward shift in the hybrid zone. Using a combination of spatially explicit, individual‐based simulations and linkage disequilibrium variance partitioning, we note a significant contribution of adaptive introgression towards this northward movement, despite the potential for differences in regional population size to aid hybrid zone movement. Overall, our study demonstrates that hybridization between recently diverged species can increase genetic diversity and generate novel allelic combinations. These novel combinations may allow range margin populations to track favourable climatic conditions or facilitate adaptive evolution to ongoing and future climate change.

 

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 betweenPinus strobiformisandPinus 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.