A genetics-based Universal Community Transfer Function for predicting the impacts of climate change on future communities

Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts

Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here, we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (Populus angustifolia) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) P. angustifolia is differentiated into six genetic groups across its range from México to Canada and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically informed ecological niche models (gENMs) outperformed the standard species-level ENM (3-14% increase in AUC; 1-23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species' capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, P. fremontii. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly "adaptive management" approach to support conservation genetic management of species facing global change.

Intraspecific trait variation across elevation predicts a widespread tree species' climate niche and range limits

Global change is widely altering environmental conditions which makes accurately predicting species range limits across natural landscapes critical for conservation and management decisions. If climate pressures along elevation gradients influence the distribution of phenotypic and genetic variation of plant functional traits, then such trait variation may be informative of the selective mechanisms and adaptations that help define climatic niche limits. Using extensive field surveys along 16 elevation transects and a large common garden experiment, we tested whether functional trait variation could predict the climatic niche of a widespread tree species (Populus angustifolia) with a double quantile regression approach. We show that intraspecific variation in plant size, growth, and leaf morphology corresponds with the species' total climate range and certain climatic limits related to temperature and moisture extremes. Moreover, we find evidence of genetic clines and phenotypic plasticity at environmental boundaries, which we use to create geographic predictions of trait variation and maximum values due to climatic constraints across the western US. Overall, our findings show the utility of double quantile regressions for connecting species distributions and climate gradients through trait-based mechanisms. We highlight how new approaches like ours that incorporate genetic variation in functional traits and their response to climate gradients will lead to a better understanding of plant distributions as well as identifying populations anticipated to be maladapted to future environments.

Eco-evolutionary community turnover following environmental change

Co-occurring species often differ in intraspecific genetic diversity, which in turn can affect adaptation in response to environmental change. Specifically, the simultaneous evolutionary responses of co-occurring species to temporal environmental change may influence community dynamics. Local adaptation along environmental gradients combined with gene flow can enhance genetic diversity of traits within populations. Quantitative genetic theory shows that having greater gene flow results in (a) lower equilibrium population size due to maladaptive immigrant genotypes (migration load), but (b) faster adaptation to changing environments. Here, I build off this theory to study community dynamics of locally adapted species in response to temporal environmental changes akin to warming temperatures. Although an abrupt environmental change leaves all species initially maladapted, high gene flow species subsequently adapt faster due to greater genetic diversity. As a result, species can transiently reverse their relative abundances, but sometimes only after long lag periods. If constant temporal environmental change is applied, the community exhibits a shift toward stable dominance by species with intermediate gene flow. Notably, fast-adapting high gene flow species can increase in absolute abundance under environmental change (although often only for a transient period) because the change suppresses superior competitors with lower gene flow. This eco-evolutionary competitive release stabilizes ecosystem function. The eco-evolutionary community turnover studied here parallels the purely ecological successional dynamics following disturbances. My results demonstrate how interspecific variation in life history can have far-reaching impacts on eco-evolutionary community response to environmental change.

Climate-driven reduction of genetic variation in plant phenology alters soil communities and nutrient pools

We examined the hypothesis that climate-driven evolution of plant traits will influence associated soil microbiomes and ecosystem function across the landscape. Using a foundation tree species, Populus angustifolia, observational and common garden approaches, and a base population genetic collection that spans 17 river systems in the western United States, from AZ to MT, we show that (a) as mean annual temperature (MAT) increases, genetic and phenotypic variation for bud break phenology decline; (b) soil microbiomes, soil nitrogen (N), and soil carbon (C) vary in response to MAT and conditioning by trees; and (c) with losses of genetic variation due to warming, population-level regulation of community and ecosystem functions strengthen. These results demonstrate a relationship between the potential evolutionary response of populations and subsequent shifts in ecosystem function along a large temperature gradient.

Common garden experiments disentangle plant genetic and environmental contributions to ectomycorrhizal fungal community structure

The interactions among climate change, plant genetic variation and fungal mutualists are poorly understood, but probably important to plant survival under drought. We examined these interactions by studying the ectomycorrhizal fungal (EMF) communities of pinyon pine seedlings (Pinus edulis) planted in a wildland ecosystem experiencing two decades of climate change-related drought. We established a common garden containing P. edulis seedlings of known maternal lineages (drought tolerant, DT; drought intolerant, DI), manipulated soil moisture and measured EMF community structure and seedling growth. Three findings emerged: EMF community composition differed at the phylum level between DT and DI seedlings, and diversity was two-fold greater in DT than in DI seedlings. EMF communities of DT seedlings did not shift with water treatment and were dominated by an ascomycete, Geopora sp. By contrast, DI seedlings shifted to basidiomycete dominance with increased moisture, demonstrating a lineage by environment interaction. DT seedlings grew larger than DI seedlings in high (28%) and low (50%) watering treatments. These results show that inherited plant traits strongly influence microbial communities, interacting with drought to affect seedling performance. These interactions and their potential feedback effects may influence the success of trees, such as P. edulis, in future climates.

Genetic-Based Susceptibility of a Foundation Tree to Herbivory Interacts With Climate to Influence Arthropod Community Composition, Diversity, and Resilience

Understanding how genetic-based traits of plants interact with climate to affect associated communities will help improve predictions of climate change impacts on biodiversity. However, few community-level studies have addressed such interactions. Pinyon pine (Pinus edulis) in the southwestern U.S. shows genetic-based resistance and susceptibility to pinyon needle scale (Matsucoccus acalyptus). We sought to determine if susceptibility to scale herbivory influenced the diversity and composition of the extended community of 250+ arthropod species, and if this influence would be consistent across consecutive years, an extreme drought year followed by a moderate drought year. Because scale insects alter the architecture of susceptible trees, it is difficult to separate the direct influences of susceptibility on arthropod communities from the indirect influences of scale-altered tree architecture. To separate these influences, scales were experimentally excluded from susceptible trees for 15 years creating susceptible trees with the architecture of resistant trees, hereafter referred to as scale-excluded trees. Five patterns emerged. (1) In both years, arthropod abundance was 3-4X lower on susceptible trees compared to resistant and scale-excluded trees. (2) Species accumulation curves show that alpha and gamma diversity were 2-3X lower on susceptible trees compared to resistant and scale-excluded trees. (3) Reaction norms of arthropod richness and abundance on individual tree genotypes across years showed genotypic variation in the community response to changes in climate. (4) The genetic-based influence of susceptibility on arthropod community composition is climate dependent. During extreme drought, community composition on scale-excluded trees resembled susceptible trees indicating composition was strongly influenced by tree genetics independent of tree architecture. However, under moderate drought, community composition on scale-excluded trees resembled resistant trees indicating traits associated with tree architecture became more important. (5) One year after extreme drought, the arthropod community rebounded sharply. However, there was a much greater rebound in richness and abundance on resistant compared to susceptible trees suggesting that reduced resiliency in the arthropod community is associated with susceptibility. These results argue that individual genetic-based plant-herbivore interactions can directly and indirectly impact community-level diversity, which is modulated by climate. Understanding such interactions is important for assessing the impacts of climate change on biodiversity.

Bud phenology and growth are subject to divergent selection across a latitudinal gradient in Populus angustifolia and impact adaptation across the distributional range and associated arthropods

Temperate forest tree species that span large geographical areas and climatic gradients often have high levels of genetic variation. Such species are ideal for testing how neutral demographic factors and climate‐driven selection structure genetic variation within species, and how this genetic variation can affect ecological communities. Here, we quantified genetic variation in vegetative phenology and growth traits in narrowleaf cottonwood, Populus angustifolia, using three common gardens planted with genotypes originating from source populations spanning the species' range along the Rocky Mountains of North America (ca. 1700 km). We present three main findings. First, we found strong evidence of divergent selection (Q_ST > F_ST) on fall phenology (bud set) with adaptive consequences for frost avoidance. We also found evidence for selection on bud flush duration, tree height, and basal diameter, resulting in population differentiation. Second, we found strong associations with climate variables that were strongly correlated with latitude of origin. More strongly differentiated traits also showed stronger climate correlations, which emphasizes the role that climate has played in divergent selection throughout the range. We found population × garden interaction effects; for some traits, this accounted for more of the variance than either factor alone. Tree height was influenced by the difference in climate of the source and garden locations and declined with increasing transfer distance. Third, growth traits were correlated with dependent arthropod community diversity metrics. Synthesis. Overall, we conclude that climate has influenced genetic variation and structure in phenology and growth traits and leads to local adaptation in P. angustifolia, which can then impact dependent arthropod species. Importantly, relocation of genotypes far northward or southward often resulted in poor growth, likely due to a phenological mismatch with photoperiod, the proximate cue for fall growth cessation. Genotypes moved too far southward suffer from early growth cessation, whereas those moved too far northward are prone to fall frost and winter dieback. In the face of current and forecasted climate change, habitat restoration, forestry, and tree breeding efforts should utilize these findings to better match latitudinal and climatic source environments with management locations for optimal future outcomes.

Plants adapted to warmer climate do not outperform regional plants during a natural heat wave

With ongoing climate change, many plant species may not be able to adapt rapidly enough, and some conservation experts are therefore considering to translocate warm‐adapted ecotypes to mitigate effects of climate warming. Although this strategy, called assisted migration, is intuitively plausible, most of the support comes from models, whereas experimental evidence is so far scarce. Here we present data on multiple ecotypes of six grassland species, which we grew in four common gardens in Germany during a natural heat wave, with temperatures 1.4–2.0°C higher than the long‐term means. In each garden we compared the performance of regional ecotypes with plants from a locality with long‐term summer temperatures similar to what the plants experienced during the summer heat wave. We found no difference in performance between regional and warm‐adapted plants in four of the six species. In two species, regional ecotypes even outperformed warm‐adapted plants, despite elevated temperatures, which suggests that translocating warm‐adapted ecotypes may not only lack the desired effect of increased performance but may even have negative consequences. Even if adaptation to climate plays a role, other factors involved in local adaptation, such as biotic interactions, may override it. Based on our results, we cannot advocate assisted migration as a universal tool to enhance the performance of local plant populations and communities during climate change.

Species Introductions and Their Cascading Impacts on Biotic Interactions in desert riparian ecosystems

Desert riparian ecosystems of North America are hotspots of biodiversity that support many sensitive species, and are in a region experiencing some of the highest rates of climatic alteration in North America. Fremont cottonwood, Populus fremontii, is a foundation tree species of this critical habitat, but it is threatened by global warming and regional drying, and by a non-native tree/shrub, Tamarix spp., all of which can disrupt the mutualism between P. fremontii and its beneficial mycorrhizal fungal communities. Specialist herbivorous leaf beetles (Diorhabda spp.) introduced for biocontrol of Tamarix are altering the relationship between this shrub and its environment. Repeated episodic feeding on Tamarix foliage by Diorhabda results in varying rates of dieback and mortality, depending on genetic variation in allocation of resources, growing conditions, and phenological synchrony between herbivore and host plant. In this article, we review the complex interaction between climatic change and species introductions and their combined impacts on P. fremontii and their associated communities. We anticipate that (1) certain genotypes of P. fremontii will respond more favorably to the presence of Tamarix and to climatic change due to varying selection pressures to cope with competition and stress; (2) the ongoing evolution of Diorhabda's life cycle timing will continue to facilitate its expansion in North America, and will over time enhance herbivore impact to Tamarix; (3) defoliation by Diorhabda will reduce the negative impact of Tamarix on P. fremontii associations with mycorrhizal fungi; and (4) spatial variability in climate and climatic change will modify the capacity for Tamarix to survive episodic defoliation by Diorhabda, thereby altering the relationship between Tamarix and P. fremontii, and its associated mycorrhizal fungal communities. Given the complex biotic/abiotic interactions outlined in this review, conservation biologists and riparian ecosystem managers should strive to identify and conserve the phenotypic traits that underpin tolerance and resistance to stressors such as climate change and species invasion. Such efforts will greatly enhance conservation restoration efficacy for protecting P. fremontii forests and their associated communities.

Incorporating climate change and exotic species into forecasts of riparian forest distribution

We examined the impact climate change (CC) will have on the availability of climatically suitable habitat for three native and one exotic riparian species. Due to its increasing prevalence in arid regions throughout the western US, we predicted that an exotic species, Tamarix, would have the greatest increase in suitable habitat relative to native counterparts under CC. We used an ecological niche model to predict range shifts of Populus fremontii, Salix gooddingii, Salix exigua and Tamarix, from present day to 2080s, under five general circulation models and one climate change scenario (A1B). Four major findings emerged. 1) Contrary to our original hypothesis, P. fremontii is projected to have the greatest increase in suitable habitat under CC, followed closely by Tamarix. 2) Of the native species, S. gooddingii and S. exigua showed the greatest loss in predicted suitable habitat due to CC. 3) Nearly 80 percent of future P. fremontii and Salix habitat is predicted to be affected by either CC or Tamarix by the 2080s. 4) By the 2080s, 20 percent of S. gooddingii habitat is projected to be affected by both Tamarix and CC concurrently, followed by S. exigua (19 percent) and P. fremontii (13 percent). In summary, while climate change alone will negatively impact both native willow species, Tamarix is likely to affect a larger portion of all three native species' distributions. We discuss these and other results in the context of prioritizing restoration and conservation efforts to optimize future productivity and biodiversity. As we are accounting for only direct effects of CC and Tamarix on native habitat, we present a possible hierarchy of effects- from the direct to the indirect- and discuss the potential for the indirect to outweigh the direct effects. Our results highlight the need to account for simultaneous challenges in the face of CC.

Species-level view of population structure and gene flow for a critically endangered primate (Varecia variegata)

Lemurs are among the world's most threatened mammals. The critically endangered black-and-white ruffed lemur (Varecia variegata), in particular, has recently experienced rapid population declines due to habitat loss, ecological sensitivities to habitat degradation, and extensive human hunting pressure. Despite this, a recent study indicates that ruffed lemurs retain among the highest levels of genetic diversity for primates. Identifying how this diversity is apportioned and whether gene flow is maintained among remnant populations will help to diagnose and target conservation priorities. We sampled 209 individuals from 19 sites throughout the remaining V. variegata range. We used 10 polymorphic microsatellite loci and ∼550 bp of mtDNA sequence data to evaluate genetic structure and population dynamics, including dispersal patterns and recent population declines. Bayesian cluster analyses identified two distinct genetic clusters, which optimally partitioned data into populations occurring on either side of the Mangoro River. Localities north of the Mangoro were characterized by greater genetic diversity, greater gene flow (lower genetic differentiation) and higher mtDNA haplotype and nucleotide diversity than those in the south. Despite this, genetic differentiation across all sites was high, as indicated by high average F ST (0.247) and ΦST (0.544), and followed a pattern of isolation-by-distance. We use these results to suggest future conservation strategies that include an effort to maintain genetic diversity in the north and restore connectivity in the south. We also note the discordance between patterns of genetic differentiation and current subspecies taxonomy, and encourage a re-evaluation of conservation management units moving forward.

Convergence in mycorrhizal fungal communities due to drought, plant competition, parasitism, and susceptibility to herbivory: consequences for fungi and host plants

Plants and mycorrhizal fungi influence each other's abundance, diversity, and distribution. How other biotic interactions affect the mycorrhizal symbiosis is less well understood. Likewise, we know little about the effects of climate change on the fungal component of the symbiosis or its function. We synthesized our long-term studies on the influence of plant parasites, insect herbivores, competing trees, and drought on the ectomycorrhizal fungal communities associated with a foundation tree species of the southwestern United States, pinyon pine (Pinus edulis), and described how these changes feed back to affect host plant performance. We found that drought and all three of the biotic interactions studied resulted in similar shifts in ectomycorrhizal fungal community composition, demonstrating a convergence of the community towards dominance by a few closely related fungal taxa. Ectomycorrhizal fungi responded similarly to each of these stressors resulting in a predictable trajectory of community disassembly, consistent with ecological theory. Although we predicted that the fungal communities associated with trees stressed by drought, herbivory, competition, and parasitism would be poor mutualists, we found the opposite pattern in field studies. Our results suggest that climate change and the increased importance of herbivores, competitors, and parasites that can be associated with it, may ultimately lead to reductions in ectomycorrhizal fungal diversity, but that the remaining fungal community may be beneficial to host trees under the current climate and the warmer, drier climate predicted for the future.

Climate relicts and their associated communities as natural ecology and evolution laboratories

Climate relicts, marginal populations that have become isolated via climate-driven range shifts, preserve ecological and evolutionary histories that can span millennia. Studies point to climate relicts as 'natural laboratories' for investigating how long-term environmental change impacts species and populations. However, we propose that such research should be expanded to reveal how climate change affects 'interacting' species in ways that reshape community composition and evolution. Biotic interactions and their community and ecosystem effects are often genetically based and driven by associations with foundation species. We discuss evolution in climate relicts within the context of the emerging fields of community and ecosystem genetics, exploring the idea that foundation relicts are also natural community and ecosystem laboratories and windows to future landscapes.