DNA methylation is environment-sensitive and can mediate stress responses. In long-lived trees, changing environments might cumulatively shape the methylome landscape over their lifetime. However, because high-resolution methylome studies usually focus on single environmental cues, it remains unclear to what extent the methylation responses are generic or stress-specific, and how this relates to their long-term stability. Here, we studied the methylome plasticity of a Populus nigra cv. 'Italica' clone that is widespread across Europe. Adult trees from a variety of geographic locations were clonally propagated in a common garden experiment, and the ramets were exposed to cold, heat, drought, herbivory, rust infection, and salicylic acid treatments. Through comprehensive whole-genome bisulfite sequencing, we analyzed stress-induced and naturally occurring DNA methylation variants. Stress-induced methylation changes predominantly targeted transposable elements. When occurring in CG/CHG contexts, the same regions were often affected by multiple stresses, suggesting a generic response of the methylome. Drought stress caused a distinct CHH hypermethylation response in transposable elements, affecting entire TE superfamilies near drought-responsive genes. Methylation differences in CG/CHG contexts that were induced by stress treatments showed striking overlap with methylation differences observed between trees from distinct geographical locations. Thus, we revealed genomic hotspots of methylation change that are not stress-specific and that contribute to natural DNA methylation variation, and we identified specific transposable element superfamilies that respond to a specific stress with possible functional consequences. Our results underscore the importance of studying the effects of multiple stressors in a single experiment for recognizing general versus stress-specific methylome responses.
PREMISE: Vertical stratification is a key feature of tropical forests and plant-frugivore interactions. However, it is unclear whether equally strong patterns of vertical stratification exist for plant-nectarivore interactions and, if so, which factors drive these patterns. Further, nectar-inhabiting bacteria, acting as "hidden players" in plant-nectarivore interactions, might be vertically stratified, either in response to differences among strata in microenvironmental conditions or to the nectarivore community serving as vectors. METHODS: We observed visitations by a diverse nectarivore community to the liana Marcgravia longifolia in a Peruvian rainforest and characterized diversity and community composition of nectar-inhabiting bacteria. Unlike most other plants, M. longifolia produces inflorescences across forest strata, enabling us to study effects of vertical stratification on plant-nectarivore interactions without confounding effects of plant species and stratum. RESULTS: A significantly higher number of visits were by nectarivorous bats and hummingbirds in the midstory than in the understory and canopy, and the visits were strongly correlated to flower availability and nectar quantity and quality. Trochiline hummingbirds foraged across all strata, whereas hermits remained in the lower strata. The Shannon diversity index for nectar-inhabiting bacterial communities was highest in the midstory. CONCLUSIONS: Our findings suggest that vertical niche differentiation in plant-nectarivore interactions seems to be partly driven by resource abundance, but other factors such as species-specific preferences of hummingbirds, likely caused by competition, play an important role. We conclude that vertical stratification is an important driver of a species' interaction niche highlighting its role for promoting biodiversity and ecosystem functioning.
Ecosystem , Plant Nectar , Animals , Forests , Biodiversity , Flowers , Birds/physiology
Sakis (genus Pithecia) are frugivorous primates with a preference for seeds that complete their diet with leaves and insects. Fruit pulp and seeds are known to have different nutritional characteristics that change during the process of ripening. The consumption of seeds can be an adaptation to changes in resource availability, as unripe seeds are a more steadily available resource than ripe pulp or young leaves. Here, we present the first study of the feeding ecology of monk sakis (Pithecia monachus). We investigated dietary composition and identified important feeding plants in a seasonally flooded forest within the Área de Conservación Regional Comunal Tamshiyacu-Tahuayo in Peruvian Amazonia. Throughout 20 months, we followed groups of monk sakis by foot and canoe and recorded 459 feeding events. Seeds were the most frequently consumed food item (49%), followed by pulp (mesocarp, pericarp or aril; 25%) and arthropods (22%). Leaves, bark, and flowers were ingested only sporadically. The importance of ripe seeds and arthropods in the diet of the monk sakis differed from other studies: we recorded the consumption of mostly ripe seeds and the share of arthropods was relatively high.
Arthropods , Pitheciidae , Animals , Feeding Behavior , Ecology , Fruit , Diet , Forests
The question whether or not tropical lianas infest host trees randomly or they exert host selection has implications for the structure and dynamics of tropical rainforests, particularly if colonization by lianas impacts host fitness. In this study, we present evidence that the Neotropical liana Marcgravia longifolia (Marcgraviaceae) infests host trees non-randomly. We identified host trees to species or genus level for 87 of the 100 M. longifolia individuals found in the study area of the Estación Biológica Quebrada Blanco (EBQB) in north-eastern Peruvian Amazonia. Data on host availability were taken from two 1-ha plots sampled at EBQB as part of a large-scale tree inventory in western Amazonia. Of the total of 88 tree genera with two or more individuals present in the inventory, 18 were represented amongst hosts. Host genera with a probability of colonization higher than expected by chance were Eschweilera (Lecythidaceae), Pouteria (Sapotaceae), Brosimum (Moraceae), and Hymenaea (Fabaceae). These findings suggest that M. longifolia exerts some level of host selectivity, but the mechanisms for this are completely unknown. Given the large number of animal species (41 bird species, three primate species) that are dispersing the seeds of M. longifolia and that have diverse ecological strategies, directed seed dispersal is unlikely to account for the observed patterns of host infestation.
Rainforest , Tropical Climate , Animals , Probability , Seeds , Peru
Climate change is increasing the frequency and intensity of drought events in many boreal forests. Trees are sessile organisms with a long generation time, which makes them vulnerable to fast climate change and hinders fast adaptations. Therefore, it is important to know how forests cope with drought stress and to explore the genetic basis of these reactions. We investigated three natural populations of white spruce (Picea glauca) in Alaska, located at one drought-limited and two cold-limited treelines with a paired plot design of one forest and one treeline plot. We obtained individual increment cores from 458 trees and climate data to assess dendrophenotypes, in particular the growth reaction to drought stress. To explore the genetic basis of these dendrophenotypes, we genotyped the individual trees at 3000 single nucleotide polymorphisms in candidate genes and performed genotype-phenotype association analysis using linear mixed models and Bayesian sparse linear mixed models. Growth reaction to drought stress differed in contrasting treeline populations. Therefore, the populations are likely to be unevenly affected by climate change. We identified 40 genes associated with dendrophenotypic traits that differed among the treeline populations. Most genes were identified in the drought-limited site, indicating comparatively strong selection pressure of drought-tolerant phenotypes. Contrasting patterns of drought-associated genes among sampled sites and in comparison to Canadian populations in a previous study suggest that drought adaptation acts on a local scale. Our results highlight genes that are associated with wood traits which in turn are critical for the establishment and persistence of future forests under climate change.
Picea , Tracheophyta , Bayes Theorem , Canada , Climate Change , Droughts , Forests
Rapid human-induced environmental changes like climate warming represent a challenge for forest ecosystems. Due to their biological complexity and the long generation time of their keystone tree species, genetic adaptation in these ecosystems might not be fast enough to keep track with conditions changing at such a fast pace. The study of adaptation to environmental change and its genetic mechanisms is therefore key for ensuring a sustainable support and management of forests. The 4-day conference of the European Research Group EvolTree (https://www.evoltree.eu) on the topic of "Genomics and Adaptation in Forest Ecosystems" brought together over 130 scientists to present and discuss the latest developments and findings in forest evolutionary research. Genomic studies in forest trees have long been hampered by the lack of high-quality genomics resources and affordable genotyping methods. This has dramatically changed in the last few years; the conference impressively showed how such tools are now being applied to study past demography, adaptation and interactions with associated organisms. Moreover, genomic studies are now finally also entering the world of conservation and forest management, for example by measuring the value or cost of interspecific hybridization and introgression, assessing the vulnerability of species and populations to future change, or accurately delineating evolutionary significant units. The newly launched conference series of EvolTree will hopefully play a key role in the exchange and synthesis of such important investigations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11295-022-01542-1.
Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we present an EWAS implementation tested for non-model plant species and describe its use.
Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations' resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine-scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east-west isolation-by-distance pattern consistent with the post-glacial colonization history of the species. Genetic differentiation among sites (FCT = 0.148) was an order of magnitude greater than between elevations within sites (FSC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post-glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non-spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.
Abies , Abies/genetics , Ecosystem , Forests , Genetic Structures , Genetic Variation , Trees/genetics
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.
Pinus sylvestris , Pinus , Acclimatization , Climate Change , Seedlings , Temperature
Knowledge on the adaptation of trees to rapid environmental changes is essential to preserve forests and their ecosystem services under climate change. Treeline populations are particularly suitable for studying adaptation processes in trees, as environmental stress together with reduced gene flow can enhance local adaptation. We investigated white spruce (Picea glauca) populations in Alaska on one moisture-limited and two cold-limited treeline sites with a paired plot design of one forest and one treeline population each, resulting in six plots. Additionally, one forest plot in the middle of the distribution range complements the study design. We combined spatial, climatic and dendrochronological data with neutral genetic marker of 2203 trees to investigate population genetic structure and drivers of tree growth. We used several individual-based approaches including random slope mixed-effects models to test the influence of genetic similarity and microenvironment on growth performance. A high degree of genetic diversity was found within each of the seven plots associated with high rates of gene flow. We discovered a low genetic differentiation between the three sites which was better explained by geographic distances than by environmental differences, indicating genetic drift as the main driver of population differentiation. Our findings indicated that microenvironmental features had an overall larger influence on growth performances than genetic similarity among individuals. The effects of climate on growth differed between sites but were smaller than the effect of tree size. Overall, our results suggest that the high genetic diversity of white spruce may result in a wider range of phenotypes which enhances the efficiency of selection when the species is facing rapid climatic changes. In addition, the large intra-individual variability in growth responses may indicate the high phenotypic plasticity of white spruce which can buffer short-term environmental changes and, thus, allow enduring the present changing climate conditions.
Picea , Climate Change , Ecosystem , Forests , Humans , Picea/genetics , Trees
Global warming is predicted to exert negative impacts on plant growth due to the damaging effect of high temperatures on plant physiology. Revealing the genetic architecture underlying the heat stress response is therefore crucial for the development of conservation strategies, and for breeding heat-resistant plant genotypes. Here we investigated the transcriptional changes induced by heat in Nothofagus pumilio, an emblematic tree species of the sub-Antarctic forests of South America. Through the performance of RNA-seq of leaves of plants exposed to 20°C (control) or 34°C (heat shock), we generated the first transcriptomic resource for the species. We also studied the changes in protein-coding transcripts expression in response to heat. We found 5,214 contigs differentially expressed between temperatures. The heat treatment resulted in a down-regulation of genes related to photosynthesis and carbon metabolism, whereas secondary metabolism, protein re-folding and response to stress were up-regulated. Moreover, several transcription factor families like WRKY or ERF were promoted by heat, alongside spliceosome machinery and hormone signaling pathways. Through a comparative analysis of gene regulation in response to heat in Arabidopsis thaliana, Populus tomentosa and N. pumilio we provide evidence of the existence of shared molecular features of heat stress responses across angiosperms, and identify genes of potential biotechnological application.
Fagales/genetics , Gene Expression Profiling/methods , Plant Proteins/genetics , Gene Expression Regulation, Plant , Gene Regulatory Networks , Heat-Shock Response , Plant Leaves/genetics , Sequence Analysis, RNA , South America
BACKGROUND: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. FINDINGS: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species' geographic ranges and reflecting local environmental gradients. CONCLUSION: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.
Fagus , Picea , Pinus sylvestris , Forests , Trees
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
Vertical stratification (VS) is a widespread phenomenon in plant and animal communities in forests and a key factor for structuring their species richness and biodiversity, particularly in tropical forests. The organisms composing forest communities adjust and shape the complex three-dimensional structure of their environment and inhabit a large variety of niches along the vertical gradient of the forest. Even though the degree of VS varies among different vertebrate groups, patterns of compositional stratification can be observed across taxa. Communities of birds, bats, primates, and non-flying small mammals are vertically stratified in terms of abundance, species richness, diversity, and community composition. Frugivorous members of these taxa play important roles as seed dispersers and forage on fruit resources that, in turn, vary in quantity and nutritional value along the vertical gradient. As a consequence, plant-seed disperser interaction networks differ among strata, which is manifested in differences in interaction frequencies and the degree of mutual specialization. In general, the canopy stratum is composed of strong links and generalized associations, while the lower strata comprise weaker links and more specialized interactions. Investigating the VS of communities can provide us with a better understanding of species habitat restrictions, resource use, spatial movement, and species interactions. Especially in the face of global change, this knowledge will be important as these characteristics can imply different responses of species and taxa at a fine spatial scale.
Ecosystem , Forests , Animals , Birds , Plants , Seeds
Understanding the dynamics of selection is key to predicting the response of tree species to new environmental conditions in the current context of climate change. However, selection patterns acting on early recruitment stages and their climatic drivers remain largely unknown in most tree species, despite being a critical period of their life cycle. We measured phenotypic selection on Pinus sylvestris seed mass, emergence time and early growth rate over 2 yr in four common garden experiments established along the latitudinal gradient of the species in Europe. Significant phenotypic plasticity and among-population genetic variation were found for all measured phenotypic traits. Heat and drought negatively affected fitness in the southern sites, but heavy rainfalls also decreased early survival in middle latitudes. Climate-driven directional selection was found for higher seed mass and earlier emergence time, while the form of selection on seedling growth rates differed among sites and populations. Evidence of adaptive and maladaptive phenotypic plasticity was found for emergence time and early growth rate, respectively. Seed mass, emergence time and early growth rate have an adaptive role in the early stages of P. sylvestris and climate strongly influences the patterns of selection on these fitness-related traits.
Pinus sylvestris , Pinus , Climate Change , Europe , Phenotype , Pinus sylvestris/genetics , Temperature
Apple proliferation is an economically important disease and a threat for commercial apple cultivation. The causative pathogen, the bacterium 'Candidatus Phytoplasma mali', is mainly transmitted by Cacopsylla picta, a phloem-feeding insect that develops on the apple tree (Malus spp.). To investigate the feeding behavior of adults of the phytoplasma vector Cacopsylla picta in more detail, we used deep sequencing technology to identify plant-specific DNA ingested by the insect. Adult psyllids were collected in different apple orchards in the Trentino-South Tyrol region of northern Italy. DNA from the whole body of the insect was extracted and analyzed for the presence of plant DNA by performing PCR with two plant-specific primers that target the chloroplast regions trnH-psbA and rbcLa. DNA from 23 plant genera (trnH) and four plant families (rbcLa) of woody and herbaceous plant taxa was detected. Up to six and three plant genera and families, respectively, could be determined in single specimens. The results of this study contribute to a better understanding of the feeding behavior of adult Cacopsylla picta.
Given that the ecological niche of tree species is typically narrower for earlier life stages, intraspecific genetic variation at early fitness traits may greatly influence the adaptive response of tree populations to changing environmental conditions. In this study, we evaluated genetic variation in early fitness traits among 12 populations of Betula pendula from a wide latitudinal range in Europe (41-55°N). We first conducted a chamber experiment to test for population differences in germination and the effect of pre-chilling treatment on seed dormancy release. We then established three common gardens spread across the species latitudinal range in order to evaluate levels of quantitative genetic variation and genotype-by-environment interaction at different early life traits. Our results showed significant variation in chamber germination rates among populations (0-60 %), with southern populations exhibiting lower germination. Pre-chilling treatments did not generally improve germination success. Population seedling emergence rates in the field were correlated with chamber germination rates, though being an order of magnitude lower, with an average ranging from 0 to 1.3 % across gardens. Highly significant variation was found in field emergence rates among populations, and between seed-crop years within populations, but not among families within populations. Populations differed in seedling height, diameter, slenderness and budburst date, with significant among-family variation. Population latitude was positively associated with chamber germination rate and with seedling emergence rate in one of the central field sites. Overall, genetic, environmental and demographic factors seem to influence the observed high levels of variation in early fitness traits among B. pendula populations. Our results suggest limited regeneration capacity for the study species under drier conditions, but further field trials with sufficient replication over environments and seed crops will improve our understanding of its vulnerability to climate change.
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Quantifying the individual reproductive success and understanding its determinants is a central issue in evolutionary research for the major consequences that the transmission of genetic variation from parents to offspring has on the adaptive potential of populations. Here, we propose to distil the myriad of information embedded in tree-ring time series into a set of tree-ring-based phenotypic traits to be investigated as potential drivers of reproductive success in forest trees. By using a cross-disciplinary approach that combines parentage analysis and a thorough dendrophenotypic characterisation of putative parents, we assessed sex-specific relationships between such dendrophenotypic traits (i.e., age, growth rate and parameters describing sensitivity to climate and to extreme climatic events) and reproductive success in Norway spruce. We applied a full probability method for reconstructing parent-offspring relationships between 604 seedlings and 518 adult trees sampled within five populations from southern and central Europe. We found that individual female and male reproductive success was positively associated with tree growth rate and age. Female reproductive success was also positively influenced by the correlation between growth and the mean temperature of the previous vegetative season. Overall, our results showed that Norway spruce individuals with the highest fitness are those who are able to keep high-growth rates despite potential growth limitations caused by reproductive costs and climatic limiting conditions. Identifying such functional links between the individual ecophysiological behaviour and its evolutionary gain would increase our understanding on how natural selection shapes the genetic composition of forest tree populations over time.
Picea , Temperature , Europe , Forests , Picea/genetics , Picea/growth & development , Reproduction
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
