Adjusting to Global Change through Clonal Growth and Epigenetic Variation

The earth is experiencing major changes in global and regional climates and changes are predicted to accelerate in the future. Many species will be under considerable pressure to evolve, to migrate, or be faced with extinction. Clonal plants would appear to be at a particular disadvantage due to their limited mobility and limited capacity for adaptation. However, they have outlived previous environmental shifts and clonal species have persisted for millenia. Clonal spread offers unique ecological advantages, such as resource sharing, risk sharing, and economies of scale among ramets within genotypes. We suggest that ecological attributes of clonal plants, in tandem with variation in gene regulation through epigenetic mechanisms that facilitate and optimize phenotype variation in response to environmental change may permit them to be well suited to projected conditions.


INTRODUCTION
Rapid and extreme climate changes are predicted, raising questions as to the capacity of plants to adjust to and survive the new environments. In clonal plants, limited dispersal and lack of recombination as a source of new gene combinations might compromise their capacity to migrate or evolve fast enough. Recent work in epigenetics has revealed an alternative path to adaptation involving variation in gene regulation, whereby genotypes can respond to environmental change without genetic recombination (Richards, 2006;Jablonka and Raz, 2009;Massicotte and Angers, 2012), that has consequences for clonal plants (Verhoeven and Preite, 2014;Douhovnikoff and Dodd, 2015). We suggest that ecological advantages to the clonal growth strategy, in tandem with epigenetically regulated accommodation through plasticity (acclimation) could position many clonal plant species well for future ecological success.
The most recent IPCC report (IPCC, 2014) predicts increasing temperatures among a range of carbon emission scenarios, with greatest changes occurring at higher latitudes and elevations. A second prediction from the IPCC report is increased frequency of extreme climatic events, such as heat, droughts, floods and storm damage. Indirect effects of these extreme events will include reduced plant defenses, increased attacks from pests and diseases and subsequent episodes of fire and soil erosion. Rates of climate change predicted by the climate models for the next century are unprecedented and may exceed by an order of magnitude the rates of climate warming during the Holocene deglaciation (Diffenbaugh and Field, 2013). The last major period of climatic change, during the Pleistocene, saw major species' distributional shifts (Hewitt, 2004), and changes in community structure as a result of unequal species' responses (Huntley, 1999). Ecologists have already monitored plant responses to recent climate change that include (1) colonization, as altitudinal and latitudinal displacements occur (Parmesan and Yohe, 2003) and (2) adaptation, such as spring-time advances in phenological processes (Hughes, 2000). Currently, mortality through increased attacks by pests and diseases following drought stress is putting some ecosystems at risk (Woods et al., 2005;Hicke et al., 2006). Because of the anticipated rates of climate change, population re-locations through dispersal and colonization are expected to be more successful responses than survival through adaptation in situ (Aitken et al., 2008). Community structure will likely change as species respond unequally; modeling suggests that community diversity decreases and non-analog communities are most likely to form when dispersal differences among species are high (Urban et al., 2012). Those species with limited ranges, or low dispersal potential are the most likely to face extinction.
The sedentary nature of plants imposes constraints on the velocity of response to rapidly changing environmental conditions. The potential for plants to track climate change depends on long distance dispersal events that allow colonization of new habitat and added genetic variation on the colonizing front (Kremer et al., 2012). For many clonal plants that spread vegetatively from attached organs (rhizomes, roots, stem bases), the opportunity for populations to track environmental change through long distance dispersal will be limited (Winkler and Fischer, 2002;Winkler and Stöcklin, 2002). If clonal plants are limited in their ability to disperse, will species that depend on this mode of reproduction be able to take advantage of in situ adaptation as a response to climate change? In the absence of meiotic recombination, adaptation requires fitness-beneficial mutations (mitotic recombination is unlikely to provide a sufficient source of genotypic variation that could be selectively advantageous.). Accumulation of beneficial mutations is slow and, for phenotypic traits, antagonistic interactions among traits are likely to impede adaptation (Etterson and Shaw, 2001). Nevertheless, clonal plants have persisted for thousands, or even millions of years during past environmental changes (Neiman et al., 2009), and clonal plants have been successful in colonizing new habitats (Ahmad et al., 2008;Zhang et al., 2013), occupying broad geographic ranges (Geng et al., 2007;Ganie et al., 2016) and have come to dominate some ecosystems (Hollingsworth and Bailey, 2000).
So, how do the classic paradigms for clonal plants fail to capture their ecological potential in a dynamic world? First, obligate clonality is rare in nature (Savidan, 2010). Even in extreme environments where clonal reproduction is expected to predominate (Eckert, 2002), high genetic diversity can be maintained by episodes of sexual recruitment (de Witte and Stöcklin, 2010). Second, clonal growth permits a range of advantageous ecological strategies including resource sharing (Alpert, 1990), niche specialization (Gómez and Stuefer, 2006;Louâpre et al., 2012) and rapid vegetative growth, particularly in pioneer habitats. Thirdly, plastic phenotypic responses may include an adaptive component that to some extent substitutes for, and can be far more rapid than adaptation through genetic selection (Verhoeven and Preite, 2014;Douhovnikoff and Dodd, 2015). Accommodation through plasticity has commonly been invoked as important in permitting clonal plants to respond to heterogeneous environments (Parker et al., 2003;Geng et al., 2007). Furthermore, phenotypic accommodation to changing environments ultimately can lead to evolutionary change through selection on elevations and slopes of norms of reaction (West-Eberhard, 2005;Lande, 2009). Recently, an increasing number of studies have shown that plastic responses can be mediated through epigenetic modifications (Jaenisch and Bird, 2003;Richards et al., 2006), the most commonly studied being DNA methylation that results in changes in gene expression. These epigenetic marks may be stable across somatic generations (Bossdorf et al., 2008;Castonguay and Angers, 2012) and across germlines (Jablonka and Raz, 2009;Richards et al., 2012;Verhoeven and Preite, 2014;Douhovnikoff and Dodd, 2015); the latter known as transgenerational (Boyko et al., 2010). Stable epigenetic variations that result in phenotypic variation are thought to offer both short and long-term possibilities for plants to be buffered against their environment Nicotra et al., 2010;Verhoeven et al., 2010;Zhang et al., 2013) and provide an alternative, or are complementary to genomic adaptations. Because epigenetic variations can be heritable and reversible (Bossdorf et al., 2008;Richards et al., 2008Richards et al., , 2012Jablonka and Raz, 2009;Nicotra et al., 2010;Verhoeven and Preite, 2014;Douhovnikoff and Dodd, 2015), they offer a potentially flexible mechanism for plant adaptation. Therefore, epigenetic diversity could provide a crucial source of adaptive potential in asexual plants (Castonguay and Angers, 2012;Verhoeven and Preite, 2014;Douhovnikoff and Dodd, 2015).
Here, we provide some perspectives on the possible success of clonal plants under the predictions of future climate change. We examine how epigenetic changes and their inheritance may contribute to resilience of clonal plants under progressive climate change and climatic extremes.

Colonization on the Advancing Front
Studies of plant responses to past climate changes suggest that rare long-distance seed dispersal events have been important in facilitating population migrations (Clark et al., 2003;Petit et al., 2004). The success of these founder populations depends on the chance that suitable genotypes are among the migrant pool and that sufficient genetic diversity can rapidly be incorporated in the population (Kremer et al., 2012). The latter requires a continuous supply of migrants, or the capability of the founder individuals to support environmental conditions through phenotypic plasticity for long enough that genetic variation can accumulate (Fischer et al., 2000;Petit et al., 2003;Mimura and Aitken, 2007). Contrary to the common belief that clonal plants have low dispersal capability, elevated levels of genotypic diversity in many clonal species suggest recruitment from seedlings (Douhovnikoff et al., 2004), even at altitudinal and elevational extremes (de Witte and Stöcklin, 2010), allowing opportunities for long distance dispersal. The maintenance and growth of a population founded by a single propagule and subsequent variations in plastic response, as it accommodates to the new environment, constitutes an important ecological advantage. Two sources of epigenetic variation help founder populations to adjust. The first is through environmentally-induced epigenetic change and the second is through stochastic epimutations (Verhoeven and Preite, 2014).
Environmentally-induced epigenetic changes are direct responses to environmental stresses that are heritable across generations and distinct from common environmental effects such as on gametes or seeds subject to the same environment as the parent. Such effects have been shown for salt-stressed invasive knotweeds , environmentally-stressed dandelions (Verhoeven et al., 2010) and pathogen-infected Arabidopsis (Dowen et al., 2012). Because these epigenetic changes are likely to be directional, as long as epigenetic changes are rapid enough and are stable across generations, serial epimutations could maintain populations at the same fitness level as the environment progressively changes. High rates of methylation of cytosine at the CG position, five times greater than genetic mutations in Arabidopsis, were estimated by Ossowski et al. (2010). Although lack of stability resulting from high epimutation rates has been argued as a reason that epigenetic changes are unlikely to have long-term evolutionary consequences (Furrow, 2014), van der Graaf et al. (2015), have shown that epimutation-selection equilibria are comparable to those expected for genetic mutations, suggesting their potential role in long-term evolution. In addition, a form of midterm acclimation, the dosage regulation of genes in addition to simple activation and silencing, and reversals at different rates allows for a broad range of fine-tuned modifications (Bräutigam et al., 2013). This increased epigenetic variation permits plants to adjust to change as they encounter new conditions through space, or changing conditions over time; two highly likely circumstances for clonal plants that are often broadly distributed and long lived (Douhovnikoff and Dodd, 2015).
Stochastic epimutations can be beneficial, or deleterious, and provided that they are stable across enough generations, can be acted upon in similar ways as genetic mutations (Slatkin, 2009). Indeed, there is evidence that stochastic epimutations accumulate in a clock-like manner, resembling the accumulation of genetic mutations (Hagmann et al., 2015). Elevated levels of epimutations have been associated with environmental stress (Rapp and Wendel, 2005;Verhoeven et al., 2010) and therefore provide an important source of variation under climate change (Platt et al., 2015). For clonal plants, the higher rate of epimutations over genetic mutations offers an increased possibility for different epialleles to be selected for among ramets of the same founding genotype, permitting both spatial and temporal scales of heterogeneity to develop that may be exploited rapidly by clonal spread (Douhovnikoff and Dodd, 2015). For example, at a spatial scale, as clones forage across the landscape, ramets could become differentially specialized in the uptake of resources (Hutchings and de Kroon, 1994;Wang et al., 2011). At a temporal scale, serial epigenetic mutations can lead to a greater range of phenotypes available for response to climatic variations; high forward and backward epimutation rates leads to much greater variation in epialles than genetic alleles (van der Graaf et al., 2015).
The rapidity at which epigenetic changes can occur and their stability will confer considerable advantages to both sexual and asexual plants under rapid environmental changes, relative to the slower accumulation of genetic diversity through mutations and recombination. Is there any evidence that epigenetic variation has indeed played a role in response to climatic variations across species ranges or in response to climate changes? Preite et al. (2015) tested for a signal of DNA methylation with northward colonization following the last glaciation in apomictic dandelions. Although they failed to detect any signal that would confirm clinal epigenetic adaptation, some epigenetic variants were uncorrelated with genetic variation and may have been a source for local phenotypic adaptations. They concluded that clinal epigenetic changes may be transitory and, over long periods of time genetic adaptation would erase any epigenetic signal. In the California oak Quercus lobata, seed dispersal distances are limited and post-glacial advances have probably been over relatively short distances. Platt et al. (2015) showed significant CpG methylation associated with climatically distinct populations of valley oak, suggesting epigenetic adaptation, or that the epialleles were tightly linked to adaptive genes. An interesting role for epigenetics on transcriptomic variations according to clone history was reported for Populus by Raj et al. (2011). Cuttings from clonally propagated Populus trees that had been planted in different geographic locations were grown in a common environment and exposed to drought stress. Transcriptome-level patterns were paralleled by differences in genome-wide DNA methylation and were most pronounced in clones with the longest time since establishment and last common propagation. This suggests an epigenomic basis for the transcriptome variation in drought stress response associated with clone history. The synchronization of plant phenology with environmental conditions is under strong selection pressure because of the need to maximize the growing season, while minimizing the risks of cold injury (Savolainen et al., 2004) and is important in the adaptation of plants during range shifts. Epigenetic-based "memory" of environmental conditions during seed development has been shown to determine bud phenology in progeny of Picea abies (Yakovlev et al., 2011). Below normal temperatures during seed development led to earlier bud phenology and above normal temperatures led to later bud phenology. Only recently, have we begun to examine variations in epigenetic responses to environmental variations in non-model plants, but these and other examples are beginning to emerge that point to an important role that epigenetic modifications may play in plant acclimation to climatic variation.

Extreme Climatic Events
Extreme climatic events can be the most devastating for plant survival by pushing systems beyond thresholds of tolerance (Feder et al., 2000). The predicted increase in extreme events will place many organisms under stress (i.e., drought) and impose episodes of extreme environmental events (i.e., fire) and potentially devastating biotic interactions (i.e., pests and diseases). It has been suggested that extreme events may have impacts on ecosystems even before the progressive changes in temperature or rainfall (Gaines and Denny, 1993). Evolutionary responses to select for stress-tolerant genotypes are unlikely to be rapid enough to protect populations against extinction in the face of extreme stresses. However, the potential for epigenetic responses to stress may provide the phenotypic variation necessary to sustain populations during events that could push plants past threshold tolerance levels. We now know that environmental stresses can elicit changes in DNA methylation. Examples mostly from in vitro tests on well-studied systems such as crop plants or Arabidopsis have been reviewed by Chinnusamy and Zhu (2009). In many cases, these involve histone mediated epigenetic changes that are reversed when the environmental cue is removed. The reversibility of epigenetic changes can provide an important additional source of variation. It would be interesting to test whether reversals can provide a preadaptation to future change. In other words, once an epigenetic change has occurred, even if reversed, could it be easier for the same change to occur again in the future (a form of hormesis, Douhovnikoff and Dodd, 2015). Further studies of stress-induced DNA methylation in genetically identical apomictic dandelions revealed more than 75% of epigenetic modifications to be transmitted to offspring not exposed to the environmental stress (Verhoeven et al., 2010). These epigenetic changes may be stresstargeted or random (subject to natural selection), but in either case they contribute to the overall response to environmental stimuli and indicate an added potential for phenotypic diversity (Verhoeven and Preite, 2014).
Although the potential for stress-related epigenetic changes may occur in both sexual and asexual plants, the combination of these responses and the ecology of clonal species can explain in part the success of clonality in environments subject to severe stresses. Many species are particularly vulnerable during the seed development, germination and seedling establishment phase, particularly in drought-prone habitats. Indeed, the switch from sexual to asexual reproduction is commonly associated with the risks associated with sexual reproduction (Eckert, 2002). Clonal reproduction provides an escape from the seedling phase, coupled with rapid vegetative growth because of the existing root system. The moderating effect epigenetic variation has on reduced genetic recombination, to some extent tempers the genetic disadvantage of this sex-avoidance strategy. Increased fire frequencies and severity are expected to be the new norm in many parts of the world as a result of higher temperature and increased drought (Westerling et al., 2011;Brando et al., 2014). Although some sexual reproductive systems are fire-adapted, in a great many resprouting systems, clonal reproduction provides the most rapid recovery after fire (Bond and Midgley, 2001). Another effect of drought-stress is the increased incidence of disease and pest outbreaks (Woods et al., 2005;Hicke et al., 2006). The search for heritable variation in disease resistance traits usually assumes variations in DNA sequence. However, recently Latzel et al. (2012) reported the epigenetic inheritance of response to the defense hormones, jasmonic acid and salicylic acid, in Arabidopsis thaliana (Latzel et al., 2012). The role of epigenetics in plant defense to pests and diseases is an area that deserves much more attention as it seems likely to hold considerable promise in understanding disease dynamics in natural populations.
The assumption that resistance is genetically based would suggest that clonal genotypes may be at a disadvantage as disease spreads through a population. However, if stress-related epimutations arise in populations, it is possible that disease outbreaks could induce defense responses regardless of the host genotype.

CONCLUSIONS
The velocity of future climate change is commonly viewed as necessitating rapid plant movements as natural selection cannot operate fast enough to generate novel beneficial gene combinations. However, the range of origins of epigenetic variation could provide phenotypic variation that would buffer against all but the most extreme climatic events. Clonal plants will continue to be an important component of ecosystems because of the attributes that they offer under heterogeneous environments, including rapid vegetative growth and multiplication, resource sharing and niche specialization among connected individuals. With our improved understanding of epigenetic systems and their mode of transmission among clonal copies and across sexual generations, we are uncovering only the superficial skin of a layer of complexity that drives phenotypic responses to the environment. The epigenome is likely to be particularly important in biological systems that lack genetic recombination, and under environmental changes, when the velocity of change exceeds the adaptation possible through natural selection. The added phenotypic diversity offered through epigenomic change should provide the buffer against environmental change that will permit more stable genetic systems to evolve.

AUTHOR CONTRIBUTIONS
RD and VD contributed equally to the ideas expressed here and to the writing of the manuscript.