Epigenetic population differentiation in field‐ and common garden‐grown Scabiosa columbaria plants

Populations often differ in phenotype and these differences can be caused by adaptation by natural selection, random neutral processes, and environmental responses. The most straightforward way to divide mechanisms that influence phenotypic variation is heritable variation and environmental‐induced variation (e.g., plasticity). While genetic variation is responsible for most heritable phenotypic variation, part of this is also caused by nongenetic inheritance. Epigenetic processes may be one of the underlying mechanisms of plasticity and nongenetic inheritance and can therefore possibly contribute to heritable differences through drift and selection. Epigenetic variation may be influenced directly by the environment, and part of this variation can be transmitted to next generations. Field screenings combined with common garden experiments will add valuable insights into epigenetic differentiation, epigenetic memory and can help to reveal part of the relative importance of epigenetics in explaining trait variation. We explored both genetic and epigenetic diversity, structure and differentiation in the field and a common garden for five British and five French Scabiosa columbaria populations. Genetic and epigenetic variation was subsequently correlated with trait variation. Populations showed significant epigenetic differentiation between populations and countries in the field, but also when grown in a common garden. By comparing the epigenetic variation between field and common garden‐grown plants, we showed that a considerable part of the epigenetic memory differed from the field‐grown plants and was presumably environmentally induced. The memory component can consist of heritable variation in methylation that is not sensitive to environments and possibly genetically based, or environmentally induced variation that is heritable, or a combination of both. Additionally, random epimutations might be responsible for some differences as well. By comparing epigenetic variation in both the field and common environment, our study provides useful insight into the environmental and genetic components of epigenetic variation.     

Phenotypic plasticity rather than locally adapted ecotypes allows the invasive alligator weed to colonize a wide range of habitats

Both phenotypic plasticity and locally adapted ecotypes may contribute to the success of invasive species in a wide range of habitats. Here, we conducted common garden experiments and molecular marker analysis to test the two alternative hypotheses in invasive alligator weed (Alternanthera philoxeroides), which colonizes both aquatic and terrestrial habitats. Ninety individuals from three pairs of aquatic versus terrestrial populations across southern China were analyzed, using inter simple sequence repeat (ISSR) marker, to examine population differentiation in neutral loci. Two common gardens simulating aquatic and terrestrial habitats were set up to examine population differentiation in quantitative traits. We found no evidence of population differentiation in both neutral loci and quantitative traits. Most individuals shared the same ISSR genotype. Meanwhile, plants from different habitats showed similar reaction norms across the two common gardens. In particular, plants allocated much more biomass to the belowground roots in the terrestrial environment, where alligator weed may lose part or all of the aboveground shoots because of periodical or accidental disturbances, than those in the aquatic environment. The combined evidence from molecular marker analysis and common garden experiments support the plasticity hypothesis rather than the ecotype hypothesis in explaining the adaptation of alligator weed in a wide range of habitats.     

Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub

Environmentally induced phenotypic plasticity is thought to play an important role in the adaption of plant populations to heterogeneous habitat conditions, and yet the importance of epigenetic variation as a mechanism of adaptive plasticity in natural plant populations still merits further research. In this study, we investigated populations of Vitex negundo var. heterophylla (Chinese chastetree) from adjacent habitat types at seven sampling sites. Using several functional traits, we detected a significant differentiation between habitat types. With amplified fragment length polymorphisms (AFLP) and methylation‐sensitive AFLP (MSAP), we found relatively high levels of genetic and epigenetic diversity but very low genetic and epigenetic differences between habitats within sites. Bayesian clustering showed a remarkable habitat‐related differentiation and more genetic loci associated with the habitat type than epigenetic, suggesting that the adaptation to the habitat is genetically based. However, we did not find any significant correlation between genetic or epigenetic variation and habitat using simple and partial Mantel tests. Moreover, we found no correlation between genetic and ecologically relevant phenotypic variation and a significant correlation between epigenetic and phenotypic variation. Although we did not find any direct relationship between epigenetic variation and habitat environment, our findings suggest that epigenetic variation may complement genetic variation as a source of functional phenotypic diversity associated with adaptation to the heterogeneous habitat in natural plant populations.     

DNA methylation in adults and during development of the self‐fertilizing mangrove rivulus,Kryptolebias marmoratus

In addition to genetic variation, epigenetic mechanisms such as DNA methylation might make important contributions to heritable phenotypic diversity in populations. However, it is often difficult to disentangle the contributions of genetic and epigenetic variation to phenotypic diversity. Here, we investigated global DNA methylation and mRNA expression of the methylation‐associated enzymes during embryonic development and in adult tissues of one natural isogenic lineage of mangrove rivulus fish, Kryptolebias marmoratus. Being the best‐known self‐fertilizing hermaphroditic vertebrate affords the opportunity to work with genetically identical individuals to examine, explicitly, the phenotypic effects of epigenetic variance. Using the LUminometric Methylation Assay (LUMA), we described variable global DNA methylation at CpG sites in adult tissues, which differed significantly between hermaphrodite ovotestes and male testes (79.6% and 87.2%, respectively). After fertilization, an immediate decrease in DNA methylation occurred to 15.8% in gastrula followed by re‐establishment to 70.0% by stage 26 (liver formation). Compared to zebrafish, at the same embryonic stages, this reprogramming event seems later, deeper, and longer. Furthermore, genes putatively encoding DNA methyltransferases (DNMTs), Ten‐Eleven Translocation (TET), and MeCP2 proteins showed specific regulation in adult gonad and brain, and also during early embryogenesis. Their conserved domains and expression profiles suggest that these proteins play important roles during reproduction and development. This study raises questions about mangrove rivulus’ peculiar reprogramming period in terms of epigenetic transmission and physiological adaptation of individuals to highly variable environments. In accordance with the general‐purpose genotype model, epigenetic mechanisms might allow for the expression of diverse phenotypes among genetically identical individuals. Such phenotypes might help to overcome environmental challenges, making the mangrove rivulus a valuable vertebrate model for ecological epigenetic studies. The mangrove rivulus, Kryptolebias marmoratus, is the best‐known self‐fertilizing hermaphroditic vertebrate that allows to work with genetically identical individuals to examine, explicitly, the phenotypic effects of epigenetic variance. The reprogramming event is later, more dramatic and longer than in other described vertebrates. High evolutionary conservation and expression patterns of DNMT, TET, and MeCP2 proteins in K. marmoratus suggest biological roles for each member in gametogenesis and development.     

Variation in DNA methylation transmissibility,genetic heterogeneity and fecundity‐related traits in natural populations of the perennial herb Helleborus foetidus

Inferences about the role of epigenetics in plant ecology and evolution are mostly based on studies of cultivated or model plants conducted in artificial environments. Insights from natural populations, however, are essential to evaluate the possible consequences of epigenetic processes in biologically realistic scenarios with genetically and phenotypically heterogeneous populations. Here, we explore associations across individuals between DNA methylation transmissibility (proportion of methylation‐sensitive loci whose methylation status persists unchanged after male gametogenesis), genetic characteristics (assessed with AFLP markers), seed size variability (within‐plant seed mass variance), and realized maternal fecundity (number of recently recruited seedlings), in three populations of the perennial herb Helleborus foetidus along a natural ecological gradient in southeastern Spain. Plants (sporophytes) differed in the fidelity with which DNA methylation was transmitted to descendant pollen (gametophytes). This variation in methylation transmissibility was associated with genetic differences. Four AFLP loci were significantly associated with transmissibility and accounted collectively for ~40% of its sample‐wide variance. Within‐plant variance in seed mass was inversely related to individual transmissibility. The number of seedlings recruited by individual plants was significantly associated with transmissibility. The sign of the relationship varied between populations, which points to environment‐specific, divergent phenotypic selection on epigenetic transmissibility. Results support the view that epigenetic transmissibility is itself a phenotypic trait whose evolution may be driven by natural selection, and suggest that in natural populations epigenetic and genetic variation are two intertwined, rather than independent, evolutionary factors.     

Low genetic diversity contrasts with high phenotypic variability in heptaploid Spartina densiflora populations invading the Pacific coast of North America

Species can respond to environmental pressures through genetic and epigenetic changes and through phenotypic plasticity, but few studies have evaluated the relationships between genetic differentiation and phenotypic plasticity of plant species along changing environmental conditions throughout wide latitudinal ranges. We studied inter‐ and intrapopulation genetic diversity (using simple sequence repeats and chloroplast DNA sequencing) and inter‐ and intrapopulation phenotypic variability of 33 plant traits (using field and common‐garden measurements) for five populations of the invasive cordgrass Spartina densiflora Brongn. along the Pacific coast of North America from San Francisco Bay to Vancouver Island. Studied populations showed very low genetic diversity, high levels of phenotypic variability when growing in contrasted environments and high intrapopulation phenotypic variability for many plant traits. This intrapopulation phenotypic variability was especially high, irrespective of environmental conditions, for those traits showing also high phenotypic plasticity. Within‐population variation represented 84% of the total genetic variation coinciding with certain individual plants keeping consistent responses for three plant traits (chlorophyll b and carotenoid contents, and dead shoot biomass) in the field and in common‐garden conditions. These populations have most likely undergone genetic bottleneck since their introduction from South America; multiple introductions are unknown but possible as the population from Vancouver Island was the most recent and one of the most genetically diverse. S. densiflora appears as a species that would not be very affected itself by climate change and sea‐level rise as it can disperse, establish, and acclimate to contrasted environments along wide latitudinal ranges.     

Epigenetic variation associated with responses to different habitats in the context of genetic divergence in Phragmites australis

The mechanisms underlying heritable phenotypic divergence associated with adaptation in response to environmental stresses may involve both genetic and epigenetic variations. Several prior studies have revealed even higher levels of epigenetic variation than genetic variation. However, few population‐level studies have explored the effects of epigenetic variation on species with high levels of genetic diversity distributed across different habitats. Using AFLP and methylation‐sensitive AFLP markers, we tested the hypothesis that epigenetic variation may contribute to differences in plants occupying different habitats when genetic variation alone cannot fully explain adaptation. As a cosmopolitan invasive species, Phragmites australis (common reed) together with high genetic diversity and remarkable adaptability has been suggested as a model for responses to global change and indicators of environmental fluctuations. We found high levels of genetic and epigenetic diversity and significant genetic/epigenetic structure within each of 12 studied populations sampled from four natural habitats of P. australis. Possible adaptive epigenetic variation was suggested by significant correlations between DNA methylation‐based epigenetic differentiation and adaptive genetic divergence in populations across the habitats. Meanwhile, various AMOVAs indicated that some epigenetic differences may respond to various local habitats. A partial Mantel test was used to tease out the correlations between genetic/epigenetic variation and habitat after controlling for the correlation between genetic and epigenetic variations. We found that epigenetic diversity was affected mostly by soil nutrient availability, suggesting that at least some epigenetic differentiation occurred independently of genetic variation. We also found stronger correlations between epigenetic variation and phenotypic traits than between genetic variation and such traits. Overall, our findings indicate that genetically based differentiation correlates with heterogeneous habitats, while epigenetic variation plays an important role in ecological differentiation in natural populations of P. australis. In addition, our results suggest that when assessing global change responses of plant species, intraspecific variation needs to be considered.     

Facing environmental predictability with different sources of epigenetic variation

Different sources of epigenetic changes can increase the range of phenotypic options. Environmentally induced epigenetic changes and stochastic epimutations are, respectively, associated with phenotypic plasticity and diversifying bet‐hedging. Their relative contribution is thus expected to reflect the capacity of a genotype to face distinct changes since these strategies are differentially selected according to environmental uncertainty. To test this hypothesis, we assessed the sources of epigenetic changes on clonal fish from predictable (lakes) or unpredictable (intermittent streams) environments. DNA methylation of clones from natural conditions revealed contrasting contribution of environmentally induced versus stochastic changes according to their origins. These differences were validated in common garden experiments. Consistent with theoretical models, distinct sources of epigenetic variation prevail according to the environmental uncertainty. However, both sources act conjointly, suggesting that plasticity and random processes are complementary strategies. This represents a rigorous approach for further exploring the capacity of organisms to respond to environmental conditions.     

不同水陆环境中喜旱莲子草甲基化调控因子表达水平和差异表达基因启动子区甲基化状态分析

DNA甲基化是一种重要的表观遗传调控方式,参与对植物生长发育的调控,并在植物逆境胁迫响应中发挥作用。DNA甲基化的建立和维持是胞嘧啶甲基转移酶、染色质重塑酶、组蛋白修饰因子和去甲基化因子等协同作用的结果,环境胁迫能诱导植物体内DNA甲基化状态改变,进而改变基因表达水平和式样,影响植物的适应性。喜旱莲子草是一种恶性入侵植物,种内遗传多样性很低,主要依靠极强的表型可塑性侵占不同水陆生境。对克隆繁殖的喜旱莲子草个体进行不同时间的淹水处理,并用定量PCR方法检测16个DNA甲基化调控基因在不同处理条件下的表达水平和变化趋势,发现其中13个基因在不同处理时间点的表达水平有明显变化,且在淹水植株中多数基因在处理前期被强烈诱导上调表达。运用亚硫酸氢钠测序技术对两个在不同水陆条件下明显差异表达基因(Contig942和Contig23336)的上游启动子区甲基化动态进行分析,发现启动子区多个胞嘧啶位点的甲基化修饰状态在不同水陆条件下及淹水处理的不同时期呈现快速且可逆的动态变化,可能影响这些基因在不同环境条件下的表达水平。本研究结果能帮助了解喜旱莲子草表型可塑性变异和适应性发生的分子机理。     

Dynamic changes in DNA methylation during embryonic and postnatal development of an altricial wild bird

DNA methylation could shape phenotypic responses to environmental cues and underlie developmental plasticity. Environmentally induced changes in DNA methylation during development can give rise to stable phenotypic traits and thus affect fitness. In the laboratory, it has been shown that the vertebrate methylome undergoes dynamic reprogramming during development, creating a critical window for environmentally induced epigenetic modifications. Studies of DNA methylation in the wild are lacking, yet are essential for understanding how genes and the environment interact to affect phenotypic development and ultimately fitness. Furthermore, our knowledge of the establishment of methylation patterns during development in birds is limited. We quantified genome‐wide DNA methylation at various stages of embryonic and postnatal development in an altricial passerine bird, the great tit Parus major. While, there was no change in global DNA methylation in embryonic tissue during the second half of embryonic development, a twofold increase in DNA methylation in blood occurred between 6 and 15 days posthatch. Though not directly comparable, DNA methylation levels were higher in the blood of nestlings compared with embryonic tissue at any stage of prenatal development. This provides the first evidence that DNA methylation undergoes global change during development in a wild bird, supporting the hypothesis that methylation mediates phenotypic development. Furthermore, the plasticity of DNA methylation demonstrated during late postnatal development, in the present study, suggests a wide window during which DNA methylation could be sensitive to environmental influences. This is particularly important for our understanding of the mechanisms by which early‐life conditions influence later‐life performance. While, we found no evidence for differences in genome‐wide methylation in relation to habitat of origin, environmental variation is likely to be an important driver of variation in methylation at specific loci.     

Epigenetic correlates of plant phenotypic plasticity: DNA methylation differs between prickly and nonprickly leaves in heterophyllous Ilex aquifolium (Aquifoliaceae) trees

Phenotypic plasticity is central to the persistence of populations and a key element in the evolution of species and ecological interactions, but its mechanistic basis is poorly understood. This article examines the hypothesis that epigenetic variation caused by changes in DNA methylation are related to phenotypic plasticity in a heterophyllous tree producing two contrasting leaf types. The relationship between mammalian browsing and the production of prickly leaves was studied in a population of Ilex aquifolium (Aquifoliaceae). DNA methylation profiles of contiguous prickly and nonprickly leaves on heterophyllous branchlets were compared using a methylation‐sensitive amplified polymorphism (MSAP) method. Browsing and the production of prickly leaves were correlated across trees. Within heterophyllous branchlets, pairs of contiguous prickly and nonprickly leaves differed in genome‐wide DNA methylation. The mean per‐marker probability of methylation declined significantly from nonprickly to prickly leaves. Methylation differences between leaf types did not occur randomly across the genome, but affected predominantly certain specific markers. The results of this study, although correlative in nature, support the emerging three‐way link between herbivory, phenotypic plasticity and epigenetic changes in plants, and also contribute to the crystallization of the consensus that epigenetic variation can complement genetic variation as a source of phenotypic variation in natural plant populations. © 2012 The Linnean Society of London     

Natural epigenetic variation in the female great roundleaf bat (Hipposideros armiger) populations

Epigenetic modifications are considered to have an important role in evolution. DNA methylation is one of the best studied epigenetic mechanisms and methylation variability is crucial for promoting phenotypic diversification of organisms in response to environmental variation. A critical first step in the assessment of the potential role of epigenetic variation in evolution is the identification of DNA methylation polymorphisms and their relationship with genetic variations in natural populations. However, empirical data is scant in animals, and particularly so in wild mammals. Bats are considered as bioindicators because of their sensitivity to environmental perturbations and they may present an opportunity to explore epigenetic variance in wild mammalian populations. Our study is the first to explore these questions in the female great roundleaf bat (Hipposideros armiger) populations using the methylation-sensitive amplified polymorphism (MSAP) technique. We obtained 868 MSAP sites using 18 primer combinations and found (1) a low genomic methylation level (21.3?% on average), but extensive DNA methylation polymorphism (90.2?%) at 5'-CCGG-3' sites; (2) epigenetic variation that is structured into distinct between- (29.8?%) and within- (71.2?%) population components, as does genetic variation; and (3) a significant correlation between epigenetic and genetic variations (P?相似文献   

不同土壤水分和养分条件下喜旱莲子草与同属种生长状况的比较研究

喜旱莲子草(Alternanthera philoxeroides)入侵已在中国造成巨大的生态和经济损失。为揭示喜旱莲子草成功入侵的生态机制并预测其种群扩张趋势及其与环境因子的关系, 作者比较了喜旱莲子草与其同属的外来弱入侵种刺花莲子草(A. pungens)以及土著种莲子草(A. sessilis)在不同土壤水分、养分条件下的生长状况。结果显示: 在高水高肥条件下, 喜旱莲子草的生物量要高于刺花莲子草和莲子草, 而在低水低肥条件下却不如这两个同属种; 弱入侵种刺花莲子草在低水条件下的生物量要高于强入侵种喜旱莲子草和土著种莲子草, 说明植物的入侵性受环境条件的影响。另外, 强入侵种喜旱莲子草形态学性状的可塑性较高, 在各种条件下都具有较高的比叶面积, 暗示这两个指标可作为莲子草属外来植物入侵性的预测指标。     

Effects of simulated herbivory and resource availability on the invasive plant, Alternanthera philoxeroides in different habitats

In biological control programs, the insect natural enemy’s ability to suppress the plant invader may be affected by abiotic factors, such as resource availability, that can influence plant growth and reproduction. Understanding plant tolerance to herbivory under different environmental conditions will help to improve biocontrol efficacy. The invasive alligator weed (Alternanthera philoxeroides) has been successfully controlled by natural enemies in many aquatic habitats but not in terrestrial environments worldwide. This study examined the effects of different levels of simulated leaf herbivory on the growth of alligator weed at two levels of fertilization and three levels of soil moisture (aquatic, semi-aquatic, and terrestrial habitats). Increasing levels of simulated (manual) defoliation generally caused decreases in total biomass in all habitats. However, the plant appeared to respond differently to high levels of herbivory in the three habitats. Terrestrial plants showed the highest below–above ground mass ratio (R/S), indicating the plant is more tolerant to herbivory in terrestrial habitats than in aquatic habitats. The unfertilized treatment exhibited greater tolerance than the fertilized treatment in the terrestrial habitat at the first stage of this experiment (day 15), but fertilizer appears not to have influenced tolerance at the middle and last stages of the experiment. No such difference was found in semi-aquatic and aquatic habitats. These findings suggest that plant tolerance is affected by habitats and soil nutrients and this relationship could influence the biological control outcome. Plant compensatory response to herbivory under different environmental conditions should, therefore, be carefully considered when planning to use biological control in management programs against invasive plants.     

The epigenetic footprint of poleward range‐expanding plants in apomictic dandelions

Epigenetic modifications, such as DNA methylation variation, can generate heritable phenotypic variation independent of the underlying genetic code. However, epigenetic variation in natural plant populations is poorly documented and little understood. Here, we test whether northward range expansion of obligate apomicts of the common dandelion (Taraxacum officinale) is associated with DNA methylation variation. We characterized and compared patterns of genetic and DNA methylation variation in greenhouse‐reared offspring of T. officinale that were collected along a latitudinal transect of northward range expansion in Europe. Genetic AFLP and epigenetic MS‐AFLP markers revealed high levels of local diversity and modest but significant heritable differentiation between sampling locations and between the southern, central and northern regions of the transect. Patterns of genetic and epigenetic variation were significantly correlated, reflecting the genetic control over epigenetic variation and/or the accumulation of lineage‐specific spontaneous epimutations, which may be selectively neutral. In addition, we identified a small component of DNA methylation differentiation along the transect that is independent of genetic variation. This epigenetic differentiation might reflect environment‐specific induction or, in case the DNA methylation variation affects relevant traits and fitness, selection of heritable DNA methylation variants. Such generated epigenetic variants might contribute to the adaptive capacity of individual asexual lineages under changing environments. Our results highlight the potential of heritable DNA methylation variation to contribute to population differentiation along ecological gradients. Further studies are needed using higher resolution methods to understand the functional significance of such natural occurring epigenetic differentiation.     

Genome‐wide epigenetic isolation by environment in a widespread Anolis lizard

Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression. However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it. Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population processes contribute to epigenetic divergence across heterogeneous landscapes. Here, we perform a comparative analysis of spatial genetic and epigenetic variation based on 8,459 single nucleotide polymorphisms (SNPs) and 8,580 single methylation variants (SMVs) from eight populations of the Puerto Rican crested anole, Anolis cristatellus, an abundant lizard in the adaptive radiations of anoles on the Greater Antilles that occupies a diverse range of habitats. Using generalized dissimilarity modelling and multiple matrix regression, we found that genome‐wide epigenetic differentiation is strongly correlated with environmental divergence, even after controlling for the underlying genetic structure. We also detected significant associations between key environmental variables and 96 SMVs, including 42 located in promoter regions or gene bodies. Our results suggest an environmental basis for population‐level epigenetic differentiation in this system and contribute to better understanding how environmental gradients structure epigenetic variation in nature.     

Learning from methylomes: epigenomic correlates of Populus balsamifera traits based on deep learning models of natural DNA methylation

Epigenomes have remarkable potential for the estimation of plant traits. This study tested the hypothesis that natural variation in DNA methylation can be used to estimate industrially important traits in a genetically diverse population of Populus balsamifera L. (balsam poplar) trees grown at two common garden sites. Statistical learning experiments enabled by deep learning models revealed that plant traits in novel genotypes can be modelled transparently using small numbers of methylated DNA predictors. Using this approach, tissue type, a nonheritable attribute, from which DNA methylomes were derived was assigned, and provenance, a purely heritable trait and an element of population structure, was determined. Significant proportions of phenotypic variance in quantitative wood traits, including total biomass (57.5%), wood density (40.9%), soluble lignin (25.3%) and cell wall carbohydrate (mannose: 44.8%) contents, were also explained from natural variation in DNA methylation. Modelling plant traits using DNA methylation can capture tissue‐specific epigenetic mechanisms underlying plant phenotypes in natural environments. DNA methylation‐based models offer new insight into natural epigenetic influence on plants and can be used as a strategy to validate the identity, provenance or quality of agroforestry products.     

Epigenetic inheritance and plant evolution

Being sessile organisms, plants show a high degree of developmental plasticity to cope with a constantly changing environment. While plasticity in plants is largely controlled genetically, recent studies have demonstrated the importance of epigenetic mechanisms, especially DNA methylation, for gene regulation and phenotypic plasticity in response to internal and external stimuli. Induced epigenetic changes can be a source of phenotypic variations in natural plant populations that can be inherited by progeny for multiple generations. Whether epigenetic phenotypic changes are advantageous in a given environment, and whether they are subject to natural selection is of great interest, and their roles in adaptation and evolution are an area of active research in plant ecology. This review is focused on the role of heritable epigenetic variation induced by environmental changes, and its potential influence on adaptation and evolution in plants.     

Within-genotype epigenetic variation enables broad niche width in a flower living yeast

Niche theory is one of the central organizing concepts in ecology. Generally, this theory defines a given species niche as all of the factors that effect the persistence of the species as well as the impact of the species in a given location ( Hutchinson 1957 ; Chase 2011 ). Many studies have argued that phenotypic plasticity enhances niche width because plastic responses allow organisms to express advantageous phenotypes in a broader range of environments ( Bradshaw 1965 ; Van Valen 1965 ; Sultan 2001 ). Further, species that exploit habitats with fine‐grained variation, or that form metapopulations, are expected to develop broad niche widths through phenotypic plasticity ( Sultan & Spencer 2002 ; Baythavong 2011 ). Although a long history of laboratory, greenhouse and reciprocal transplant experiments have provided insight into how plasticity contributes to niche width ( Pigliucci 2001 ), recent advances in molecular approaches allow for a mechanistic understanding of plasticity at the molecular level ( Nicotra et al. 2010 ). In particular, variation in epigenetic effects is a potential source of the within‐genotype variation that underlies the phenotypic plasticity associated with broad niche widths. Epigenetic mechanisms can alter gene expression and function without altering DNA sequence ( Richards 2006 ) and may be stably transmitted across generations ( Jablonka & Raz 2009 ; Verhoeven et al. 2010 ). Also, epigenetic mechanisms may be an important component of an individual’s response to the environment ( Verhoeven et al. 2010 ). While these ideas are intriguing, few studies have made a clear connection between genome‐wide DNA methylation patterns and phenotypic plasticity (e.g. Bossdorf et al. 2010 ). In this issue of Molecular Ecology, Herrera et al. (2012) present a study that demonstrates epigenetic changes in genome‐wide DNA methylation are causally active in a species’ ability to exploit resources from a broad range of environments and are particularly important in harsh environments.     

Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations

Intraspecific trait variation within natural populations (i.e. intra‐population trait variation, IPTV) is the basic source for selection and can have significant ecological consequences. Higher IPTV may increase a population's niche breath and benefit interspecies competition under a resource‐limited environment, thus affecting the ability of a species to move into novel habitats. However, the reciprocal influences of variation in environmental conditions and phenotypic trait expression in spreading plant populations are not clearly defined. We propose that during invasion, IPTV and its relative change in response to key resource enrichment may increase with the resource deficit of invaded sites, and that this relationship may facilitate plant invasions into resource‐limited environments. We analyzed the invasion trend, IPTV and its response to water enrichment, and moisture variability among populations of an annual grass Brachypodium hybridum in California, United States. We incorporated a genotyping‐by‐sequencing approach, a common garden experiment that had two water level treatments, and public plant and climate databases. Our hypothesis was supported by the observation that for populations that invaded sites with higher spring moisture deficit, both their seed biomass IPTV (for the water‐enriched treatment only) and relative change of the IPTV across water treatments were larger when examined in the common garden experiment. A generally north to south spreading direction was found in these B. hybridum populations, towards a drier and warmer climate exhibiting higher moisture deficit for plant growth. Our results suggest a role for interactions between IPTV (rather than trait means) and environmental resource availability in promoting plant invasions, providing new insights into the significance of IPTV in shaping plant geographic distributions.