Natural selection and climate change: temperature-linked spatial and temporal trends in gene frequency in Fagus sylvatica

Immigration and seasonal bottlenecks: high inbreeding despite high genetic diversity in an oscillating population of Culicoides sonorensis (Diptera: Ceratopogonidae)

Most population genetic studies concern spatial genetic differentiation, but far fewer aim at analyzing the temporal genetic changes that occur within populations. Vector species, including mosquitoes and biting midges, are often characterized by oscillating adult population densities, which may affect their dispersal, selection, and genetic diversity over time. Here, we used a population of Culicoides sonorensis from a single site in California to investigate short-term (intra-annual) and long-term (inter-annual) temporal variation in genetic diversity over a 3 yr period. This biting midge species is the primary vector of several viruses affecting both wildlife and livestock, thus a better understanding of the population dynamics of this species can help inform epidemiological studies. We found no significant genetic differentiation between months or years, and no correlation between adult populations and the inbreeding coefficient (FIS). However, we show that repeated periods of low adult abundance during cooler winter months resulted in recurring bottleneck events. Interestingly, we also found a high number of private and rare alleles, which suggests both a large, stable population, as well as a constant influx of migrants from nearby populations. Overall, we showed that the high number of migrants maintains a high level of genetic diversity by introducing new alleles, while this increased diversity is counterbalanced by recurrent bottleneck events potentially purging unfit alleles each year. These results highlight the temporal influences on population structure and genetic diversity in C. sonorensis and provide insight into factors effecting genetic variation that may occur in other vector species with fluctuating populations.

Warming appears as the main risk of non-adaptedness for western Mediterranean relict fir forests under expected climate change scenarios

Circum-Mediterranean firs are considered among the most drought-sensitive species to climate change. Understanding the genetic basis of trees' adaptive capacity and intra-specific variability to drought avoidance is mandatory to define conservation measures, thus potentially preventing their extinction. We focus here on Abies pinsapo and Abies marocana, both relict tree species, endemic from south Spain and north Morocco, respectively. A total of 607 samples were collected from eight nuclei: six from Spanish fir and two from Moroccan fir. A genotyping by sequencing technique called double digestion restriction site-associated DNA sequencing (ddRAD-seq) was performed to obtain a genetic matrix based on single-nucleotide polymorphisms (SNPs). This matrix was utilized to study the genetic structure of A. pinsapo populations and to carry out selection signature studies. In order to understand how Spanish fir and Moroccan fir cope with climate change, genotype-environment associations (GEAs) were identified. Further, the vulnerability of these species to climate variations was estimated by the risk of non-adaptedness (RONA). The filtering of the de novo assembly of A. pinsapo provided 3,982 SNPs from 504 out of 509 trees sequenced. Principal component analysis (PCA) genetically separated Grazalema from the rest of the Spanish populations. However, FST values showed significant differences among the sampling points. We found 51 loci potentially under selection. Homolog sequences were found for some proteins related to abiotic stress response, such as dehydration-responsive element binding transcription factor, regulation of abscisic acid signaling, and methylation pathway. A total of 15 associations with 11 different loci were observed in the GEA studies, with the maximum temperature of the warmest month being the variable with the highest number of associated loci. This temperature sensitivity was also supported by the risk of non-adaptedness, which yielded a higher risk for both A. pinsapo and A. marocana under the high emission scenario (Representative Concentration Pathway (RCP) 8.5). This study sheds light on the response to climate change of these two endemic species.

Assessment of Genetic Diversity and Genetic Structure of Saussurea medusa (Asteraceae), a "Sky Island" Plant in the Qinghai-Tibet Plateau, Using SRAP Markers

Saussurea medusa Maxim. is a typical "sky island" species and one with the highest altitude distributions among flowering plants. The present study aimed at analyzing the genetic diversity and population structure of 300 S. medusa accessions collected from 20 populations in the Qilian Mountains in the northeastern Qinghai-Tibet Plateau (QTP), using sequence-related amplified polymorphism (SRAP) markers. A total of 14 SRAP primer combinations were employed to analyze genetic diversity and population structure across all accessions. Out of 511 amplified bands, 496 (97.06%) were polymorphic. The populations in the eastern Qilian Mountains had significantly higher genetic diversity than those in the central and western groups. Population structure analysis revealed greater genetic differentiation among populations with a Gst of 0.4926. UPGMA-based clustering classified the 300 S. medusa accessions into 3 major clusters, while the Bayesian STRUCTURE analysis categorized them into 2 groups. Correlation analyses showed that the genetic affinity of the populations was based on differences in geographical distance, moisture conditions, and photothermal conditions between the habitats. This study represents the first comprehensive genetic assessment of S. medusa and provides important genetic baseline data for the conservation of the species.

Genome-environment associations along elevation gradients in two snowbed species of the North-Eastern Calcareous Alps

BACKGROUND

Anthropogenic climate change leads to increasing temperatures and altered precipitation and snowmelt patterns, especially in alpine ecosystems. To understand species' responses to climate change, assessment of genetic structure and diversity is crucial as the basis for the evaluation of migration patterns, genetic adaptation potential as well as the identification of adaptive alleles.

RESULTS

We studied genetic structure, diversity and genome-environment associations of two snowbed species endemic to the Eastern Alps with a large elevational range, Achillea clusiana Tausch and Campanula pulla L. Genotyping-by-sequencing was employed to assemble loci de novo, call variants and perform population genetic analyses. Populations of either species were distinguishable by mountain, and to some extent by elevation. We found evidence for gene flow between elevations. Results of genome-environment associations suggested similar selective pressures acting on both species, emanating mainly from precipitation and exposition rather than temperature.

CONCLUSIONS

Given their genetic structure and amount of gene flow among populations the two study species are suitable to serve as a model for genetic monitoring of climate change adaptation along an elevation gradient. Consequences of climate change will predominantly manifest via changes in precipitation and, thus, duration of snow cover in the snowbeds and indirectly via shrub encroachment accompanied by increasing shading of snowbeds at lower range margins. Assembling genomes of the study species and studying larger sample sizes and time series will be necessary to functionally characterize and validate the herein identified genomic loci putatively involved in adaptive processes.

Big data help to define climate change challenges for the typical Mediterranean species Cistus ladanifer L

Climate change’s huge impact on Mediterranean species’ habitat suitability and spatial and temporal distribution in the coming decades is expected. The present work aimed to reconstruct rockrose (Cistus ladanifer L.) historical and future spatial distribution, a typically Mediterranean species with abundant occurrence in North Africa, Iberian Peninsula, and Southern France. The R ensemble modeling approach was made using the biomod2 package to assess changes in the spatial distribution of the species in the Last Interglacial (LIG), the Last Glacial Maximum (LGM), and the Middle Holocene (MH), in the present, and in the future (for the years 2050 and 2070), considering two Representative Concentration Pathways (RCP 4.5 and RCP 8.5). The current species potential distribution was modeled using 2,833 occurrences, six bioclimatic variables, and four algorithms, Generalized Linear Model (GLM), MaxEnt, Multivariate Adaptive Regression Splines (MARS), and Artificial Neural Networks (ANN). Two global climate models (GCMs), CCSM4 and MRI-CGCM3, were used to forecast past and future suitability. The potential area of occurrence of the species is equal to 15.8 and 14.1% of the study area for current and LIG conditions, while it decreased to 3.8% in the LGM. The species’ presence diaminished more than half in the RCP 4.5 (to 6.8% in 2050 and 7% in 2070), and a too low figure (2.2%) in the worst-case scenario (RCP 8.5) for 2070. The results suggested that the current climatic conditions are the most suitable for the species’ occurrence and that future changes in environmental conditions may lead to the loss of suitable habitats, especially in the worst-case scenario. The information unfolded by this study will help to understand future predictable desertification in the Mediterranean region and to help policymakers to implement possible measures for biodiversity maintenance and desertification avoidance.

Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles

Quaternary climate fluctuations drove many species to shift their geographic ranges, in turn shaping their genetic structures. Recently, it has been argued that adaptation may have accompanied species range shifts via the "sieving" of genotypes during colonisation and establishment. However, this has not been directly demonstrated, and knowledge remains limited on how different evolutionary forces, which are typically investigated separately, interacted to jointly mediate species responses to past climatic change. Here, through whole-genome re-sequencing of over 1200 individuals of the carnation Dianthus sylvestris coupled with integrated population genomic and gene-environment models, we reconstruct the past neutral and adaptive landscape of this species as it was shaped by the Quaternary glacial cycles. We show that adaptive responses emerged concomitantly with the post-glacial range shifts and expansions of this species in the last 20 thousand years. This was due to the heterogenous sieving of adaptive alleles across space and time, as populations expanded out of restrictive glacial refugia into the broader and more heterogeneous range of habitats available in the present-day inter-glacial. Our findings reveal a tightly-linked interplay of migration and adaptation under past climate-induced range shifts, which we show is key to understanding the spatial patterns of adaptive variation we see in species today.

Genomic signals of local adaptation and hybridization in Asian white birch

Disentangling the numerous processes that affect patterns of genome-wide diversity in widespread tree species has important implications for taxonomy, conservation, and forestry. Here, we investigate the population genomic structure of Asian white birch (Betula platyphylla) in China and seek to explain it in terms of hybridization, demography and adaptation. We generate whole genome sequence data from 83 individuals across the species range in China. Combining this with an existing data set for 79 European and Russian white birches, we show a clear distinction between B. pendula and B. platyphylla, which have sometimes been lumped taxonomically. Genomic diversity of B. platyphylla in north-western China and Central Russia is affected greatly by hybridization with B. pendula. Excluding these hybridized populations, B. platyphylla in China has a linear distribution from north-eastern to south-western China, along the edge of the inland mountainous region. Within this distribution, three genetic clusters are found, which we model as long diverged with subsequent episodes of gene flow. Patterns of covariation between allele frequencies and environmental variables in B. platyphylla suggest the role of natural selection in the distribution of diversity at 7609 SNPs of which 3767 were significantly differentiated among the genetic clusters. The putative adaptive SNPs are distributed throughout the genome and span 1633 genic regions. Of these genic regions, 87 were previously identified as candidates for selective sweeps in Eurasian B. pendula. We use the 7609 environmentally associated SNPs to estimate the risk of nonadaptedness for each sequenced B. platyphylla individual under a scenario of future climate change, highlighting areas where populations may be under future threat from rising temperatures.

Modeling the effect of adaptation to future climate change on spring phenological trend of European beech (Fagus sylvatica L.)

Temperate trees could cope with climate change through phenotypic plasticity of phenological key events or adaptation in situ via selection on genetic variation. However, the relative contribution of local adaptation and phenotypic plasticity to phenological change is unclear for many ecologically important tree species. Here, we analyzed the leaf-out data of European beech (Fagus sylvatica L.) from 50 provenances planted in 7 trial sites. We first constructed a function between chilling accumulation (CA) and photoperiod-associated heat requirement (PHR) of leaf-out date for each provenance and quantified the relationship between parameters of the CA-PHR function and climatic variables at provenance origins by using the random forest model. Furthermore, we used the provenance-specific CA-PHR function to simulate future leaf-out dates under two climate change scenarios (RCP 4.5 and 8.5) and two assumptions (no adaptation and adaptation). The results showed that both CA, provenance, and their interactions affected the PHR of leaf-out. The provenances from southeastern Europe exhibited a stronger response of PHR to CA and thus flushed earlier than northwestern provenances. The parameters of the CA-PHR function were connected with climatic variables (e.g., mean diurnal temperature range, temperature seasonality) at the originating sites of each provenance. If only considering the phenotypic plasticity, the leaf-out date of European beech in 2070-2099 will advance by 6.8 and 9.0 days on average relative to 1951-2020 under RCP 4.5 and RCP 8.5, respectively. However, if F. sylvatica adapts to future climate change by adopting the current strategy, the advance of the leaf-out date will weaken by 1.4 and 3.4 days under RCP 4.5 and RCP 8.5, respectively. Our results suggest that the European beech could slow down its spring phenological advances and reduce its spring frost risk if it adopts the current strategy to adapt to future climate change.

Multi-Year Monitoring of Deciduous Forests Ecophysiology and the Role of Temperature and Precipitation as Controlling Factors

Two deciduous forest ecosystems, one dominated by Fagus sylvatica and a mixed one with Quercus cerris and Quercus frainetto, were monitored from an ecophysiological perspective during a five-year period, in order to assess seasonal fluctuations, establish links between phenology and ecophysiology, and reveal climatic controls. Field measurements of leaf area index (LAI), chlorophyll content, leaf specific mass (LSM), water potential (Ψ) and leaf photosynthesis (Aleaf) were performed approximately on a monthly basis. LAI, chlorophylls and LSM fluctuations followed a recurrent pattern yearly, with increasing values during spring leaf burst and expansion, relatively stable values during summer and decreasing values during autumn senescence. However, pre-senescence leaf fall and chlorophyll reductions were evident in the driest year. The dynamically responsive Aleaf and Ψ presented considerable inter-annual variation. Both oak species showed more pronounced depressions of Aleaf and Ψ compared to beech, yet the time-point of their appearance coincided and was the same for all species each year. Spring temperature had a positive role in the increasing phase of all ecophysiological processes while rising autumn temperature resulted in retarded senescence. Precipitation showed asymmetric effects on the measured ecophysiological parameters. The between-species differences in responses, climate sensitivity and climate memory are identified and discussed.

Reproduction and genetic diversity of Juniperus squamata along an elevational gradient in the Hengduan Mountains

Elevation plays a crucial factor in the distribution of plants, as environmental conditions become increasingly harsh at higher elevations. Previous studies have mainly focused on the effects of large-scale elevational gradients on plants, with little attention on the impact of smaller-scale gradients. In this study we used 14 microsatellite loci to survey the genetic structure of 332 Juniperus squamata plants along elevation gradient from two sites in the Hengduan Mountains. We found that the genetic structure (single, clonal, mosaic) of J. squamata shrubs is affected by differences in elevational gradients of only 150 m. Shrubs in the mid-elevation plots rarely have a clonal or mosaic structure compared to shrubs in lower- or higher-elevation plots. Human activity can significantly affect genetic structure, as well as reproductive strategy and genetic diversity. Sub-populations at mid-elevations had the highest yield of seed cones, lower levels of asexual reproduction and higher levels of genetic diversity. This may be due to the trade-off between elevational stress and anthropogenic disturbance at mid-elevation since there is greater elevational stress at higher-elevations and greater intensity of anthropogenic disturbance at lower-elevations. Our findings provide new insights into the finer scale genetic structure of alpine shrubs, which may improve the conservation and management of shrublands, a major vegetation type on the Hengduan Mountains and the Qinghai-Tibet Plateau.

Adaptation Strategies and Approaches for Managing Fire in a Changing Climate

As the effects of climate change accumulate and intensify, resource managers juggle existing goals and new mandates to operationalize adaptation. Fire managers contend with the direct effects of climate change on resources in addition to climate-induced disruptions to fire regimes and subsequent ecosystem effects. In systems stressed by warming and drying, increased fire activity amplifies the pace of change and scale of severe disturbance events, heightening the urgency for management action. Fire managers are asked to integrate information on climate impacts with their professional expertise to determine how to achieve management objectives in a changing climate with altered fire regimes. This is a difficult task, and managers need support as they incorporate climate adaptation into planning and operations. We present a list of adaptation strategies and approaches specific to fire and climate based on co-produced knowledge from a science–management partnership and pilot-tested in a two-day workshop with natural resource managers and regional stakeholders. This “menu” is a flexible and useful tool for fire managers who need to connect the dots between fire ecology, climate science, adaptation intent, and management implementation. It was created and tested as part of an adaptation framework used widely across the United States and should be applicable and useful in many fire-prone forest ecosystems.

Differentiation of Cold Tolerance in an Artificial Population of a Mangrove Species, Kandelia obovata, Is Associated With Geographic Origins

Temperature is one of the climatic factors that shape the geographic distribution of plant populations. Mangroves are temperature-sensitive plants, and their distributions are severely limited by low temperatures. It is unknown, however, to what extent temperature contributes to their population differentiation and evolution. Kandelia obovata (Rhizophoraceae) is a mangrove species with high cold tolerance in the Northern Hemisphere. We investigated the phenotypic responses of an artificial population of K. obovata, with plants transplanted from different source populations, to extremely low temperatures during winter of 2015-2016 in Yueqing County (28°20'N), Zhejiang Province of China. Using two binary traits, "with/without leaves alive on the branches" and "with/without alive buds on the tips of branches," we classified plants in this artificial population into strong, moderate and poor cold resistance groups. We further assessed the genetic diversity, structure and differentiation of these three groups, as well as five natural populations along a latitudinal gradient using ten nuclear and six plastid microsatellite markers. Microsatellite data revealed genetic differentiation among the natural populations along the latitudinal gradient. Molecular data indicated that the cold tolerance of three groups in the artificial population was associated with their geographic origins, and that the most cold-tolerant group came from the northernmost natural population. Our study thus indicates that natural populations of K. obovata may have evolved divergent capacity of cold tolerance.

Intriguing effects of selection intensity on the evolution of prosocial behaviors

In many models of evolving populations, genetic drift has an outsized role relative to natural selection, or vice versa. While there are many scenarios in which one of these two assumptions is reasonable, intermediate balances between these forces are also biologically relevant. In this study, we consider some natural axioms for modeling intermediate selection intensities, and we explore how to quantify the long-term evolutionary dynamics of such a process. To illustrate the sensitivity of evolutionary dynamics to drift and selection, we show that there can be a “sweet spot” for the balance of these two forces, with sufficient noise for rare mutants to become established and sufficient selection to spread. This balance allows prosocial traits to evolve in evolutionary models that were previously thought to be unconducive to the emergence and spread of altruistic behaviors. Furthermore, the effects of selection intensity on long-run evolutionary outcomes in these settings, such as when there is global competition for reproduction, can be highly non-monotonic. Although intermediate selection intensities (neither weak nor strong) are notoriously difficult to study analytically, they are often biologically relevant; and the results we report suggest that they can elicit novel and rich dynamics in the evolution of prosocial behaviors.

Theoretical models of populations have been useful for assessing when and how traits spread, in large part because they are simple. Rather than being used to reproduce empirical data, these idealized models involve relatively few parameters and are utilized to gain a qualitative understanding of what promotes or suppresses a trait. For prosocial traits, which entail a cost to self to help another, one thing that mathematical models often suggest is that competition to reproduce must be localized, meaning an individual must be fitter than just a small subset of the population in order to produce an offspring. We show here that this finding is not robust. Such traits can indeed proliferate when there is global competition for reproduction, which we demonstrate by increasing the degree to which payoffs from games affect birth rates. Since this kind of “stronger selection” has also been observed empirically, we discuss how it is incorporated into theoretical models more broadly.

Adaptive responses to temperature and precipitation variation at the early-life stages of Pinus sylvestris

Early-stage fitness variation has been seldom evaluated at broad scales in forest tree species, despite the long tradition of studying climate-driven intraspecific genetic variation. In this study, we evaluated the role of climate in driving patterns of population differentiation at early-life stages in Pinus sylvestris and explored the fitness and growth consequences of seed transfer within the species range. We monitored seedling emergence, survival and growth over a 2-yr period in a multi-site common garden experiment which included 18 European populations and spanned 25° in latitude and 1700 m in elevation. Climate-fitness functions showed that populations exhibited higher seedling survival and growth at temperatures similar to their home environment, which is consistent with local adaptation. Northern populations experienced lower survival and growth at warmer sites, contrary to previous studies on later life stages. Seed mass was higher in populations from warmer areas and was positively associated with survival and growth at more southern sites. Finally, we did not detect a survival-growth trade-off; on the contrary, bigger seedlings exhibited higher survival probabilities under most climatic conditions. In conclusion, our results reveal that contrasting temperature regimes have played an important role in driving the divergent evolution of P. sylvestris populations at early-life stages.

Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv

Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.

Differences in Thermal Tolerance between Parental Species Could Fuel Thermal Adaptation in Hybrid Wood Ants

AbstractGenetic variability is essential for adaptation and could be acquired via hybridization with a closely related lineage. We use ants to investigate thermal adaptation and the link between temperature and genetic variation arising from hybridization. We test for differences in cold and heat tolerance between Finnish Formica polyctena and Formica aquilonia wood ants and their naturally occurring hybrids. Using workers, we find that the parental individuals differ in both cold and heat tolerances and express thermal limits that reflect their global distributions. Hybrids, however, cannot combine thermal tolerance of parental species as they have the same heat tolerance as F. polyctena but not the same cold tolerance as F. aquilonia. We then focus on a single hybrid population to investigate the relationship between temperature variation and genetic variation across 16 years using reproductive individuals. On the basis of the thermal tolerance results, we expected the frequency of putative F. polyctena alleles to increase in warm years and F. aquilonia alleles to increase in cold years. We find support for this in hybrid males but not in hybrid females. These results contribute to understanding the outcomes of hybridization, which may be sex specific or depend on the environment. Furthermore, genetic variability resulting from hybridization could help hybrid wood ants cope with changing thermal conditions.

Genetic Diversity and Association Analysis among Germplasms of Diospyros kaki in Zhejiang Province Based on SSR Markers

In subtropical to temperate regions, persimmon (Diospyros kaki Thunb.) is an economically important fruit crop cultivated for its edible fruits. Persimmons are distributed abundantly and widely in Zhejiang Province, representing a valuable resource for the breeding of new cultivars and studying the origin and evolution of persimmon. In this study, we elucidated the genetic structures and diversity patterns of 179 persimmon germplasms from 16 different ecologic populations in Zhejiang Province based on the analysis of 17 SSR markers. The results show that there was a medium degree of genetic diversity for persimmon found in Zhejiang Province. With the exception of the Tiantai Mountain and Xin’an River populations, we found extensive gene exchange had occurred among the other populations. The 179 D. kaki germplasms from the 16 populations could be separated into three distinct clusters (I, II, and III) with a higher mean pairwise genetic differentiation index (FST) (0.2714). Nearly all samples of Cluster-I were distributed inland. Cluster-II and Cluster-III contained samples that were widely distributed throughout Zhejiang Province including all samples from the coastal populations and the Northeast Plain populations. In addition, we performed association mapping with nine traits (fruit crude fiber content, fruit calcium content, fruit water content, fruit longitudinal diameter, fruit aspect ratio, seed width, seed length, leaf aspect ratio, and number of lateral veins) using these markers. This led to the identification of 13 significant marker–trait associations (MTAs; p < 0.00044, 0.1/228) using a general linear model, of which, six MTAs with a correlation coefficient (R2) >10% were consistently represented in the general linear model with p < 0.00044 in the two models. The genetic structures and diversity patterns of the persimmon germplasms revealed in this study will provide a reference for the efficient conservation and further utilization of persimmon germplasms. The MTAs identified in this study will be useful for future marker-assisted breeding of persimmon.

Genomic vulnerability to rapid climate warming in a tree species with a long generation time

The ongoing increase in global temperature affects biodiversity, especially in mountain regions where climate change is exacerbated. As sessile, long-lived organisms, trees are especially challenged in terms of adapting to rapid climate change. Here, we show that low rates of allele frequency shifts in Swiss stone pine (Pinus cembra) occurring near the treeline result in high genomic vulnerability to future climate warming, presumably due to the species' long generation time. Using exome sequencing data from adult and juvenile cohorts in the Swiss Alps, we found an average rate of allele frequency shift of 1.23 × 10^-2 /generation (i.e. 40 years) at presumably neutral loci, with similar rates for putatively adaptive loci associated with temperature (0.96 × 10^-2 /generation) and precipitation (0.91 × 10^-2 /generation). These recent shifts were corroborated by forward-in-time simulations at neutral and adaptive loci. Additionally, in juvenile trees at the colonisation front we detected alleles putatively beneficial under a future warmer and drier climate. Notably, the observed past rate of allele frequency shift in temperature-associated loci was decidedly lower than the estimated average rate of 6.29 × 10^-2 /generation needed to match a moderate future climate scenario (RCP4.5). Our findings suggest that species with long generation times may have difficulty keeping up with the rapid climate change occurring in high mountain areas and thus are prone to local extinction in their current main elevation range.

Ecosystem Processes Show Uniform Sensitivity to Winter Soil Temperature Change Across a Gradient from Central to Cold Marginal Stands of a Major Temperate Forest Tree

The magnitude and frequency of soil frost events might increase in northern temperate regions in response to climate warming due to reduced insulation caused by declining snow cover. In temperate deciduous forests, increased soil frost severity can hamper tree growth and increase the mortality of fine roots, soil fauna and microorganisms, thus altering carbon and nutrient cycling. From single-site studies, however, it is unclear how the sensitivities of these responses change along continental gradients from regions with low to high snowfall. We conducted a gradient design snow cover and soil temperature manipulation experiment across a range of lowland beech forest sites to assess the site-specific sensitivity of tree growth and biogeochemical cycling to soil cooling. Even mild and inconsistent soil frost affected tree increment, germination, litter decomposition and the retention of added 15N. However, the sensitivity of response (treatment effect size per degree of warming or cooling) was not related to prevailing winter climate and snow cover conditions. Our results support that it may be valid to scale these responses to simulated winter climate change up from local studies to regional scales. This upscaling, however, needs to account for the fact that cold regions with historically high snowfall may experience increasingly harsh soil frost conditions, whereas in warmer regions with historically low snowfall, soil frost may diminish. Thus, despite the uniform biotic sensitivity of response, there may be opposing directions of winter climate change effects on temperate forests along continental temperature gradients due to different trends of winter soil temperature.

Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes

Signals of local adaptation have been found in many plants and animals, highlighting the heterogeneity in the distribution of adaptive genetic variation throughout species ranges. In the coming decades, global climate change is expected to induce shifts in the selective pressures that shape this adaptive variation. These changes in selective pressures will likely result in varying degrees of local climate maladaptation and spatial reshuffling of the underlying distributions of adaptive alleles. There is a growing interest in using population genomic data to help predict future disruptions to locally adaptive gene-environment associations. One motivation behind such work is to better understand how the effects of changing climate on populations’ short-term fitness could vary spatially across species ranges. Here we review the current use of genomic data to predict the disruption of local adaptation across current and future climates. After assessing goals and motivationsunderlying the approach, we review the main steps and associated statistical methods currently in use and explore our current understanding of the limits and future potential of using genomics to predict climate change (mal)adaptation.

Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis

BACKGROUND

Restrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely distributed throughout the Indian and Pacific Oceans including along the western, northern and eastern coastline of Australia, where it is an important aquaculture and fishery species. Understanding the genetic structure and the influence of environmental factors leading to adaptive differences among populations of this species is important for farm genetic improvement programs and sustainable fisheries management.

RESULTS

Based on 278 individuals obtained from seven geographically disparate Australian locations, 10,624 high-quality SNP loci were used to characterize genetic diversity, population structure, genetic connectivity, and adaptive divergence. Significant population structure and differentiation were revealed among wild populations (average F_ST = 0.001-0.107; p <  0.05). Eighty-nine putatively outlier SNPs were identified to be potentially associated with environmental variables by using both population differentiation (BayeScan and PCAdapt) and environmental association (redundancy analysis and latent factor mixed model) analysis methods. Clear population structure with similar spatial patterns were observed in both neutral and outlier markers with three genetically distinct groups identified (north Queensland, Northern Territory, and Western Australia). Redundancy, partial redundancy, and multiple regression on distance matrices analyses revealed that both geographical distance and environmental factors interact to generate the structure observed across Australian P. monodon populations.

CONCLUSION

This study provides new insights on genetic population structure of Australian P. monodon in the face of environmental changes, which can be used to advance sustainable fisheries management and aquaculture breeding programs.

Microgeographic adaptation and the effect of pollen flow on the adaptive potential of a temperate tree species

In species with long-distance dispersal capacities and inhabiting a large ecological niche, local selection and gene flow are expected to be major evolutionary forces affecting the genetic adaptation of natural populations. Yet, in species such as trees, evidence of microgeographic adaptation and the quantitative assessment of the impact of gene flow on adaptive genetic variation are still limited. Here, we used extensive genetic and phenotypic data from European beech seedlings collected along an elevation gradient, and grown in a common garden, to study the signature of selection on the divergence of eleven potentially adaptive traits, and to assess the role of gene flow in resupplying adaptive genetic variation. We found a significant signal of adaptive differentiation among plots separated by < 1 km, with selection acting on growth and phenological traits. Consistent with theoretical expectations, our results suggest that pollen dispersal contributes to increase genetic diversity for these locally differentiated traits. Our results thus highlight that local selection is an important evolutionary force in natural tree populations and suggest that management interventions to facilitate movement of gametes along short ecological gradients would boost genetic diversity of individual tree populations, and enhance their adaptive potential to rapidly changing environments.

Small spaces, big impacts: contributions of micro-environmental variation to population persistence under climate change

Individuals within natural populations can experience very different abiotic and biotic conditions across small spatial scales owing to microtopography and other micro-environmental gradients. Ecological and evolutionary studies often ignore the effects of micro-environment on plant population and community dynamics. Here, we explore the extent to which fine-grained variation in abiotic and biotic conditions contributes to within-population variation in trait expression and genetic diversity in natural plant populations. Furthermore, we consider whether benign microhabitats could buffer local populations of some plant species from abiotic stresses imposed by rapid anthropogenic climate change. If microrefugia sustain local populations and communities in the short term, other eco-evolutionary processes, such as gene flow and adaptation, could enhance population stability in the longer term. We caution, however, that local populations may still decline in size as they contract into rare microhabitats and microrefugia. We encourage future research that explicitly examines the role of the micro-environment in maintaining genetic variation within local populations, favouring the evolution of phenotypic plasticity at local scales and enhancing population persistence under global change.

Climate-associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Local adaptation patterns have been found in many plants and animals, highlighting the genetic heterogeneity of species along their range of distribution. In the next decades, global warming is predicted to induce a change in the selective pressures that drive this adaptive variation, forcing a reshuffling of the underlying adaptive allele distributions. For species with low dispersion capacity and long generation time such as trees, the rapidity of the change could impede the migration of beneficial alleles and lower their capacity to track the changing environment. Identifying the main selective pressures driving the adaptive genetic variation is thus necessary when investigating species capacity to respond to global warming. In this study, we investigate the adaptive landscape of Fagus sylvatica along a gradient of populations in the French Alps. Using a double-digest restriction-site-associated DNA (ddRAD) sequencing approach, we identified 7,000 SNPs from 570 individuals across 36 different sites. A redundancy analysis (RDA)-derived method allowed us to identify several SNPs that were strongly associated with climatic gradients; moreover, we defined the primary selective gradients along the natural populations of F. sylvatica in the Alps. Strong effects of elevation and humidity, which contrast north-western and south-eastern site, were found and were believed to be important drivers of genetic adaptation. Finally, simulations of future genetic landscapes that used these findings allowed identifying populations at risk for F. sylvatica in the Alps, which could be helpful for future management plans.

Geographical Gradients of Genetic Diversity and Differentiation among the Southernmost Marginal Populations of Abies sachalinensis Revealed by EST-SSR Polymorphism

Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than in central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and Methods: A total of 1189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations, namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were genetically differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.

Phenology and growth of Fagus sylvatica and Quercus robur seedlings in response to temperature variation in the parental versus offspring generation

Plants are known to respond to warming temperatures. Few studies, however, have included the temperature experienced by the parent plant in the experimental design, in spite of the importance of this factor for population dynamics. We investigated the phenological and growth responses of seedlings of two key temperate tree species (Fagus sylvatica and Quercus robur) to spatiotemporal temperature variation during the reproductive period (parental generation) and experimental warming of the offspring. To this end, we sampled oak and beech seedlings of different ages (1-5 years) from isolated mother trees and planted the seedlings in a common garden. Warming of the seedlings advanced bud burst in both species. In oak seedlings, higher temperatures experienced by mother trees during the reproductive period delayed bud burst in control conditions, but advanced bud burst in heated seedlings. In beech seedlings, bud burst timing advanced both with increasing temperatures during the reproductive period of the parents and with experimental warming of the seedlings. Relative diameter growth was enhanced in control oak seedlings but decreased with warming when the mother plant experienced higher temperatures during the reproductive period. Overall, oak displayed more plastic responses to temperatures than beech. Our results emphasise that temperature during the reproductive period can be a potential determinant of tree responses to climate change.

Gene Flow and Genetic Variation Explain Signatures of Selection across a Climate Gradient in Two Riparian Species

Many species occur across environmental gradients and it is expected that these species will exhibit some signals of adaptation as heterogeneous environments and localized gene flow may facilitate local adaptation. While riparian zones can cross climate gradients, many of which are being impacted by climate change, they also create microclimates for the vegetation, reducing environmental heterogeneity. Species with differing distributions in these environments provide an opportunity to investigate the importance of genetic connectivity in influencing signals of adaptation over relatively short geographical distance. Association analysis with genomic data was used to compare signals of selection to climate variables in two species that have differing distributions along a river traversing a climate gradient. Results demonstrate links between connectivity, standing genetic variation, and the development of signals of selection. In the restricted species, the combination of high gene flow in the middle and lower catchment and occurrence in a microclimate created along riverbanks likely mitigated the development of selection to most climatic variables. In contrast the more widely distributed species with low gene flow showed a stronger signal of selection. Together these results strengthen our knowledge of the drivers and scale of adaptation and reinforce the importance of connectivity across a landscape to maintain adaptive potential of plant species.

Do atmospheric CO2 concentration increase, climate and forest management affect iWUE of common beech? Evidences from carbon isotope analyses in tree rings

Beech is one of the most important forest tree species in Europe, hence possible adverse factors affecting its physiology and productivity can have strong ecological and economic impacts. In this context, four beech forests along a latitudinal gradient from southern Apennines to middle European lowlands were selected for chronological determinations of carbon isotope composition (δ13C) in tree-ring cellulose. The main objectives of this study were to assess (i) the effect of climate on the carbon signature of tree-ring cellulose (δ13C); (ii) the physiological response to recent CO2 concentration increment and to climatic variation; and (iii) the relationship between intrinsic water-use efficiency (iWUE, here the average long-term ratio of net photosynthesis to stomatal conductance) and growth of trees in different sites since 1950. Our results demonstrated that site climatic conditions peculiarly affect δ13C. In northern sites, a climatic control of summer precipitation and temperature on stomatal conductance was demonstrated by their opposite correlations with δ13C, negative and positive, respectively. Furthermore, an 'earliness effect' was suggested by a significant relationship between spring temperature and δ13C in the coldest sites and by a positive one between winter temperature and δ13C in the warmest ones. In all the study sites, during the maturity phase, a positive correlation between the increment of CO2 and iWUE was observed, due to an active response of trees to CO2 increment. This increment of CO2 was the main driver of the long term increasing trend of iWUE, resulting by an active response of trees to CO2 fertilization. Moreover, precipitation mostly influences positively and negatively the inter-annual variations of iWUE of the southernmost and northernmost sites, respectively. Overall, we observed a mean increment of 40% of iWUE. Moreover, the sensitivity of iWUE to the increase of CO2 was different between the northernmost and southernmost sites. Increasing iWUE was correlated to growth in the two sites during the release phase and we hypothesize a positive effect of silvicultural treatments.

Soil environment is a key driver of adaptation in Medicago truncatula: new insights from landscape genomics

Spatial differences in environmental selective pressures interact with the genomes of organisms, ultimately leading to local adaptation. Landscape genomics is an emergent research area that uncovers genome-environment associations, thus allowing researchers to identify candidate loci for adaptation to specific environmental variables. In the present study, we used latent factor mixed models (LFMMs) and Moran spectral outlier detection/randomization (MSOD-MSR) to identify candidate loci for adaptation to 10 environmental variables (climatic, soil and atmospheric) among 43 515 single nucleotide polymorphisms (SNPs) from 202 accessions of the model legume Medicago truncatula. Soil variables were associated with a large number of candidate loci identified through both LFMMs and MSOD-MSR. Genes tagged by candidate loci associated with drought and salinity are involved in the response to biotic and abiotic stresses, while those tagged by candidates associated with soil nitrogen and atmospheric nitrogen, participate in the legume-rhizobia symbiosis. Candidate SNPs identified through both LFMMs and MSOD-MSR explained up to 56% of variance in flowering traits. Our findings highlight the importance of soil in driving adaptation in the system and elucidate the basis of evolutionary potential of M. truncatula to respond to global climate change and anthropogenic disruption of the nitrogen cycle.

Invoking adaptation to decipher the genetic legacy of past climate change

Persistence of natural populations during periods of climate change is likely to depend on migration (range shifts) or adaptation. These responses were traditionally considered discrete processes and conceptually divided into the realms of ecology and evolution. In a milestone paper, Davis and Shaw (2001) Science 292:673 argued that the interplay of adaptation and migration was central to biotic responses to Quaternary climate, but since then there has been no synthesis of efforts made to set up this research program. Here we review some of the salient findings from molecular genetic studies assessing ecological and evolutionary responses to Quaternary climate change. These studies have revolutionized our understanding of population processes associated with past species migration. However, knowledge remains limited about the role of natural selection for local adaptation of populations to Quaternary environmental fluctuations and associated range shifts, and for the footprints this might have left on extant populations. Next-generation sequencing technologies, high-resolution paleoclimate analyses, and advances in population genetic theory offer an unprecedented opportunity to test hypotheses about adaptation through time. Recent population genomics studies have greatly improved our understanding of the role of contemporary adaptation to local environments in shaping spatial patterns of genetic diversity across modern-day landscapes. Advances in this burgeoning field provide important conceptual and methodological bases to decipher the historical role of natural selection and assess adaptation to past environmental variation. We suggest that a process called "temporal conditional neutrality" has taken place: some alleles favored in glacial environments become selectively neutral in modern-day conditions, whereas some alleles that had been neutral during glacial periods become under selection in modern environments. Building on this view, we present a new integrative framework for addressing the interplay of demographic and adaptive evolutionary responses to Quaternary climate dynamics, the research agenda initially envisioned by Davis and Shaw (2001) Science 292:673.

Seed origin and warming constrain lodgepole pine recruitment, slowing the pace of population range shifts

Understanding how climate warming will affect the demographic rates of different ecotypes is critical to predicting shifts in species distributions. Here, we present results from a common garden, climate change experiment in which we measured seedling recruitment of lodgepole pine, a widespread North American conifer that is also planted globally. Seeds from a low-elevation provenance had more than three-fold greater recruitment to their third year than seeds from a high-elevation provenance across sites within and above its native elevation range and across climate manipulations. Heating halved recruitment to the third year of both low- and high-elevation seed sources across the elevation gradient, while watering more than doubled recruitment, alleviating some of the negative effects of heating. Demographic models based on recruitment data from the climate manipulations and long-term observations of adult populations revealed that heating could effectively halt modeled upslope range expansion except when combined with watering. Simulating fire and rapid postfire forest recovery at lower elevations accelerated lodgepole pine expansion into the alpine, but did not alter final abundance rankings among climate scenarios. Regardless of climate scenario, greater recruitment of low-elevation seeds compensated for longer dispersal distances to treeline, assuming colonization was allowed to proceed over multiple centuries. Our results show that ecotypes from lower elevations within a species' range could enhance recruitment and facilitate upslope range shifts with climate change.

Life-History Traits Evolved Jointly with Climatic Niche and Disturbance Regime in the Genus Leucadendron (Proteaceae)

Organisms have evolved a diversity of life-history strategies to cope with variation in their environment. Persistence as adults and/or seeds across recruitment events allows species to dampen the effects of environmental fluctuations. The evolution of life cycles with overlapping generations should thus permit the colonization of environments with uncertain recruitment. We tested this hypothesis in Leucadendron (Proteaceae), a genus with high functional diversity native to fire-prone habitats in the South African fynbos. We analyzed the joint evolution of life-history traits (adult survival and seed-bank strategies) and ecological niches (climate and fire regime), using comparative methods and accounting for various sources of uncertainty. In the fynbos, species with canopy seed banks that are unable to survive fire as adults display nonoverlapping generations. In contrast, resprouters with an underground seed bank may be less threatened by extreme climatic events and fire intervals, given their iteroparity and long-lasting seed bank. Life cycles with nonoverlapping generations indeed jointly evolved with niches with less exposure to frost but not with those with less exposure to drought. Canopy seed banks jointly evolved with niches with more predictable fire return, compared to underground seed banks. The evolution of extraordinary functional diversity among fynbos plants thus reflects, at least in part, the diversity of both climates and fire regimes in this region.

Postglacial range expansion and the role of ecological factors in driving adaptive evolution of Musa basjoo var. formosana

Genetic variation evolves during postglacial range expansion of a species and is important for adapting to varied environmental conditions. It is crucial for the future survival of a species. We investigate the nuclear DNA sequence variation to provide evidence of postglacial range expansion of Musa basjoo var. formosana, a wild banana species, and test for adaptive evolution of amplified fragment length polymorphic (AFLP) loci underlying local adaptation in association with environmental variables. Postglacial range expansion was suggested by phylogeographical analyses based on sequence variation of the second intron of copper zinc superoxide dismutase 2 gene. Two glacial refugia were inferred by the average F_ST parameter (mean F_ST of a population against the remaining populations). Using variation partitioning by redundancy analysis, we found a significant amount of explained AFLP variation attributed to environmental and spatially-structured environmental effects. By combining genome scan methods and multiple univariate logistic regression, four AFLP loci were found to be strongly associated with environmental variables, including temperature, precipitation, soil moisture, wet days, and surface coverage activity representing vegetation greenness. These environmental variables may have played various roles as ecological drivers for adaptive evolution of M. basjoo var. formosana during range expansion after the last glacial maximum.

Discrimination of Picea chihuahuana Martinez populations on the basis of climatic, edaphic, dendrometric, genetic and population traits

Background

Picea chihuahuana, which is endemic to Mexico, is currently listed as “Endangered” on the Red List. Chihuahua spruce is only found in the Sierra Madre Occidental (SMO), Mexico. About 42,600 individuals are distributed in forty populations. These populations are fragmented and can be classified into three geographically distinct clusters in the SMO. The total area covered by P. chihuahuana populations is less than 300 ha. A recent study suggested assisted migration as an alternative to the ex situ conservation of P. chihuahuana, taking into consideration the genetic structure and diversity of the populations and the predictions regarding the future climate of the habitat. However, detailed background information is required to enable development of plans for protecting and conserving species and for successful assisted migration. Thus, it is important to identify differences between populations in relation to environmental conditions. The genetic diversity of populations, which affect vigor, evolution and adaptability of the species, must also be considered. In this study, we examined 14 populations of P. chihuahuana, with the overall aim of discriminating the populations and form clusters of this species.

Methods

Each population was represented by one 50 × 50 m plot established in the center of its respective location. Climate, soil, dasometric, density variables and genetic and species diversities were assessed in these plots for further analyses. The putatively neutral and adaptive AFLP markers were used to calculate genetic diversity. Affinity Propagation (AP) clustering technique and k-means clustering algorithm were used to classify the populations in the optimal number of clusters. Later stepwise binomial logistic regression was applied to test for significant differences in variables of the southern and northern P. chihuahuana populations. Spearman’s correlation test was used to analyze the relationships among all variables studied.

Results

The binomial logistic regression analysis revealed that seven climate variables, the geographical longitude and sand proportion in the soil separated the southern from northern populations. The northern populations grow in more arid and continental conditions and on soils with lower sand proportion. The mean genetic diversity using all AFLP studied of P. chihuahuana was significantly correlated with the mean temperature in the warmest month, where warmer temperatures are associated to larger genetic diversity. Genetic diversity of P. chihuahuana calculated with putatively adaptive AFLP was not statistically significantly correlated with any environmental factor.

Discussion

Future reforestation programs should take into account that at least two different groups (the northern and southern cluster) of P. chihuahuana exist, as local adaptation takes place because of different environmental conditions.

Continental divide: Predicting climate-mediated fragmentation and biodiversity loss in the boreal forest

Climate change threatens natural landscapes through shifting distribution and abundance of species and attendant change in the structure and function of ecosystems. However, it remains unclear how climate-mediated variation in species’ environmental niche space may lead to large-scale fragmentation of species distributions, altered meta-population dynamics and gene flow, and disrupted ecosystem integrity. Such change may be especially relevant when species distributions are restricted either spatially or to a narrow environmental niche, or when environments are rapidly changing. Here, we use range-wide environmental niche models to posit that climate-mediated range fragmentation aggravates the direct effects of climate change on species in the boreal forest of North America. We show that climate change will directly alter environmental niche suitability for boreal-obligate species of trees, birds and mammals (n = 12), with most species ranges becoming smaller and shifting northward through time. Importantly, species distributions will become increasingly fragmented, as characterized by smaller mean size and greater isolation of environmentally-suitable landscape patches. This loss is especially pronounced along the Ontario-Québec border, where the boreal forest is narrowest and roughly 78% of suitable niche space could disappear by 2080. Despite the diversity of taxa surveyed, patterns of range fragmentation are remarkably consistent, with our models predicting that spruce grouse (Dendragapus canadensis), boreal chickadee (Poecile hudsonicus), moose (Alces americanus) and caribou (Rangifer tarandus) could have entirely disjunct east-west population segments in North America. These findings reveal potentially dire consequences of climate change on population continuity and species diversity in the boreal forest, highlighting the need to better understand: 1) extent and primary drivers of anticipated climate-mediated range loss and fragmentation; 2) diversity of species to be affected by such change; 3) potential for rapid adaptation in the most strongly-affected areas; and 4) potential for invasion by replacement species.

Substantial heritable variation for susceptibility to Dothistroma septosporum within populations of native British Scots pine (Pinus sylvestris)

The threat from pests and pathogens to native and commercially planted forest trees is unprecedented and expected to increase under climate change. The degree to which forests respond to threats from pathogens depends on their adaptive capacity, which is determined largely by genetically controlled variation in susceptibility of the individual trees within them and the heritability and evolvability of this trait. The most significant current threat to the economically and ecologically important species Scots pine (Pinus sylvestris) is dothistroma needle blight (DNB), caused by the foliar pathogen Dothistroma septosporum. A progeny-population trial of 4-year-old Scots pine trees, comprising six populations from native Caledonian pinewoods each with three to five families in seven blocks, was artificially inoculated using a single isolate of D. septosporum. Susceptibility to D. septosporum, assessed as the percentage of non-green needles, was measured regularly over a period of 61 days following inoculation, during which plants were maintained in conditions ideal for DNB development (warm; high humidity; high leaf wetness). There were significant differences in susceptibility to D. septosporum among families indicating that variation in this trait is heritable, with high estimates of narrow-sense heritability (0.38-0.75) and evolvability (genetic coefficient of variation, 23.47). It is concluded that native Scots pine populations contain sufficient genetic diversity to evolve lower susceptibility to D. septosporum through natural selection in response to increased prevalence of this pathogen.

Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe

BACKGROUND

Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales.

METHODS

A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical 'within-site' approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM).

RESULTS

HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species' southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches.

CONCLUSION

Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales.

AFLP Genome Scanning Reveals Divergent Selection in Natural Populations of Liriodendron chinense (Magnoliaceae) along a Latitudinal Transect

Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci) provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined Amplified Fragment Length Polymorphism (AFLP) genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae) along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Both frequency-based (Dfdist and BayeScan) and correlation-based (MLM) methods were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity toward the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation, and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies.

Detecting long-term metabolic shifts using isotopomers: CO2-driven suppression of photorespiration in C3 plants over the 20th century

Terrestrial vegetation currently absorbs approximately a third of anthropogenic CO2 emissions, mitigating the rise of atmospheric CO2. However, terrestrial net primary production is highly sensitive to atmospheric CO2 levels and associated climatic changes. In C3 plants, which dominate terrestrial vegetation, net photosynthesis depends on the ratio between photorespiration and gross photosynthesis. This metabolic flux ratio depends strongly on CO2 levels, but changes in this ratio over the past CO2 rise have not been analyzed experimentally. Combining CO2 manipulation experiments and deuterium NMR, we first establish that the intramolecular deuterium distribution (deuterium isotopomers) of photosynthetic C3 glucose contains a signal of the photorespiration/photosynthesis ratio. By tracing this isotopomer signal in herbarium samples of natural C3 vascular plant species, crops, and a Sphagnum moss species, we detect a consistent reduction in the photorespiration/photosynthesis ratio in response to the ∼100-ppm CO2 increase between ∼1900 and 2013. No difference was detected in the isotopomer trends between beet sugar samples covering the 20th century and CO2 manipulation experiments, suggesting that photosynthetic metabolism in sugar beet has not acclimated to increasing CO2 over >100 y. This provides observational evidence that the reduction of the photorespiration/photosynthesis ratio was ca. 25%. The Sphagnum results are consistent with the observed positive correlations between peat accumulation rates and photosynthetic rates over the Northern Hemisphere. Our results establish that isotopomers of plant archives contain metabolic information covering centuries. Our data provide direct quantitative information on the "CO2 fertilization" effect over decades, thus addressing a major uncertainty in Earth system models.

Adapting through glacial cycles: insights from a long-lived tree (Taxus baccata)

Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long-lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation-by-distance) and selective (isolation-by-adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present-day patterns of genetic diversity.

Rapid genetic divergence in response to 15 years of simulated climate change

Genetic diversity may play an important role in allowing individual species to resist climate change, by permitting evolutionary responses. Our understanding of the potential for such responses to climate change remains limited, and very few experimental tests have been carried out within intact ecosystems. Here, we use amplified fragment length polymorphism (AFLP) data to assess genetic divergence and test for signatures of evolutionary change driven by long-term simulated climate change applied to natural grassland at Buxton Climate Change Impacts Laboratory (BCCIL). Experimental climate treatments were applied to grassland plots for 15 years using a replicated and spatially blocked design and included warming, drought and precipitation treatments. We detected significant genetic differentiation between climate change treatments and control plots in two coexisting perennial plant study species (Festuca ovina and Plantago lanceolata). Outlier analyses revealed a consistent signature of selection associated with experimental climate treatments at individual AFLP loci in P. lanceolata, but not in F. ovina. Average background differentiation at putatively neutral AFLP loci was close to zero, and genomewide genetic structure was associated neither with species abundance changes (demography) nor with plant community-level responses to long-term climate treatments. Our results demonstrate genetic divergence in response to a suite of climatic environments in reproductively mature populations of two perennial plant species and are consistent with an evolutionary response to climatic selection in P. lanceolata. These genetic changes have occurred in parallel with impacts on plant community structure and may have contributed to the persistence of individual species through 15 years of simulated climate change at BCCIL.