Correlations between genetic, epigenetic and phenotypic variation of an introduced clonal herb

DNA methylation variation and growth in the clonal Duchesnea indica is regulated by both past and present lead environments

Studies suggest that clonal plants' ability to select habitats and forage in a heterogeneous environment is influenced by their past environment, with stress legacy potentially playing a crucial role. In this study, we examined parental ramets of Duchesnea indica Focke that were subject to either a control or lead-contaminated environment (past environment), and their newborn offspring were then transplanted into control, homogeneous lead or heterogeneous lead environment (present environment). We analysed how past and present environments affect plant growth and DNA methylation in offspring. The result shown that the DNA methylation loci composition of offspring was affected by the interaction of parental environment and offspring environment, and DNA methylation levels were higher in heterogeneous environments. Moreover, our findings indicate that offspring would thrive in the heterogeneous lead environment if they did not experience lead pollution in the past, their progeny will avoid lead toxicity by reducing underground biomass allocation. However, when the parents experienced lead stress environment, their biomass allocation strategies disappeared, and they prefer to grow in favourable patches to avoid lead-contaminated patches. We concluded that the integration of historical parental exposure to lead-contaminated and current information about their offspring's environment are impacting plant phenotypes. It is possible that the stress legacy from the parents has been transmitted to their offspring ramets, and the stress legacy is at least partly based on heritable epigenetic variation. The phenotypic variation regulated by the stress legacy affects the growth performance, biomass allocation strategy, and even the behaviour of D. indica.

The evolutionary consequences of interactions between the epigenome, the genome and the environment

The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.

Microbiome and epigenetic variation in wild fish with low genetic diversity

Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.

The complete chloroplast genome sequence of Hydrocotyle vulgaris L. (Araliaceae)

Hydrocotyle vulgaris is a perennial wetland clonal plant in the Araliaceae family, which was introduced to China as an ornamental plant in the 1990s. Although H. vulgaris is now considered a potential invasiveness species in China, it also plays a significant role in the remediation of water pollution. Here, we reported its complete chloroplast genome and analyzed the basic characteristics. The chloroplast genome was 153,165 bp in length, including a pair of inverted repeat (IR) regions of 25,072 bp separated by a large single-copy (LSC) region of 84,291 bp and a small single-copy (SSC) region of 18,730 bp. The H. vulgaris chloroplast genome contained 132 predicted genes, and its overall GC content was 37.60%. Phylogenetic analysis revealed that H. vulgaris was closely related to H. verticillata. The H. vulgaris chloroplast genome presented in this study will lay a foundation for further genetic and genomic studies of the genus Hydrocotyle.

Three-year study of DNA cytosine methylation dynamics in transplanted Malbec grapevines

DNA cytosine methylation, an epigenetic mechanism involved in gene regulation and genome stability, remains poorly understood in terms of its role under changing environmental conditions. Previous research using methylation-sensitive amplified polymorphism (MSAP) markers in a Vitis vinifera L. cv. Malbec clone showed vineyard-specific DNA methylation polymorphism, but no change in overall methylation levels. To complement these findings, the present study investigates the intra-seasonal epigenetic dynamics between genetically identical plants grown in different vineyards through a transplanting experiment. Cuttings of the same clone, showing differential methylation patterns imposed by the vineyard of origin (Agrelo and Gualtallary), were cultivated in a common vineyard (Lunlunta). Using high-performance liquid chromatography-ultraviolet detection, the quantification of global DNA 5-methylcytosine (5-mC) levels revealed relatively low overall 5-mC percentages in grapevines, with higher levels in Agrelo (5.8%) compared to Gualtallary plants (3.7%). The transplanted plants maintained the 5-mC levels differences between vineyards (9.8% vs 6.2%), which equalized in subsequent seasons (7.5% vs 7%). Additionally, the study examined 5-mC polymorphism using MSAP markers in Lunlunta transplanted plants over three seasons. The observed differences between vineyards in MSAP patterns during the initial growing season gradually diminished, suggesting a reprogramming of the hemimethylated pattern following implantation in the common vineyard. In contrast, the non-methylated pattern exhibited greater stability, indicating a potential memory effect. Overall, this study provides valuable insights into the dynamic nature of DNA methylation in grapevines under changing environmental conditions, with potential implications for crop management and breeding strategies.

Clonal functional traits favor the invasive success of alien plants into native communities

Functional traits are frequently proposed to determine the invasiveness of alien species. However, few empirical studies have directly manipulated functional traits and tested their importance in the invasion success of alien species into native plant communities, particularly under global change. We manipulated clonal integration (a key clonal functional trait) of four alien clonal plants by severing inter-ramet connections or keeping them intact and simulated their invasion into native plant communities with two levels of species diversity, population density and nutrient availability. High community diversity and density impeded the invasion success of the alien clonal plants. Clonal integration of the alien plants promoted their invasion success, particularly in the low-density communities associated with low species diversity or nutrient addition, which resulted in a negative correlation between the performance of alien plants and native communities, as expected under global change. Thus, clonal integration can favor the invasion success of alien clonal plants into degraded resident communities with a high degree of disturbance and eutrophication. Our findings confirm the role of clonal functional traits in facilitating alien plant invasions into native plant communities and suggest that clonal functional traits should be considered to efficiently restore degraded communities heavily invaded by alien clonal plants.

Does genotypic diversity of Hydrocotyle vulgaris affect CO2 and CH4 fluxes?

Biodiversity plays important roles in ecosystem functions and genetic diversity is a key component of biodiversity. While effects of genetic diversity on ecosystem functions have been extensively documented, no study has tested how genetic diversity of plants influences greenhouse gas fluxes from plant-soil systems. We assembled experimental populations consisting of 1, 4 or 8 genotypes of the clonal plant Hydrocotyle vulgaris in microcosms, and measured fluxes of CO2 and CH4 from the microcosms. The fluxes of CO2 and CO2 equivalent from the microcosms with the 1-genotype populations of H. vulgaris were significantly lower than those with the 4- and 8-genotype populations, and such an effect increased significantly with increasing the growth period. The cumulative CO2 flux was significantly negatively related to the growth of the H. vulgaris populations. However, genotypic diversity did not significantly affect the flux of CH4. We conclude that genotypic diversity of plant populations can influence CO2 flux from plant-soil systems. The findings highlight the importance of genetic diversity in regulating greenhouse gas fluxes.

Water temperature and chlorophyll a density drive the genetic and epigenetic variation of Vallisneria natans across a subtropical freshwater lake

Plant genetic diversity differs in habitat's oscillations, especially species distributed under heterogeneous environmental conditions. Freshwater ecosystems are vulnerable to biotic and abiotic impacts, which affect the genetic and epigenetic variations in aquatic plants. The extent of environmental heterogeneous attributes can be examined based on genetic and epigenetic variations. Such variations under environmental gradient can provide evidence for understanding the correlations between rapid environmental changes and species evolution. In this study, we performed amplified fragment polymorphism length and methylated-sensitive amplified polymorphism analysis to depict the genetic and epigenetic variations of Vallisneria natans in a subtropical lake. Results showed that this species maintained a relatively high genetic diversity (mean H E = 0.320, I = 0.474, PPL = 85.93%) and epigenetic variation (mean eH E = 0.282, eI = 0.428, ePPL = 83.91%). Water body temperature and chlorophyll a density were positively correlated to the genetic and epigenetic variations. The clonal generates of V. natans depicted a relative high methylation level and shew ancestral scenario between the genet and the second clonal generation. These findings revealed that species diversity is unevenly distributed under environmental heterogeneity, even at a fine geographic scale. Environmental characteristics in relation to temperature and chlorophyll a should be considered in the analysis of the genetic and epigenetic variations. Additionally, epigenetic variations between genets and ramets should be considered with caution when applied to analysis of other aquatic species.

Co-contamination by heavy metal and organic pollutant alters impacts of genotypic richness on soil nutrients

Co-contamination by heavy metal and organic pollutant may negatively influence plant performance, and increasing the number of genotypes for a plant population may reduce this negative effect. To test this hypothesis, we constructed experimental populations of Hydrocotyle vulgaris consisting of single, four or eight genotypes in soils contaminated by cadmium, cypermethrin or both. Biomass, leaf area and stem internode length of H. vulgaris were significantly lower in the soil contaminated by cypermethrin and by both cadmium and cypermethrin than in the soil contaminated by cadmium only. A reverse pattern was found for specific internode length and specific leaf area. In general, genotypic richness or its interaction with soil contamination did not influence plant growth or morphology. However, soil nutrients varied in response to soil contamination and genotypic richness. Moreover, plant population growth was positively correlated to soil total nitrogen, but negatively correlated to total potassium and organic matter. We conclude that co-contamination by cadmium and cypermethrin may suppress the growth of H. vulgaris population compared to contamination by cadmium only, but genotypic richness may play little role in regulating these effects.

Cadmium stress interacts with nutrient availability and light condition to affect the growth of Hydrocotyle vulgaris

Heavy metal pollution is becoming a serious problem in wetland and often co-occurs with nutrient availability and light conditions variation. We hypothesized that nutrient availability and light condition can affect the growth of wetland plants under heavy metal stress. To test this hypothesis, single ramets of a common, clonal wetland plant Hydrocotyle vulgaris were grown for four weeks at three levels of cadmium with three levels of nutrient availability under 30% or 100% light conditions. High level of nutrient availability and high light condition overall promoted growth of H. vulgaris under Cd stress. Under the two light conditions, responses of H. vulgaris to Cd treatments differed among three nutrient levels. Under 30% light condition, 2 mg L-1 Cd2+ treatment decreased total mass at the low nutrient level and decreased ramet number at the medium nutrient level; 0.5 and 2 mg L-1 Cd2+ treatments decreased leaf mass ratio at the low and the medium nutrient levels. Under 100% light condition, 2 mg L-1 Cd2+ treatments significantly decreased total mass at the high level of nutrients; 2 mg L-1 Cd2+ treatment decreased ramet number at the medium and the high nutrient levels and decreased leaf mass ratio at the medium nutrient levels. Our results suggested that Cd stress can interact with nutrient availability and light condition to affect the performance of wetland plants such as H. vulgaris.

Effect of DNA methylation, modified by 5-azaC, on ecophysiological responses of a clonal plant to changing climate

Epigenetic regulation of gene expression is expected to be an important mechanism behind phenotypic plasticity. Whether epigenetic regulation affects species ecophysiological adaptations to changing climate remains largely unexplored. We compared ecophysiological traits between individuals treated with 5-azaC, assumed to lead to DNA demethylation, with control individuals of a clonal grass originating from and grown under different climates, simulating different directions and magnitudes of climate change. We linked the ecophysiological data to proxies of fitness. Main effects of plant origin and cultivating conditions predicted variation in plant traits, but 5-azaC did not. Effects of 5-azaC interacted with conditions of cultivation and plant origin. The direction of the 5-azaC effects suggests that DNA methylation does not reflect species long-term adaptations to climate of origin and species likely epigenetically adjusted to the conditions experienced during experiment set-up. Ecophysiology translated to proxies of fitness, but the intensity and direction of the relationships were context dependent and affected by 5-azaC. The study suggests that effects of DNA methylation depend on conditions of plant origin and current climate. Direction of 5-azaC effects suggests limited role of epigenetic modifications in long-term adaptation of plants. It rather facilitates fast adaptations to temporal fluctuations of the environment.

Spectroscopic profiling-based geographic herb identification by neural network with random weights

Daodi medicinal material plays an important role in traditional Chinese medicine (TCM). This study researches and validates the NNRW (neural network with random weights) model on spectroscopic profiling data for geographical origin identification. NNRW is a special neural network model that does not require an iterative training process. It has been proved effective in various resource-limited data-driven applications. However, whether NNRW works for spectroscopic profiling data remains to be explored. In this study, the Raman and UV (ultraviolet) profiling data of 160 radix astragali samples from four geographic regions are trained and evaluated by four classification models, i.e., NNRW, MLP (multi-layer perceptron), SVM (support vector machine), and DTC (decision tree classifier). Their validation accuracies are 96.3%, 98.0%, 98.4%, and 92.8% respectively. The training/fitting times are 0.372 ms (milli-seconds), 57.9 ms, 2.033 ms, and 3.351 ms, respectively. This study shows that NNRW has a significant training time cut while keeping a high prediction accuracy, and it is a promising solution to resource-limited edge computing applications.

Phenoplasticity of Essential Oils from Two Species of Piper (Piperaceae): Comparing Wild Specimens and Bi-Generational Monoclonal Cultivars

This study tested the hypothesis that “clonal chemical heritability is a crucial factor for the conservation of chemical uniformity of Piper essential oils in controlled monoclonal cultivation”. We asexually propagated first and second-generation clones of two medicinal and aromatic species, Piper gaudichaudianum Kunth and Piper mollicomum Kunth (Piperaceae), for use as experimental models since they show high chemical plasticity in the wild. Leaves from wild specimens of both species, and their respective cultivated specimens, were hydrodistilled in a Clevenger-type apparatus to produce essential oils (EOs). EOs were chemically characterised by GC-MS and GC-FID. The analysis identified 63 compounds in EO of P. mollicomum, which were predominantly monoterpenes, and 59 in EO of P. gaudichaudianum, which were predominantly sesquiterpenes. Evaluation of chemical diversity and oxi-reduction indices showed a loss of chemical homology across the intergenerational cline. Chemometric analysis indicated higher chemical plasticity between wild and intergenerational specimens of P. mollicomum, than for P. gaudichaudianum. EO compounds were significantly less oxidized throughout the generations in both species. Therefore, while clonal heritability is crucial to chemical homology, significant chemical plasticity is likely to occur when cultivated from wild specimens.

Density Alters Impacts of Genotypic Evenness on Productivity in an Experimental Plant Population

Genetic diversity plays important roles in maintaining population productivity. While the impact of genotypic richness on productivity has been extensively tested, the role of genotypic evenness has not been considered. Plant density can also affect population productivity, but its interaction with genotypic diversity has not been tested. We constructed experimental populations of the clonal plant Hydrocotyle vulgaris with either low or high richness (consisting of four vs. eight genotypes), either low or high evenness (each genotype had a different number vs. the same number of ramets), and either low or high density (consisting of 16 vs. 32 ramets) in a full factorial design. Total biomass of plant populations did not differ between four- and eight-genotype mixtures. When the initial plant density was low, total biomass of populations with high genotypic evenness was significantly greater than total biomass of those with low genotypic evenness. However, this difference disappeared when the initial plant density was high. Moreover, total biomass increased linearly with increasing plant density at harvest, but was negatively correlated to variation in leaf area. We conclude that genotypic evenness but not genotypic richness can benefit population productivity, and that plant density can alter the impact of genotypic evenness on population productivity.

Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora

Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.

Epigenetics in Ecology, Evolution, and Conservation

Epigenetic variation is often characterized by modifications to DNA that do not alter the underlying nucleotide sequence, but can influence behavior, morphology, and physiological phenotypes by affecting gene expression and protein synthesis. In this review, we consider how the emerging field of ecological epigenetics (eco-epi) aims to use epigenetic variation to explain ecologically relevant phenotypic variation and predict evolutionary trajectories that are important in conservation. Here, we focus on how epigenetic data have contributed to our understanding of wild populations, including plants, animals, and fungi. First, we identified published eco-epi literature and found that there was limited taxonomic and ecosystem coverage and that, by necessity of available technology, these studies have most often focused on the summarized epigenome rather than locus- or nucleotide-level epigenome characteristics. We also found that while many studies focused on adaptation and heritability of the epigenome, the field has thematically expanded into topics such as disease ecology and epigenome-based ageing of individuals. In the second part of our synthesis, we discuss key insights that have emerged from the epigenetic field broadly and use these to preview the path toward integration of epigenetics into ecology. Specifically, we suggest moving focus to nucleotide-level differences in the epigenome rather than whole-epigenome data and that we incorporate several facets of epigenome characterization (e.g., methylation, chromatin structure). Finally, we also suggest that incorporation of behavior and stress data will be critical to the process of fully integrating eco-epi data into ecology, conservation, and evolutionary biology.

Genotypic Diversity Improves Photosynthetic Traits of Hydrocotyle vulgaris and Alters Soil Organic Matter and N2O Emissions of Wetland Microecosystems

In plant communities, genotypic diversity can impact the plant community structure and ecosystem functions, but related research has focused on native plants. Therefore, whether genotypic diversity affects the growth of invasive plants and then changes the wetland microecosystem remains unresolved. In this study, six different genotypes of Hydrocotyle vulgaris, a common invasive plant in China, were selected to construct populations with three different genotypic diversity levels (one, three, and six genotype combinations, respectively) to explore the effects of different genotypic diversity levels on the growth and physiological traits of H. vulgaris, and soil nutrients and greenhouse gas emissions of the wetland microecosystem under flooding conditions. We found that genotypic diversity improved the leaf area, root to shoot ratio and photosynthetic physiological traits of H. vulgaris, especially under flooding. Moreover, genotypic diversity increased soil organic matter (SOM) contents in the wetland microecosystem, while it reduced the cumulative nitrous oxide emissions under flooding conditions. Overall, genotype diversity improved photosynthetic traits of H. vulgaris, further increased SOM, and reduced the N2O emissions of the wetland microecosystem. The results of this study can provide a theoretical basis for exploring how genotypic diversity levels affect the invasiveness of invasive plants and ecosystems in wetland microecosystems.

DNA Methylation Correlates With Responses of Experimental Hydrocotyle vulgaris Populations to Different Flood Regimes

Epigenetic mechanisms such as DNA methylation are considered as an important pathway responsible for phenotypic responses and rapid acclimation of plants to different environments. To search for empirical evidence that DNA methylation is implicated in stress-responses of non-model species, we exposed genetically uniform, experimental populations of the wetland clonal plant Hydrocotyle vulgaris to two manipulated flood regimes, i.e., semi-submergence vs. submergence, measured phenotypic traits, and quantified different types of DNA methylation using MSAP (methylation-sensitive amplified polymorphism). We found different epi-phenotypes and significant epigenetic differentiation between semi-submerged and submerged populations. Compared to subepiloci (denoting DNA methylation conditions) for the CG-methylated state, unmethylation and CHG-hemimethylation subepiloci types contribute more prominently to the epigenetic structure of experimental populations. Moreover, we detected some epimarker outliers potentially facilitate population divergence between two flood regimes. Some phenotypic variation was associated with flood-induced DNA methylation variation through different types of subepiloci. Our study provides the indication that DNA methylation might be involved in plant responses to environmental variation without altering DNA sequences.

Heterogeneous Nitrogen Supply With High Frequency and Ramet Damage Increases the Benefits of Clonal Integration in Invasive Hydrocotyle vulgaris

Nitrogen (N) deposition significantly affects the growth and the function of invasive clonal plants. However, the effects of heterogeneous N supply with different frequencies on the growth and the potential contribution of clonal integration in invasion plants are still unclear, especially in the complex environment considering ramet damage. To address this question, apical and basal ramets of the clonal invader Hydrocotyle vulgaris were connected or disconnected, N was added to the basal ramets with a high frequency, a low frequency, or no supply, and the total N quantity was the same for the different frequency. Furthermore, 8 aphids were placed on the apical ramets, and 30% of each leaf was cut off to cause damage. The connection between ramets significantly increased the biomass, total carbon (C), and total N of the basal and apical ramets. Higher frequency N supply significantly increased the biomass, total C, and total N of the basal ramets and the entire clonal fragment biomass. The damage had no significant effect on the growth of basal and apical ramets. Especially, under the high N frequency and ramet damage condition, the connection between ramets more significantly increased the biomass, total C, and total N of the apical ramets and the entire clonal fragment biomass. In addition, the uptake rates of ¹⁵ NH 4 + and ¹⁵ NO 3 - in H. vulgaris had no significant difference, and N supply increased the uptake rates of ¹⁵ NH 4 + and ¹⁵ NO 3 - of the basal ramets. Our results suggest that both higher frequency N supply and clonal integration are beneficial to the growth of H. vulgaris. Moreover, the heterogeneous N supply with high frequency and ramet damage increases the benefits of clonal integration in H. vulgaris. These findings improve our understanding of the response of clonal invader H. vulgaris to nitrogen deposition and ramet damage.

Human activity strongly influences genetic dynamics of the most widespread invasive plant in the sub-Antarctic

The link between the successful establishment of alien species and propagule pressure is well-documented. Less known is how humans influence the post-introduction dynamics of invasive alien populations. The latter requires studying parallel invasions by the same species in habitats that are differently impacted by humans. We analysed microsatellite and genome size variation, and then compared the genetic diversity and structure of invasive Poa annua L. on two sub-Antarctic islands: human-occupied Marion Island and unoccupied Prince Edward Island. We also carried out niche modelling to map the potential distribution of the species on both islands. We found high levels of genetic diversity and evidence for extensive admixture between genetically distinct lineages of P. annua on Marion Island. By contrast, the Prince Edward Island populations showed low genetic diversity, no apparent admixture, and had smaller genomes. On both islands, high genetic diversity was apparent at human landing sites, and on Marion Island, also around human settlements, suggesting that these areas received multiple introductions and/or acted as initial introduction sites and secondary sources (bridgeheads) for invasive populations. More than 70 years of continuous human activity associated with a meteorological station on Marion Island led to a distribution of this species around human settlements and along footpaths, which facilitates ongoing gene flow among geographically separated populations. By contrast, this was not the case for Prince Edward Island, where P. annua populations showed high genetic structure. The high levels of genetic variation and admixture in P. annua facilitated by human activity, coupled with high habitat suitability on both islands, suggest that P. annua is likely to increase its distribution and abundance in the future.

Genetic variation and population structure of clonal Zingiber zerumbet at a fine geographic scale: a comparison with two closely related selfing and outcrossing Zingiber species

BACKGROUND

There has always been controversy over whether clonal plants have lower genetic diversity than plants that reproduce sexually. These conflicts could be attributed to the fact that few studies have taken into account the mating system of sexually reproducing plants and their phylogenetic distance. Moreover, most clonal plants in these previous studies regularly produce sexual progeny. Here, we describe a study examining the levels of genetic diversity and differentiation within and between local populations of fully clonal Zingiber zerumbet at a microgeographical scale and compare the results with data for the closely related selfing Z. corallinum and outcrossing Z. nudicarpum. Such studies could disentangle the phylogenetic and sexually reproducing effect on genetic variation of clonal plants, and thus contribute to an improved understanding in the clonally reproducing effects on genetic diversity and population structure.

RESULTS

The results revealed that the level of local population genetic diversity of clonal Z. zerumbet was comparable to that of outcrossing Z. nudicarpum and significantly higher than that of selfing Z. corallinum. However, the level of microgeographic genetic diversity of clonal Z. zerumbet is comparable to that of selfing Z. corallinum and even slightly higher than that of outcrossing Z. nudicarpum. The genetic differentiation among local populations of clonal Z. zerumbet was significantly lower than that of selfing Z. corallinum, but higher than that of outcrossing Z. nudicarpum. A stronger spatial genetic structure appeared within local populations of Z. zerumbet compared with selfing Z. corallinum and outcrossing Z. nudicarpum.

CONCLUSIONS

Our study shows that fully clonal plants are able not only to maintain a high level of within-population genetic diversity like outcrossing plants, but can also maintain a high level of microgeographic genetic diversity like selfing plant species, probably due to the accumulation of somatic mutations and absence of a capacity for sexual reproduction. We suggest that conservation strategies for the genetic diversity of clonal and selfing plant species should be focused on the protection of all habitat types, especially fragments within ecosystems, while maintenance of large populations is a key to enhance the genetic diversity of outcrossing species.

How is epigenetics predicted to contribute to climate change adaptation? What evidence do we need?

Transgenerational effects that are interpreted in terms of epigenetics have become an important research focus at a time when rapid environmental changes are occurring. These effects are usually interpreted as enhancing fitness extremely rapidly, without depending on the slower process of natural selection changing DNA-encoded (fixed) genetic variants in populations. Supporting evidence comes from a variety of sources, including environmental associations with epialleles, cross-generation responses of clonal material exposed to different environmental conditions, and altered patterns of methylation or frequency changes in epialleles across time. Transgenerational environmental effects have been postulated to be larger than those associated with DNA-encoded genetic changes, based on (for instance) stronger associations between epialleles and environmental conditions. Yet environmental associations for fixed genetic differences may always be weak under polygenic models where multiple combinations of alleles can lead to the same evolutionary outcome. The ultimate currency of adaptation is fitness, and few transgenerational studies have robustly determined fitness effects, particularly when compared to fixed genetic variants. Not all transgenerational modifications triggered by climate change will increase fitness: stressful conditions often trigger negative fitness effects across generations that can eliminate benefits. Epigenetic responses and other transgenerational effects will undoubtedly play a role in climate change adaptation, but further, well-designed, studies are required to test their importance relative to DNA-encoded changes. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

Ultraviolet B Radiation Triggers DNA Methylation Change and Affects Foraging Behavior of the Clonal Plant Glechoma longituba

Clonal plants in heterogeneous environments can benefit from their habitat selection behavior, which enables them to utilize patchily distributed resources efficiently. It has been shown that such behavior can be strongly influenced by their memories on past environmental interactions. Epigenetic variation such as DNA methylation was proposed to be one of the mechanisms involved in the memory. Here, we explored whether the experience with Ultraviolet B (UV-B) radiation triggers epigenetic memory and affects clonal plants' foraging behavior in an UV-B heterogeneous environment. Parental ramets of Glechoma longituba were exposed to UV-B radiation for 15 days or not (controls), and their offspring ramets were allowed to choose light environment enriched with UV-B or not (the species is monopodial and can only choose one environment). Sizes and epigenetic profiles (based on methylation-sensitive amplification polymorphism analysis) of parental and offspring plants from different environments were also analyzed. Parental ramets that have been exposed to UV-B radiation were smaller than ramets from control environment and produced less and smaller offspring ramets. Offspring ramets were placed more often into the control light environment (88.46% ramets) than to the UV-B light environment (11.54% ramets) when parental ramets were exposed to UV-B radiation, which is a manifestation of "escape strategy." Offspring of control parental ramets show similar preference to the two light environments. Parental ramets exposed to UV-B had lower levels of overall DNA methylation and had different epigenetic profiles than control parental ramets. The methylation of UV-B-stressed parental ramets was maintained among their offspring ramets, although the epigenetic differentiation was reduced after several asexual generations. The parental experience with the UV-B radiation strongly influenced foraging behavior. The memory on the previous environmental interaction enables clonal plants to better interact with a heterogeneous environment and the memory is at least partly based on heritable epigenetic variation.

Polyploidy and high environmental tolerance increase the invasive success of plants

Ploidy level and genome size (GS) could affect the invasive capacity of plants, although these parameters can be contradictory. While small GS seems to favor dispersion, polyploidy-which increases the GS-also seems to favor it. Using a phylogenetic path analysis, we evaluated the effects of both factors on the environmental tolerance and invasive success of plants. We selected 99 invasive plant species from public online databases and gathered information about invasive capacity (number of non-original countries in which each species occurs), tolerance to environmental factors, ploidy level, and GS. The invasive capacity varied depending on the ploidy level and tolerance to environmental factors. Polyploids and species with increased tolerance to elevated temperatures and rainfall values exhibited high invasive capacity. We found no evidence that GS affects the invasive capacity of plants. We suggest that the genetic variability provided by polyploidization has a positive impact on plant competitiveness, which may ultimately lead to an increased ability to colonize new environments. In a global warming scenario, integrative approaches using phenotypic, genetic, epigenetic, and ecological traits should be a productive route to unveil the aspects of invasive plants.

Effects of fragmentation of clones compound over vegetative generations in the floating plant Pistia stratiotes

BACKGROUND AND AIMS

Clonal plants dominate many plant communities, especially in aquatic systems, and clonality appears to promote invasiveness and to affect how diversity changes in response to disturbance and resource availability. Understanding how the special physiological and morphological properties of clonal growth lead to these ecological effects depends upon studying the long-term consequences of clonal growth properties across vegetative generations, but this has rarely been done. This study aimed to show how a key clonal property, physiological integration between connected ramets within clones, affects the response of clones to disturbance and resources in an aquatic, invasive, dominant species across multiple generations.

METHODS

Single, parental ramets of the floating stoloniferous plant Pistia stratiotes were grown for 3 weeks, during which they produced two or three generations of offspring; connections between new ramets were cut or left intact. Individual offspring were then used as parents in a second 3-week iteration that crossed fragmentation with previous fragmentation in the first iteration. A third iteration yielded eight treatment combinations, zero to three rounds of fragmentation at different times in the past. The experiment was run once at a high and once at a low level of nutrients.

RESULTS

In each iteration, fragmentation increased biomass of the parental ramet, decreased biomass of the offspring and increased number of offspring. These effects persisted and compounded from one iteration to another, though more recent fragmentation had stronger effects, and were stronger at the low than at the high nutrient level. Fragmentation did not affect net accumulation of mass by groups after one iteration but increased it after two iterations at low nutrients, and after three iterations at both nutrient levels.

CONCLUSIONS

Both the positive and negative effects of fragmentation on clonal performance can compound and persist over time and can be stronger when resource levels are lower. Even when fragmentation has no short-term net effect on clonal performance, it can have a longer-term effect. In some cases, fragmentation may increase total accumulation of mass by a clone. The results provide the first demonstration of how physiological integration in clonal plants can affect fitness across generations and suggest that increased disturbance may promote invasion of introduced clonal species via effects on integration, perhaps especially at lower nutrient levels.

Capacity for clonal integration in introduced versus native clones of the invasive plant Hydrocotyle vulgaris

Clonal plants can make up a disproportionately high number of the introduced, invasive plant species in a region. Physiological integration of connected ramets within clones is a key ecological advantage of clonal growth. To ask whether clonal integration underlies the invasiveness of clonal plants, we tested the hypothesis that introduced clones of an invasive species will show higher capacity for integration than native clones of the same species. We conduct a greenhouse experiment on the widespread, perennial herb Hydrocotyle vulgaris. Clonal fragments consisting of pairs of connected ramets from seven sites in northwestern Spain where the species is native and seven sites in southeastern China where the species is introduced and invasive were grown for 79 days with the younger, apical ramet shaded to 30% of ambient light and the connection between ramets either severed or left intact. Severance decreased the final dry mass and ramet number of the apical ramet and its offspring in nearly all clones and increased the mass or ramet number of the basal portion of the fragment in about half of the clones, but these effects did not differ consistently between native and introduced clones. Severance did affect allocation more in introduced than in native clones, decreasing root/total mass more in apical portions and increasing it more in basal portions. Maintaining the connection between ramets caused introduced, but not native, clonal fragments to produce more leaf and less root mass and thus to lower allocation to roots. Regardless of severance, introduced clones accumulated about twice as much mass as native clones. Results suggest that introduced clones of a species can show greater effects of integration on allocation than native clones. In species such as H. vulgaris, this might increase competitiveness for light.

Clonal integration in Phagmites australis mitigates effects of oil pollution on greenhouse gas emissions in a coastal wetland

Clonal integration, i.e., resource sharing within clones, enables clonal plants to maintain biomass production when ramets (asexual individuals) under stress are connected to those not under stress. Oil pollution can strongly reduce biomass production, and connected ramets within clones may experience different levels of oil pollution. Therefore, clonal integration may help plants maintain biomass production despite oil pollution. Because biomass production is often negatively correlated with greenhouse gas emissions, we hypothesized that oil pollution would increase greenhouse gas emissions and that clonal integration would reduce such an effect. We tested these hypotheses in a coastal wetland dominated by the rhizomatous grass Phragmites australis near a major site of oil production in the Yellow River Delta in China. We applied 0, 5, or 10 mm crude oil per year for two years in plots within stands of P. australis and tested effects of severing rhizomes connecting ramets inside and outside a plot (i.e. preventing clonal integration) on biomass production, soil chemistry and greenhouse gas emissions. When severed, ramets inside plots with no added oil produced about 220 g aboveground biomass m^--2 over the second growing season, and plots absorbed about 500 g total CO₂ equivalents m^-2. Adding 10 mm oil per year reduced aboveground biomass by about 30%, and caused plots to emit about 800 g CO₂ equivalents m^-2. Leaving ramets connected to those outside plots eliminated the negative effects of oil pollution on biomass production, and caused plots given 10 mm oil per year to emit about 50% fewer total CO₂ equivalents. We conclude that oil pollution can increase greenhouse gas emissions and clonal integration can reduce the effect of oil pollution on biomass production and greenhouse gas emissions. Our study provides the first experimental evidence that clonal integration in plants can reduce greenhouse gas emissions.

The Seagrass Methylome Is Associated With Variation in Photosynthetic Performance Among Clonal Shoots

Evolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management considers genetic variation as the ultimate measure of a population's ability to survive over time. However, clonal plants are among the oldest living organisms on our planet. Here, we test the hypothesis that clonal seagrass meadows display epigenetic variation that complements genetic variation as a source of phenotypic variation. In a clonal meadow of the seagrass Zostera marina, we characterized DNA methylation among 42 shoots. We also sequenced the whole genome of 10 shoots to correlate methylation patterns with photosynthetic performance under exposure to and recovery from 27°C, while controlling for somatic mutations. Here, we show for the first time that clonal seagrass shoots display DNA methylation variation that is independent from underlying genetic variation, and associated with variation in photosynthetic performance under experimental conditions. It remains unknown to what degree this association could be influenced by epigenetic responses to transplantation-related stress, given that the methylomes showed a strong shift under acclimation to laboratory conditions. The lack of untreated control samples in the heat stress experiment did not allow us to distinguish methylome shifts induced by acclimation from such induced by heat stress. Notwithstanding, the co-variation in DNA methylation and photosynthetic performance may be linked via gene expression because methylation patterns varied in functionally relevant genes involved in photosynthesis, and in the repair and prevention of heat-induced protein damage. While genotypic diversity has been shown to enhance stress resilience in seagrass meadows, we suggest that epigenetic variation plays a similar role in meadows dominated by a single genotype. Consequently, conservation management of clonal plants should consider epigenetic variation as indicator of resilience and stability.

Habitat matters - Strong genetic and epigenetic differentiation in Linum catharticum from dry and wet grasslands

Plant species differ in their ecological amplitude, with some species occurring in very different habitats under strongly differentiated environmental conditions. We were interested in to what extent the occurrence of Linum catharticum in dry calcareous grasslands (Bromion) and wet litter meadows (Molinion), two habitats on opposing ends concerning, for example, moisture level, is reflected on the genetic and epigenetic level. Using AFLP (amplified fragment length polymorphisms) and MSAP (methylation sensitive amplification polymorphisms) analyses, we studied the genetic and epigenetic variation of L. catharticum from calcareous grasslands and litter meadows. From each habitat, we included five study sites with 16 individuals per sampling location. We observed lower genetic than epigenetic diversity, but considerable differentiation among habitats, which was stronger on the genetic than the epigenetic level. Additionally, we observed a strong correlation of genetic and epigenetic distance, irrespective of geographic distance. The dataset included a large portion of fragments exclusively found in individuals from one or the other habitat. Some epigenetic fragments even occurred in different methylation states depending on the habitat. We conclude that environmental effects act on both the genetic and epigenetic level, producing the clear differentiation among plant individuals from calcareous grasslands and litter meadows. These results may also point into the direction of ecotype formation in this species.

Comparative genetic and epigenetic diversity in pairs of sympatric, closely related plants with contrasting distribution ranges in south-eastern Iberian mountains

Genetic diversity defines the evolutionary potential of a species, yet mounting evidence suggests that epigenetic diversity could also contribute to adaptation. Elucidating the complex interplay between genetic and epigenetic variation in wild populations remains a challenge for evolutionary biologists, and the intriguing possibility that epigenetic diversity could compensate for the loss of genetic diversity is one aspect that remains basically unexplored in wild plants. This hypothesis is addressed in this paper by comparing the extent and patterns of genetic and epigenetic diversity of phylogenetically closely related but ecologically disparate species. Seven pairs of congeneric species from Cazorla mountains in south-eastern Spain were studied, each pair consisting of one endemic, restricted-range species associated to stressful environments, and one widespread species occupying more favourable habitats. The prediction was tested that endemic species should have lower genetic diversity due to population fragmentation, and higher epigenetic diversity induced by environmental stress, than their widespread congeners. Genetic (DNA sequence variants) and epigenetic (DNA cytosine methylation variants) diversities and their possible co-variation were assessed in three populations of each focal species using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP). All species and populations exhibited moderate to high levels of genetic polymorphism irrespective of their ecological characteristics. Epigenetic diversity was greater than genetic diversity in all cases. Only in endemic species were the two variables positively related, but the difference between epigenetic and genetic diversity was greater at populations with low genetic polymorphism. Results revealed that the relationship between genetic and epigenetic diversity can be more complex than envisaged by the simple hypothesis addressed in this study, and highlight the need of additional research on the actual role of epigenetic variation as a source of phenotypic diversity before a realistic understanding of the evolutionary relevance of epigenetic phenomena in plant adaptation can be achieved.