SPECIAL SECTION

doi:10.1111/evo.12320

EPIGENETIC VARIATION IN ASEXUALLY REPRODUCING ORGANISMS Koen J.F. Verhoeven1,2 and Veronica Preite1 1

Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB

Wageningen, The Netherlands 2

E-mail: [email protected]

Received September 11, 2013 Accepted November 14, 2013 The role that epigenetic inheritance can play in adaptation may differ between sexuals and asexuals because (1) the dynamics of adaptation differ under sexual and asexual reproduction and the opportunities offered by epigenetic inheritance may affect these dynamics differently; and (2) in asexual reproduction epigenetic reprogramming mechanisms that are associated with meiosis can be bypassed, which could promote the buildup of epigenetic variation in asexuals. Here, we evaluate current evidence for an epigenetic contribution to adaptation in asexuals. We argue that two aspects of epigenetic variation should have particular relevance for asexuals, namely epigenetics-mediated phenotypic plasticity within and between generations, and heritable variation via stochastic epimutations. An evaluation of epigenetic reprogramming mechanisms suggests that some, but not all, forms of asexual reproduction enhance the likelihood of stable transmission of epigenetic marks across generations compared to sexual reproduction. However, direct tests of these predicted sexual–asexual differences are virtually lacking. Stable transmission of DNA methylation, transcriptomes, and phenotypes from parent to clonal offspring are demonstrated in various asexual species, and clonal genotypes from natural populations show habitat-specific DNA methylation. We discuss how these initial observations can be extended to demonstrate an epigenetic contribution to adaptation. KEY WORDS:

Apomixis, DNA methylation, epigenetic resetting, parthenogenesis, transgenerational epigenetic inheritance,

vegetative propagation.

Asexual organisms lack the variation-generating mechanisms of meiotic recombination and segregation, which reduces their potential for genetically based adaptation and makes them susceptible to the accumulation of deleterious mutations. Asexuals are therefore generally considered to be evolutionary dead ends (Lynch et al. 1993). Nevertheless, some asexuals persist and successfully expand in a range of different environments. Some of the most successful invasive plant species are clonal, with a single widespread genotype dominating the invasive process over large geographic areas (Hollingsworth and Bailey 2000; Ahmad et al. 2008; Zhang et al. 2010). The success of individual asexual lineages can be due to preadaptation of native genotypes to specific conditions in the new habitat or due to high phenotypic plasticity (general-purpose genotypes; Baker 1965). Increasingly, it is speculated that the persistence and ecological success of such  C

644

lineages can be facilitated via epigenetic variation as a source of phenotypic plasticity and selectable heritable variation (Latzel and Klimesova 2010; Castonguay and Angers 2012; Massicotte and Angers 2012; Richards et al. 2012). Epigenetic DNA modifications, specifically histone modifications and DNA methylation that are in part guided and maintained by small RNAs, allow for stable transmission of gene expression states through cell division. Epigenetic variation can be induced by environments (Dowen et al. 2012) or can arise stochastically (Becker et al. 2011; Schmitz et al. 2011). Epigenetic modifications can be reset between generations (Feng et al. 2010), however, resetting is often not complete and a subset of epigenetic modifications is transmitted through meiosis to subsequent generations (e.g., Anway et al. 2005; Jablonka and Raz 2009; Johannes et al. 2009). Several recent review papers have

C 2013 The Society for the Study of Evolution. 2013 The Author(s). Evolution  Evolution 68-3: 644–655

SPECIAL SECTION

detailed the various ways in which epigenetic inheritance has the potential to affect the process of adaptation (e.g., Jablonka 2012, 2013). Adaptation can be affected by epigenetics-mediated phenotypic plasticity within generations (Bossdorf et al. 2010; Feinberg and Irizarry 2010; Massicotte et al. 2011; Castonguay and Angers 2012) and also between generations (transgenerational effects; Bonduriansky and Day 2009; Boyko et al. 2010). Another possibility is that selection acts directly on stable epigenetic mutations to shape epigenetic adaptations (Zhang et al. 2013). Finally, epigenetic inheritance can have indirect effects on the rate and direction of genetic adaptation (Pal and Miklos 1999; Klironomos et al. 2013). Most of our knowledge of epigenetic inheritance comes from few sexual model organisms such as Arabidopsis. Several studies in Arabidopsis have provided proof-of-principle evidence that some basic requirements are met for an evolutionary role of epigenetic variation, including transgenerational stability of part of the epigenetic code (Teixeira et al. 2009), heritable epigenetic effects on phenotypes (Johannes et al. 2009), and association with fitness (Zhang et al. 2013). Beyond proof-of-principle, the epigenetic contribution to adaptation remains an open question. Important issues for which little empirical information currently exists include the stability of epigenetic mutations within and between generations and also the degree of autonomy of epigenetic variation from the underlying genetic code. Both factors have clear implications for the role that epigenetic inheritance can play in evolution (Richards 2006; Bossdorf et al. 2008). Epigenetic variation is beginning to be investigated in asexually reproducing plant and animal species in recent years (e.g. Gao et al. 2010; Verhoeven et al. 2010b; Massicotte et al. 2011; Richards et al. 2012). Thus far, the issue of how epigenetic variation affects the specifics of asexual evolution has received little attention (Gorelick et al. 2011). The question that we address in this article is if, or how, the evolutionary significance of epigenetic variation is different in asexuals compared to sexuals. The study of epigenetic variation in asexual species offers several advantages. First, it facilitates the evaluation of causes and consequences of epigenetic variation that is not confounded with genetic (DNA sequence) variation. Second, because asexual lineages cannot generate heritable variation via recombination and segregation, epigenetic variation may be relatively important for asexual evolution. Third, because asexuals circumvent meiosis, which is associated with epigenetic resetting between generations (Feng et al. 2010), asexuals could show reduced epigenetic resetting compared to sexuals. This may predispose asexuals to a larger epigenetic contribution to heritable trait variation and to adaptation. Understanding the epigenetic contribution to asexual variation and adaptation is relevant because asexual reproduction is very common, both in plants (Van Groenendael and De Kroon 1990) and animals (Bell 1982). For instance, approximately two-

thirds of the species in temperate zone plant communities are estimated to be capable of clonal propagation (Van Groenendael and De Kroon 1990; Klimes et al. 1997) and for successional series the estimates of soil cover by asexuals are even higher (Prach and Pysek 1994). Here, we review current evidence for the relevance of epigenetic variation in asexually reproducing plants and animals. Starting from differences in adaptive dynamics between sexuals and asexuals, we explore how epigenetic variation might contribute specifically to asexual adaptation. We briefly recapitulate mechanisms of epigenetic resetting and transmission at generation boundaries and discuss the influence of the mode of reproduction on epigenetic transmission between generations. We then review recent literature on epigenetic variation in asexual species, emphasizing natural systems and nonmodel species, to evaluate current evidence for the involvement of epigenetics in asexual adaptation. Although these studies hint at a role for epigenetic variation in asexual plasticity and adaptation, many questions still remain and we discuss challenges and opportunities for further research in this area. Our focus in this article is mainly on DNA methylation, the epigenetic mechanism that is most studied in the context of heritable epigenetic variation. Emphasis is on plant epigenetic literature; however we include also relevant examples from animal studies and the conceptual aspects of epigenetic contributions to asexual adaptation apply equally to plants and animals. We do not include studies of clonal unicellular organisms; see for instance Satory et al. (2011), Van der Woude (2011), Levy et al. (2012), and Herrera et al. (2012) for discussions and recent examples of epigenetic contributions to variation in clonal yeast and bacterial populations. Our bias to plant epigenetics reflects our own expertise as well as the current status of the field, in which much recent progress is made in plant models. It is also important to point out that the contrast between asexual and sexual reproduction is a convenient simplification. Many species can reproduce both sexually and asexually, and in such species the epigenetic contributions to asexual adaptation that we discuss apply only to their episodes of clonal reproduction, while in fact their overall adaptive dynamics might be strongly affected by occasional sexual reproduction (Hurst and Peck 1996).

Epigenetic Contributions to Asexual Evolution Asexual reproduction results in offspring that are genetically identical (clonal copies) of the parent. This includes the production of offspring from somatic cells or structures, such as in vegetative propagation in plants (through for instance bulbs, rhizomes, or stolons) and fragmentation or budding in animals (as found

EVOLUTION MARCH 2014

645

SPECIAL SECTION

for instance in annelids and echinoderms). Other types of asexual reproduction involve the formation of female gametes that develop into embryos/seeds without a need for fertilization, typically labeled as parthenogenesis in animals and apomixis in seed plants (Koltunow 1993; Vrijenhoek 1998). Many different variants of parthenogenesis and apomixis exist but not all of these variants result in true clonal offspring (de Meeus et al. 2007). Clonality depends on if or how meiotic divisions are suppressed and egg cell ploidy level is restored, and some variants have genetic consequences that are intermediate between true clonality and self-fertilization. In this article, we use the term generation as defined by the physiological individual; in the case of vegetative propagation, an individual ramet is considered as offspring of the parental individual from which it derived. We use the term epigenetic inheritance as the stable transmission of epigenetic marks between two or more generations, irrespective of the mode of reproduction (sexual or asexual). Thus, epigenetic inheritance in sexuals involves meiotic stability of epigenetic marks. In asexuals that reproduce through vegetative propagation, it involves only mitotic stability of epigenetic marks. Given the limited capacity of asexuals to generate genetic variation as required for genetic adaptation, can epigenetic variation rescue some of the adaptive potential of an asexual lineage? In this section, we discuss how adaptive evolution differs under sexual and asexual reproduction to explore how epigenetic variation might contribute specifically to adaptation in asexuals. We distinguish between “untargeted” epigenetic modifications and “environment-directed” epigenetic modifications. As pointed out by Shea et al. (2011), these two types of epigenetic variation may share the same molecular mechanism (e.g., DNA methylation) but their evolutionary roles are fundamentally different: (1) environment-directed epigenetic modifications are targeted (nonrandom) epigenetic changes that are environment-dependent. Such modifications can mediate phenotypic plasticity and, when faithfully transmitted to offspring, also transgenerational phenotypic plasticity (detection-based effects; Shea et al. 2011). (2) Untargeted epigenetic modifications that are heritable between generations are comparable to random genetic mutations in the sense that they may contribute to adaptive phenotypes via the action of natural selection (selection-based effects; Shea et al. 2011). AUTONOMY FROM DNA SEQUENCE VARIATION

When considering the evolutionary role of epigenetic variation, one relevant aspect is to what extent epigenetic variation is autonomous, that is, not under genetic control. Epigenetic variation can be genetically determined for instance when allelic variation in DNA methylation is strictly associated with the epigenetic silencing of a nearby transposable element (TE; Richards 2006). However, it is autonomous epigenetic variation that has obvious

646

EVOLUTION MARCH 2014

evolutionary relevance: if epigenetic variation is not autonomous but under direct genetic control then adaptation takes place at the genetic loci that control epigenetic variation, and observed epigenetic variation is a reflection of how the adapted genome expresses itself. The study of epigenetic inheritance in genetically uniform asexual lineages facilitates the identification of autonomous epigenetic variation. However, as we discuss below, epigenetic variation can also have adaptive relevance under different degrees of association between genetic and epigenetic variation. Specifically, when epigenetic mechanisms underpin phenotypic plasticity within or between generations (detection-based effects), the epigenetic variation can be under genetic control that is conditional on the current environment or on the environment experienced by previous generations. ENVIRONMENT-DIRECTED EPIGENETIC VARIATION: PHENOTYPIC PLASTICITY AND TRANSGENERATIONAL EFFECTS

Reshuffling of genomes under sexual reproduction emphasizes fitness effects of individual loci, which can be recombined into novel combinations. This can facilitate the tracking of a moving fitness peak (Burger 1999). With asexual reproduction, in contrast, the response to selection is constrained to entire genomes. This constraint is thought to affect selection on phenotypic plasticity and niche specialism (Vrijenhoek 1979; Lynch 1984). Phenotypic plasticity can evolve as an adaptive strategy when populations and individuals are exposed to variable environments. In asexuals, individual genotypes persist over multiple (somatic) generations and the same genotype is therefore likely exposed to a broad range of environments. Because each present-day clonal genome must have successfully persisted through all environments that it encountered since its incipience, Lynch (1984) argued that asexual reproduction selects, over time, for clonal genotypes that have high geometric mean fitness across different environments (Lynch 1984). Such general-purpose genotypes (Baker 1965) can cope with different environments via high phenotypic plasticity in underlying functional traits (Richards et al. 2006), which can be mediated by epigenetic mechanisms. A simple model to envision epigenetics-mediated phenotypic plasticity is that specific genes (or their regulators) are epigenetically silenced or activated upon perceiving a change in environment, resulting in a modified and environment-specific phenotype. Depending on the stability of the epigenetic changes, the modified gene expression state may or may not persist in the organism after the environmental cue has disappeared, and can potentially be transmitted to offspring if the epigenetic changes resist epigenetic resetting between generations. DNA methylation has been demonstrated to mediate phenotypic plasticity within a single generation (Bossdorf et al. 2010) and between generations (maternal or transgenerational effects; Boyko et al. 2010). The

SPECIAL SECTION

evolutionary implications and adaptive benefits of within- and between-generation phenotypic plasticity are discussed in Herman and Sultan (2011). Stability of environment-directed epigenetic changes beyond a single generation alters adaptive dynamics due to the partial uncoupling of the phenotype from the underlying genotype (Bonduriansky and Day 2009). Given their high dependency on phenotypic plasticity, the evolutionary implications of within- and between-generation phenotypic plasticity are thought to be particularly relevant for asexual taxa (Latzel and Klimesova 2010; Massicotte and Angers 2012). Thus, selection may have favored asexual genotypes with a high capacity for epigenetics-mediated plasticity. SELECTION ON STOCHASTIC EPIGENETIC MUTATIONS

In contrast to environment-directed epigenetic modifications, which are expected to occur in the same way in different individuals from the same genotype when exposed to the same environmental cue, also essentially untargeted or stochastic epigenetic variation may arise. Stochastic variation can arise, for instance, due to imperfect action of enzymes that ensure proper maintenance of epigenetic information through cell division (Schmitz and Ecker 2012), or when exposure to stressful environments triggers an enhanced rate of stochastic “epimutation” (Rapp and Wendel 2005). Transgenerational stability of such epimutations (Cubas et al. 1999; Manning et al. 2006; Verhoeven et al. 2010a) contributes to heritable variation that can, in principle, be shaped by natural selection. Asexuals can adapt via novel beneficial mutations only when these mutations arise sequentially within the same lineage, whereas sexual reproduction allows beneficial mutations from different ancestors to be recombined into single individuals. The latter can speed up adaptation (Hurst and Peck 1996; Burger 1999). Lacking the flexibility that recombination offers, can stochastic epimutations increase the level of selectable within-lineage variation and therefore enhance the adaptive potential of asexual lineages? We address two issues to explore this question. First, are enhanced rates of random epimutations beneficial or deleterious in asexual lineages? Second, how stable should epimutations be to play a role in adaptation? Most random mutations are deleterious, thus selection typically acts to minimize mutation rates in sexual populations (Sniegowski et al. 2000). In asexuals, new beneficial mutations may only fix in the population when they arise in backgrounds that are relatively free of deleterious mutations. Adaptation can be further slowed down by competition between lineages that carry different beneficial mutations (clonal interference; Gerrish and Lenski 1998). In addition, due to stochastic fluctuations also those genotypes can be lost from a population that have few deleterious mutations, leading to the inevitable accumulation of deleterious mutations over time in asexual populations (Muller’s

Ratchet; Muller 1964). The long-term expectation is therefore that obligate asexual populations are driven to extinction due to deleterious mutations (Lynch et al. 1993). Nevertheless, an increase in mutation rate can be observed in asexual populations that evolve under novel experimental conditions (Sniegowski et al. 1997). Modeling studies (Sniegowski et al. 2000) as well as empirical work (Bjedov et al. 2003) show that increased mutation rates can have short-term adaptive benefits in asexuals when they are maladapted or in changing/stressful environments. Provided that some proportion of mutations are beneficial, an optimal strategy is to enhance mutation rates only during episodes of stress: this generates enhanced levels of stochastic variation when populations are under strong selection to change but alleviates the problem that high mutation rates become disadvantageous once adaptation is achieved (Ram and Hadany 2012). Thus, the stochastic variation that is introduced by heritable epimutations (and that comes in addition to stochastic variation due to genetic mutations) has the potential to facilitate short-term adaptation in asexuals in changing or stressful environments. Epigenetic variation can be of particular relevance because stressful environments can trigger enhanced epimutation rates (Rapp and Wendel 2005; Verhoeven et al. 2010a), providing a possible mechanism for fine-tuning stochastic mutation rates to environmental conditions. Are some epialleles stable for a sufficient number of generations to permit selection-based epigenetic adaptation? In a constant environment, long-term stability for many generations may typically be required for natural selection to produce populationlevel adaptation that is based on epiallelic variation (e.g., Slatkin 2009). Less stable epialleles can be a basis for adaptation in such environments only when the strength of selection is high (Klironomos et al. 2013). In rapidly changing environments, however, epimutations that are less stable may play a relevant role. In such changing environments, epigenetic stabilities that match the rate of environmental fluctuations can contribute to transient adaptation (Lachmann and Jablonka 1996; Rando and Verstrepen 2007; Salathe et al. 2009) by allowing populations or lineages to cope with temporal variation in environments without changes to the hardcoded genome. Epimutations that are not long-term stable may also alter selection on genetic mutations and thus affect the course of genetic adaptation: both stochastic and environmentdirected epimutations may "hold" an adaptive phenotype for several generations that could affect subsequent selection on genetic mutations to stabilize the phenotype (Pal and Miklos 1999; see also True et al. 2004; Klironomos et al. 2013). There is currently limited empirical knowledge of the range of stabilities for changes in DNA methylation that are independent of changes in DNA sequence. In Arabidopsis, an analysis of spontaneous DNA methylation variation that arose in 30 generations in mutation accumulation lines showed that heritable

EVOLUTION MARCH 2014

647

SPECIAL SECTION

DNA methylation differences readily build up between lines over generations. However, the number of methylation differences between lines did not increase linearly over generations, which is interpreted as lack of long-term stability of individual mutations (Becker et al. 2011). In the same species, DNA methylation differences between genetically uniform individuals that were induced by transient deficiency in a DNA methylation maintenance enzyme showed variable stabilities but a considerable proportion of the epimutations remained stable over at least eight generations (which was the last generation tested—stability of many epimutations in this system possibly lasts much longer; Johannes et al. 2009; Teixeira et al. 2009). These observations suggest that a subset of epimutations may be sufficiently stable to play a relevant role in adaptation via selection on epiallelic variation. Importantly, if asexual reproduction circumvents some of the epigenetic resetting mechanisms that are associated with meiosis, such observations from sexual species underestimate the potential for epigenetic stability (and thus for adaptation via selection-based epigenetic effects) in asexual species. Whether epigenetic changes are environmentally directed or stochastically induced is likely to influence their adaptive value. For both sources of epigenetic variation, the stability of epigenetic changes across generations will influence their adaptive value in a manner determined by the degree of environmental variability. Moreover, the adaptive value of epigenetic variation may differ between sexual and asexual organisms, because stable epigenetic variation in asexuals has the potential to compensate for the lack of genetic changes introduced by recombination and because environment-directed epigenetic modifications can mediate (transgenerational) phenotypic plasticity, which can be particularly relevant under clonal selection.

Epigenetic Reprogramming Between Generations For epigenetic inheritance that contributes to transgenerational phenotypic plasticity or to heritable and selectable differences between individuals, a key issue is to what extent epigenetic modifications are resistant to epigenetic resetting between generations. Here we briefly review known mechanisms of epigenetic resetting between generations, to evaluate if, or to what extent, asexual reproduction facilitates epigenetic inheritance across asexual generations due to compromised resetting mechanisms.

DNA METHYLATION RESETTING BETWEEN GENERATIONS UNDER SEXUAL REPRODUCTION

DNA methylation has various functions and has different stabilities in different genomic contexts. One function of DNA methylation is to silence TEs and it is important that this function is

648

EVOLUTION MARCH 2014

not affected by epigenetic resetting. DNA methylation at TEs can be actively restored after incidental loss via a small RNA-based mechanism that detects TE transcripts and guides DNA methylation to the active TE locus to silence it (Slotkin and Martienssen 2007); this mechanism ensures stable methylation at TE loci. DNA methylation can also adjust gene expression in response to internal developmental cues and external environmental cues (Yoder et al. 1997; Jaenisch and Bird 2003; Dowen et al. 2012). Such methylation patterns that undergo modifications during life in response to developmental and environmental cues are a more dynamic type of DNA methylation that is thought of as essentially transient. Unconstrained buildup of DNA methylation variation over generations is prevented by epigenetic resetting between generations that removes DNA methylation marks that were acquired dynamically during life while at the same time ensuring proper maintenance of methylation at TE loci. In mammals, epigenetic reprogramming starts in the germline prior to gamete formation and continues into postfertilization embryonic development. Reprogramming involves erasure of DNA methylation in primordial germ cells and in early zygotes, and de novo establishment of methylation marks during gametogenesis and embryonic development (Feng et al. 2010). DNA methylation erasure in this process is extensive but not complete: a subset of genomic regions is resistant or shows variable resistance to large-scale demethylation (Seisenberger et al. 2012). Epigenetic reprogramming in plants is much less pronounced, at least for DNA methylation. There is evidence for some degree of passive demethylation during female gametogenesis (via reduced activity of enzymes that propagate methylation marks during semiconservative DNA replication) followed by de novo remethylation during early embryonic development (Jullien et al. 2012). However, much DNA methylation, especially cytosine methylation in CG contexts, is not reset and stably passes through meiosis and embryonic development (Feng et al. 2010). This may be different for DNA methylation in non-CG sequence contexts, which is more flexible and dynamic and can be less resistant to reprogramming (Paszkowski and Grossniklaus 2011; Dalakouras et al. 2012). In plants, in contrast to the gametes themselves, significant demethylation can occur in cells adjacent to gametes or developing embryos (such as in the endosperm or the pollen vegetative cell), which desuppresses TE activity (Ibarra et al. 2012; Martinez and Slotkin 2012). One hypothesized function of this desuppression is that RNA from transcriptionally reactivated TEs are converted to small RNAs, which are subsequently transported from their cells of origin (which are in terminal tissues) to gametes or the embryo where they can reinforce proper TE silencing by guiding DNA methylation to TE loci. Many of the known epialleles are associated with differentially methylated TE inserts and therefore heritable TE methylation variation is a potentially relevant source

SPECIAL SECTION

of heritable phenotypic variation (Paszkowski and Grossniklaus 2011). Differences in TE methylation between individuals can arise due to effects of environmental stress (Strand and McDonald 1985; Tittel-Elmer et al. 2010); due to some stochasticity in TE silencing (Reiss et al. 2010), and because small RNA-guided methylation of active TE loci does not happen instantly but can develop gradually and progressively over multiple generations (Teixeira et al. 2009). TE activity and silencing can be a relevant source of within-clone epigenetic (Diaz-Martinez et al. 2012) as well as genetic variation (Lushai et al. 2003). CIRCUMVENTING EPIGENETIC REPROGRAMMING UNDER ASEXUAL REPRODUCTION

The above mechanisms outline the potential for transgenerational epigenetic inheritance in sexual organisms. Vegetative propagation and fragmentation lack gametogenesis and embryonic development from zygotes. Although some epigenetic reprogramming must be required for proper cell and tissue differentiation, resetting mechanisms that operate during gametogenesis and in early zygotes are bypassed. These forms of asexual reproduction may therefore have enhanced potential for epigenetic inheritance. In contrast, parthenogenetic and apomictic forms of asexual reproduction seem less likely to bypass epigenetic resetting mechanisms. Depending on the specific type of apomixis, embryos develop from cells that have undergone aberrant meiosis or no meiosis at all (Koltunow 1993). We can speculate that in such cases epigenetic resetting mechanisms that act during early embryonic development are unaffected, while resetting mechanisms that act during gametogenesis may or may not be affected. The transient desuppression of TEs that is observed in endosperm and pollen vegetative cells may function to reinforce TE silencing in gametes and embryos (Ibarra et al. 2012). If so, then asexual reproduction that bypasses this gametophytic process can result in compromised ability to silence active TEs (unless other tissues such as meristems take over the TE silencing function; Martinez and Slotkin 2012). Individuals that are propagated clonally through tissue culture often show some level of phenotypic variation (somaclonal variation) that is correlated with epigenetic differences and that can be caused by desuppression of TE activity (Hirochika et al. 1996; Kaeppler et al. 2000). It has been proposed that the bypassing of meiotic epigenetic reprogramming in tissue culture promotes epigenetic instability, which could lead to reactivated TEs (Kaeppler et al. 2000). TESTING THE EPIGENETIC CONSEQUENCES OF ASEXUAL REPRODUCTION

If and how epigenetic resetting differs between sexual and asexual reproduction could be compared between different reproduction modes within the same species. To our knowledge no such studies exist that have compared transgenerational transmission of epige-

netic variation directly, and only very few studies provide some indirect evidence. In dandelions, which have both apomictic and sexual genotypes, higher rates of chromosomal rearrangements were observed in apomicts than in sexuals; this was interpreted to indicate increased TE activity in the apomicts (Richards 1989). Because it is unclear whether apomixis in dandelion circumvents any of the epigenetic resetting mechanisms that operate in sexuals, the underlying mechanism of enhanced TE activity in apomicts might be unrelated to epigenetic resetting. Alternatively, it could be related to less efficient selection against deleterious mutations in asexuals (Kraaijeveld et al. 2012). Comparing seed-derived and rhizome-derived offspring from the same mother plants in Solidago and Aster, it was found that phenotypic plasticity is higher in rhizome-derived offspring (Schmid and Bazzaz 1990). In arctic sedge, consistent with stable epigenetic transmission through vegetative reproduction, strong parental environmental effects on vegetative offspring traits have been observed (Schwaegerle et al. 2000). It would be interesting to test inheritance of environmentinduced phenotypes between sexual and asexual reproduction, as epigenetic mechanisms such as DNA methylation are likely candidates to mediate these transgenerational effects. Some observations on plant flowering time also hint at the enhanced potential for transmission of epigenetic states between generations in clonal organisms. Some plants require exposure to low temperatures (vernalization) to be capable of flowering later in life. Flowering ability is achieved by cold-induced epigenetic silencing of flower repressor genes (Henderson et al. 2003). After vernalization, this epigenetic state is maintained over many mitotic cell divisions and for an extended period of time, allowing for initiation of flowering long after reaching the vernalized state. The epigenetic state is reset at meiosis so that sexually produced offspring require new vernalization to flower (Sheldon et al. 2000). However, a memory of vernalization is retained in vegetatively produced offspring: plantlets grown from leaf or root cuttings can flower more readily when obtained from vernalized donor plants (Wellensiek 1964; Demeulemeester and De Proft 1999). Asexual organisms are likely to exhibit epigenetic changes that persist across clonal generations, although how epigenetic stability differs with different modes of asexual reproduction remains to be determined. Moreover, specific comparisons of the epigenetic stability of asexual and sexual organisms, or sexual and asexual phases of the same organism, have yet to be conducted.

Natural Epigenetic Variation in Asexual Organisms Evidence that epigenetic variation contributes to adaptation should ultimately come from studies in natural populations. From our discussion of adaptation and epigenetic reprogramming in

EVOLUTION MARCH 2014

649

SPECIAL SECTION

asexuals, it can be predicted that transgenerational effects and also appreciable levels of standing heritable epigenetic variation should be readily detectable in natural populations of asexuals, especially under somatic asexual reproduction. What is the current status of evidence for this prediction? Below we highlight some recent studies on asexual organisms that explore environmentinduced heritable epigenetic variation and epigenetic variation in naturally occurring clonal lineages. TRANSMISSION OF ENVIRONMENT-INDUCED EPIGENETIC VARIATION

Raj et al. (2011) investigated vegetative offspring (through stem cuttings) of the same poplar genotypes that had been raised at different nurseries under distinct environmental conditions. When tested under common environmental conditions, two of three genotypes showed within-genotype differences in global DNA methylation and in transcriptomic drought response that were related to the nursery location of the mother plants. These effects were more pronounced in genotypes that had been grown for the longest period at different locations. Thus, genetically identical ramets build up epigenetic and functional gene expression differences in different environments, and this differentiation is transmitted to vegetative offspring (Raj et al. 2011). In apomictic dandelion, genetically identical plants that were derived from the same mother through clonal seeds were exposed to different experimental conditions and their methylation variation was assessed using methylation sensitive amplified fragment length polymorphism (MS-AFLPs). At a subset of loci with labile DNA methylation, stressed plants showed increased rates of DNA methylation change and the majority of these modifications were faithfully transmitted (74–92%) to unexposed apomictic offspring (Verhoeven et al. 2010a). The function of the observed DNA methylation changes is unclear, because the MS-AFLP method is an anonymous marker locus approach. But the same stresses can also induce heritable phenotypic effects in dandelion (Verhoeven and van Gurp 2012), suggesting the possibility that stress-induced DNA methylation changes are an underlying mechanism for transgenerational effects on offspring phenotypes. It is often argued that to demonstrate environment-directed transgenerational epigenetic inheritance, persistent effects need to be shown not only in first-generation offspring but also in subsequent generations to rule out direct induction of developing embryos (Paszkowski and Grossniklaus 2011). In animals, when a gestating female is exposed to an environmental stress (F0 ) then her offspring (F1 ) and also the germline within the developing offspring (leading to the F2 ) can be exposed directly. The unequivocal demonstration of transgenerational epigenetic inheritance therefore requires demonstration of inherited effects in the F3 generation when gravid F0 females are exposed (Jirtle and Skinner 2007). In plants, which do not set apart a germline

650

EVOLUTION MARCH 2014

early in development, effects need to be demonstrated in the F2 generation. To date, studies that evaluate induced environmental effects beyond the first offspring generation are rare in asexual organisms. In the parthenogenetic springtail Folsomia candida, effects of both parental and grandparental nutrient environments were detected on life history traits (Hafer et al. 2011). However, the direction of these specific effects did not indicate adaptive significance; exposure to nutrient stress in previous generations affected but did not enhance offspring fitness under nutrient stress (Hafer et al. 2011). In parthenogenetically reproducing aphids (Acyrthosiphon pisum), unwinged individuals produce winged offspring in response to environmental cues and represent a model to study the epigenetic mechanisms involved in phenotypic plasticity and polyphenism (Srinivasan and Brisson 2012). Observations in this aphid system suggest that epigenetic variation might contribute to stable phenotypic variation within morphs. Exposure of the same aphid genotype to different environments resulted in DNA methylation differences between and within environments, which was associated with a distinct repertoire of molecular, physiological, and behavioral phenotypes (Dombrovsky et al. 2009). Such epigenetically based variation could be a basis for selection of adaptive variants within specific environments (as the authors of the study suggested; Dombrovsky et al. 2009). However, as is the case with studies that screen epigenetic variation in field-collected individuals (e.g. Massicotte et al. 2011), stable heritable transmission of epigenetic variants cannot be distinguished from nonheritable but repeated induction by the same environmental experiences in each new generation. Both within-generation and between-generation phenotypic plasticity can have adaptive relevance, but to distinguish these two possibilities it is necessary to perform controlled experiments in which offspring generations of field-collected individuals can be evaluated in a common environment.

WITHIN-CLONE EPIGENETIC VARIATION IN NATURAL POPULATIONS

If heritable epigenetic variation contributes to phenotypic variation that is adaptive, we expect to find epigenetic differentiation to habitat type between populations that consist of the same clonal genotype. Several recent studies have looked for this pattern, either in field-collected individuals, that potentially harbor an environment-induced epigenetic component that is not heritable, or in offspring grown in common environments (Gao et al. 2010; Massicotte et al. 2011; Massicotte and Angers 2012; Richards et al. 2012). These studies require DNA methylation screening at the population level and have typically used marker methods such as MS-AFLPs. The limitations with this approach lay in the functional interpretation of anonymous markers and, as with genetic variation, the challenge to distinguish adaptation

SPECIAL SECTION

from neutral processes such as epigenetic drift (Richards et al. 2010). With these limitations in mind, interesting patterns of epigenetic variation were observed in natural populations of invasive Japanese knotweed (Fallopia japonica) in northeastern USA. The species can reproduce clonally and rhizome-derived plants collected from replicated sites covering distinct habitat types show habitat-specific phenotypes when grown in common environments (Richards et al. 2008). AFLP and MS-AFLP screening in common garden experiments of plants from multiple sites from each habitat type revealed much stronger epigenetic than genetic differentiation. Additionally, epigenetic differentiation to habitat type was also found in widespread clonal genotypes for which no AFLP variation could be detected (Richards et al. 2012). Although the functional consequences and also the multigeneration stability of the observed epigenetic variation remain to be demonstrated, these observations are consistent with the idea that epigenetic variation allows a single clonal genotype to adjust its phenotype to different environments. It remains possible, however, that undetected genetic variation plays a role in habitat differentiation. Adaptive matching of a clonal phenotype to its specific environment can be brought about either through specific environment-induced epigenetic modifications, or through environmental selection of stochastically arising epigenetic variations. Induction of environment-specific epigenetic modifications is suggested by observations in Alligator weed (Alternanthera philoxeroides), an invasive weed in China that reproduces clonally through stolons. MS-AFLP analysis of natural field grown plants showed very little genetic but much epigenetic variation, with DNA methylation differentiated geographically but also between wet or dry habitat types within each sampling locality (Gao et al. 2010). In a common garden experiment, largescale DNA methylation reprogramming as well as phenotypic adjustment was observed due to experimental “dry” and “wet” treatments, resulting in many shared DNA methylation polymorphisms between plants from different origins exposed to the same treatment. Within-genotype DNA methylation variation has also been observed in natural populations of the hybrid clonal fish Chrosomus eos-neogaeus (Massicotte et al. 2011; Massicotte and Angers 2012). MS-AFLP variation within genotypes was differentiated between lakes and also correlated with an environmental variable (pH). Thus, dynamic DNA methylation might contribute to phenotypic plasticity in these clonal genotypes, allowing the clonal lineage to exploit broad ecological niches. This would be an epigenetic basis of general-purpose genotypes. Epigenetic variation exists within natural populations and between natural populations that inhabit different environments.

Experimental studies have shown that the environments can contribute to such heritable differences in epigenetic states. What remains to be tested explicitly is the adaptive significance of these epigenetic differences.

Conclusion and Perspectives Asexual organisms are convenient models to study the causes and evolutionary consequences of epigenetic variation because clonal identity controls for the confounding effects of genetic variation; when both genetic and epigenetic vary it is difficult to unravel the two and to identify the epigenetic contribution to trait variation. Furthermore, it emphasizes the effects of epigenetic variation that is autonomous, that is, not under direct genetic control. Asexuals also offer good opportunities to track epigenetic variation within genetically uniform lineages in natural populations (Gao et al. 2010; Richards et al. 2012)—although it remains challenging to distinguish epigenetic effects from the effects of genetic mutations that build up within lineages over microevolutionary time (Lushai et al. 2003). Compared to sexuals, we hypothesize that epigenetic inheritance has a larger impact on adaptive dynamics in asexuals because (1) phenotypic plasticity, both within and between generations, can be a particularly relevant adaptive strategy under clonal selection (Lynch 1984) and such plasticity can be mediated via environment-directed epigenetic modifications; and (2) stochastic epimutations can contribute random heritable variation within asexual lineages and thus may rescue some of their adaptive potential that is otherwise constrained by their inability to generate variation through recombination and segregation. In addition, and depending on the type of asexual reproduction, asexual organisms may circumvent some of the epigenetic reprogramming mechanisms that are typically operating during gametogenesis and early embryonic development in sexual species. Compared to sexuals, asexuals are therefore predicted to accumulate epigenetic differences between individuals and lineages more easily, suggesting a larger potential for an epigenetic contribution to adaptation. Research in recent years is revealing considerable potential for transgenerational epigenetic inheritance in sexual species (Jablonka and Raz 2009; Johannes et al. 2009; Becker et al. 2011; Schmitz et al. 2011). In asexual organisms this potential has remained little studied, despite a predicted enhanced relevance for epigenetic variation. Studies that have started to explore epigenetic variation in asexuals have demonstrated the transmission of environmental epigenetic modifications, transcriptomes and phenotypes from parent to asexually produced offspring (Verhoeven et al. 2010a; Hafer et al. 2011; Raj et al. 2011; Verhoeven and van Gurp 2012). These studies also show within-genotype epigenetic variation that is correlated with habitat differences and

EVOLUTION MARCH 2014

651

SPECIAL SECTION

that is stably maintained through asexual reproduction (e.g., Richards et al. 2012). None of these studies unequivocally demonstrate epigenetic adaptation in asexuals; more detailed study approaches are required for that (see below). But these initial observations in natural systems generally agree with the hypothesis that epigenetic inheritance is a relevant factor in the ecology and adaptation of asexuals. To improve our understanding of the adaptive relevance of epigenetic variation for asexual organisms, we suggest that the following topics are important research priorities. 1. Baseline data on epigenetic inheritance in asexuals, in controlled experimenta, and in natural populations Recent studies on natural epigenetic variation in asexuals represent an early stage in the research field of ecological epigenetics and there is currently very limited insight into the basic characteristics and natural patterns of epigenetic variation in asexual lineages. How readily does epigenetic variation arise within lineages? How much of this variation associates with functional and phenotypic variation? What is the range of stabilities of epigenetic modifications in asexuals? How common are correlations between habitat and epigenetic variation in asexual lineages? Because the adaptive significance of epigenetic inheritance likely depends on the time scale of environmental change (Rando and Verstrepen 2007), we expect that the study of asexuals in contexts of rapid environmental change is a promising approach, for instance during range expansions or during exposure to novel biotic and abiotic interactions in biological invasions (Richards et al. 2012). 2. Tools for epigenetic screening in nonmodel organisms Understanding the adaptive relevance of epigenetic variation requires the functional characterization from epigenetic patterns to associated gene expression effects to phenotypes and fitness, ultimately documenting selective effects of epigenetic variants in natural environments. The techniques that are used for screening DNA methylation variation present a pressing challenge to the study of ecological and evolutionary epigenetics in nonmodel species (Schrey et al. 2013). Most of the studies in this review use asexual species for which no sequenced reference genome is currently available. This severely limits the possibilities for high-resolution bisulfite sequencing approaches that can generate DNA methylation information at base pair-resolution for either specific genes of interest or even for whole genomes (e.g., Becker et al. 2011; Schmitz et al. 2011). Instead, ecological epigenetics studies typically use methylation-sensitive AFLPs, which use isoschizomers with different methylation sensitivities to probe DNA methylation at many anonymous marker loci simultaneously. This method has proved to be a very useful tool in pop-

652

EVOLUTION MARCH 2014

ulation studies for documenting global patterns of methylation variation and (dis)similarities between individuals and populations. However, further insight in the contribution of epigenetics to adaptation requires more detailed understanding of methylation variation at specific and functionally characterized loci. One approach that has been followed involves the identification, excision, and sequencing of interesting polymorphic MS-AFLP fragments, searching for sequence homology in reference databases to gain functional insight, and subsequent population-level bisulfite sequencing of selected loci (Massicotte et al. 2011). Other approaches can be envisioned (Schrey et al. 2013) including dense DNA methylation genotyping using high-throughput sequencing (Feng et al. 2011); most progress is to be expected from bringing large-scale bisulfite sequencing approaches within reach for more study systems. 3. Explicit comparison of the adaptive significance of epigenetic variation between sexuals and asexuals The predictions that epigenetic variation is both more relevant and can show more stability across generations in asexuals compared to sexuals can be tested empirically. Does an enhanced epigenetic stability in asexuals in fact confer adaptive advantages? To date explicit sexual–asexual comparisons are virtually lacking in epigenetics studies. Modeling studies that explore how adaptive dynamics are impacted by (transgenerational) phenotypic plasticity and stochastic epimutations of variable stability may be extended to contrast these impacts under sexual versus asexual reproduction. One key aspect in these models is environmental heterogeneity, both temporal and spatial. For instance, in sessile organisms such as plants, asexual reproduction through vegetative propagation results in offspring growing in similar environments as parents. It is easy to envision the advantage of inheriting the parental epigenome and transcriptome when parental gene expression profiles are fine-tuned to local environmental conditions. In contrast, parent–offspring environments will be less correlated when there is long-distance dispersal of offspring, making it less likely that inheriting the parental epigenome and transcriptome is advantageous. A difference in epigenetic transmission across generations between sexuals and asexuals can be tested empirically using species that show both types of reproduction. For instance, several plant species have both sexual and apomictic variants (van Dijk 2003) or can reproduce sexually through seeds as well as asexually through vegetative propagation (Schmid and Bazzaz 1990), and some animals switch between sexual and parthenogenetic episodes (Srinivasan and Brisson 2012). Such systems can be exploited to identify aspects of epigenetic inheritance that are specific to asexual reproduction, and can provide important general insights into the adaptive significance of epigenetic variation.

SPECIAL SECTION

ACKNOWLEDGMENTS We thank C. Richards, A. Biere, K. Slotkin, the anonymous reviewers, and the associate editor for useful discussion and comments on the manuscript. Funding was provided by the Netherlands Organisation for Scientific Research (NWO). This is publication 5530 of the Netherlands Institute of Ecology (NIOO-KNAW).

LITERATURE CITED Ahmad, R., P. S. Liow, D. F. Spencer, and M. Jasieniuk. 2008. Molecular evidence for a single genetic clone of invasive Arundo donax in the United States. Aquat. Bot. 88:113–120. Anway, M. D., A. S. Cupp, M. Uzumcu, and M. K. Skinner. 2005. Epigenetic transgenerational actions of endocrine disruptors and mate fertility. Science 308:1466–1469. Baker, H. G. 1965. Characteristics and modes of origins of weeds. Pp. 147– 172 in H. G. Baker and G. L. Stebbins, eds. The genetics of colonizing species. Academic Press, New York. Becker, C., J. Hagmann, J. Muller, D. Koenig, O. Stegle, K. Borgwardt, and D. Weigel. 2011. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480:245–249. Bell, G. 1982. The masterpiece of nature: the evolution and genetics of sexuality. Springer, Berkeley, CA. Bjedov, I., O. Tenaillon, B. Gerard, V. Souza, E. Denamur, M. Radman, F. Taddei, and I. Matic. 2003. Stress-induced mutagenesis in bacteria. Science 300:1404–1409. Bonduriansky, R., and T. Day. 2009. Nongenetic inheritance and its evolutionary implications. Annu. Rev. Ecol. Evol. Syst. 40:103–125. Bossdorf, O., D. Arcuri, C. L. Richards, and M. Pigliucci. 2010. Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana. Evol. Ecol. 24:541–553. Bossdorf, O., C. L. Richards, and M. Pigliucci. 2008. Epigenetics for ecologists. Ecol. Lett. 11:106–115. Boyko, A., T. Blevins, Y. L. Yao, A. Golubov, A. Bilichak, Y. Ilnytskyy, J. Hollander, F. Meins, and I. Kovalchuk. 2010. Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins. Plos One 5:e9514. Burger, R. 1999. Evolution of genetic variability and the advantage of sex and recombination in changing environments. Genetics 153:1055–1069. Castonguay, E., and B. Angers. 2012. The key role of epigenetics in the persistence of asexual lineages. Genet. Res. Int. 2012:534289. doi: 10.1155/2012/534289. Cubas, P., C. Vincent, and E. Coen. 1999. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401:157–161. Dalakouras, A., E. Dadami, M. Zwiebel, G. Krczal, and M. Wassenegger. 2012. Transgenerational maintenance of transgene body CG but not CHG and CHH methylation. Epigenetics 7:1071–1078. de Meeus, T., F. Prugnolle, and P. Agnew. 2007. Asexual reproduction: Genetics and evolutionary aspects. Cell. Mol. Life Sci. 64:1355–1372. Demeulemeester, M., and M. De Proft. 1999. In vivo and in vitro flowering response of chicory (Cichorium intybus L.): influence of plant age and vernalization. Plant Cell Rep. 18:781–785. Diaz-Martinez, M., A. Nava-Cedillo, J. A. Guzman-Lopez, R. EscobarGuzman, and J. Simpson. 2012. Polymorphism and methylation patterns in Agave tequilana Weber var. ‘Azul’ plants propagated asexually by three different methods. Plant Sci. 185:321–330. Dombrovsky, A., L. Arthaud, T. N. Ledger, S. Tares, and A. Robichon. 2009. Profiling the repertoire of phenotypes influenced by environmental cues that occur during asexual reproduction. Genome Res. 19:2052–2063. Dowen, R. H., M. Pelizzola, R. J. Schmitz, R. Lister, J. M. Dowen, J. R. Nery, J. E. Dixon, and J. R. Ecker. 2012. Widespread dynamic DNA

methylation in response to biotic stress. Proc. Natl. Acad. Sci. USA 109:e2183–e2191. Feinberg, A. P., and R. A. Irizarry. 2010. Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc. Natl. Acad. Sci. USA 107:1757–1764. Feng, S. H., S. E. Jacobsen, and W. Reik. 2010. Epigenetic reprogramming in plant and animal development. Science 330:622–627. Feng, S. H., L. Rubbi, S. E. Jacobsen, and M. Pellegrini. 2011. Determining DNA methylation profiles using sequencing. Pp. 223–238 in Y. M. Kwon and S. C. Ricke, eds. High-throughput next generation sequencing: methods and applications. Springer, New York. Gao, L. X., Y. P. Geng, B. Li, J. K. Chen, and J. Yang. 2010. Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation. Plant Cell Environ. 33:1820–1827. Gerrish, P. J., and R. E. Lenski. 1998. The fate of competing beneficial mutations in an asexual population. Genetica 102–103:27–144. Gorelick, R., M. Laubichler, and R. Massicotte. 2011. Asexuality and epigenetic variation. Pp. 87–102 in B. Hallgrimsson and B. K. Hall, eds. Epigenetics: linking genotype and phenotype in development and evolution. Univ. of California Press, CA. Hafer, N., S. Ebil, T. Uller, and N. Pike. 2011. Transgenerational effects of food availability on age at maturity and reproductive output in an asexual collembolan species. Biol. Lett. 7:755–758. Henderson, I. R., C. Shindo, and C. Dean. 2003. The need for winter in the switch to flowering. Annu. Rev. Genet. 37:371–392. Herman, J. J., and S. E. Sultan. 2011. Adaptive transgenerational plasticity in plants: case studies, mechanisms, and implications for natural populations. Front. Plant Sci. 2:102. doi:10.3389/fpls.2011000102. Herrera, C. M., M. I. Pozo, and P. Bazaga. 2012. Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast. Mol. Ecol. 21:2602–2616. Hirochika, H., K. Sugimoto, Y. Otsuki, H. Tsugawa, and M. Kanda. 1996. Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl. Acad. Sci. 93:7783–7788. Hollingsworth, M. L., and J. P. Bailey. 2000. Evidence for massive clonal growth in the invasive weed Fallopia japonica (Japanese Knotweed). Bot. J. Linn. Soc. 133:463–472. Hurst, L. D., and J. R. Peck. 1996. Recent advances in understanding of the evolution and maintenance of sex. Trends Ecol. Evol. 11:A46–A52. Ibarra, C. A., X. Feng, V. K. Schoft, T. F. Hsieh, R. Uzawa, J. A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R. L. Fischer, H. Tamaru, and D. Zilberman. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337:1360–1364. Jablonka, E. 2012. Epigenetic variations in heredity and evolution. Clin. Pharmacol. Therapeut. 92:683–688. Jablonka, E. 2013. Epigenetic inheritance and plasticity: the responsive germline. Prog. Biophys. Mol. Biol. 111:99–107. Jablonka, E., and G. Raz. 2009. Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. Q. Rev. Biol. 84:131–176. Jaenisch, R., and A. Bird. 2003. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 33:245–254. Jirtle, R. L., and M. K. Skinner. 2007. Environmental epigenomics and disease susceptibility. Nat. Rev. Genet. 8:253–262. Johannes, F., E. Porcher, F. K. Teixeira, V. Saliba-Colombani, M. Simon, N. Agier, A. Bulski, J. Albuisson, F. Heredia, P. Audigier, D. Bouchez, C. Dillmann, P. Guerche, F. Hospital, and V. Colot. 2009. Assessing the

EVOLUTION MARCH 2014

653

SPECIAL SECTION

impact of transgenerational epigenetic variation on complex traits. Plos Genet. 5:e1000530. Jullien, P. E., D. Susaki, R. Yelagandula, T. Higashiyama, and F. Berger. 2012. DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana. Curr. Biol. 22:1825–1830. Kaeppler, S. M., H. F. Kaeppler, and Y. Rhee. 2000. Epigenetic aspects of somaclonal variation in plants. Plant Mol. Biol. 43:179–188. Klimes, L., J. Klimesova, R. Hendriks, and J. Van Groenendael. 1997. Clonal plant architecture: a comparative analysis of form and function. Pp. 1–29 in H. De Kroon, and J. Van Groenendael, eds. The ecology and evolution of clonal plants. Backhuys, Leiden. Klironomos, F. D., J. Berg, and S. Collins. 2013. How epigenetic mutations can affect genetic evolution: model and mechanism. Bioessays 35: 571–578. Koltunow, A. M. 1993. Apomixis: Embryo sacs and embryos formed without meiosis or fertilization in ovules. Plant Cell 5:1425–1437. Kraaijeveld, K., B. Zwanenburg, B. Hubert, C. Vieira, S. De Pater, J. J. Van Alphen, J. T. Den Dunnen, and P. De Knijff. 2012. Transposon proliferation in an asexual parasitoid. Mol. Ecol. 21:3898– 3906. Lachmann, M., and E. Jablonka. 1996. The inheritance of phenotypes: an adaptation to fluctuating environments. J. Theor. Biol. 181:1–9. Latzel, V., and J. Klimesova. 2010. Transgenerational plasticity in clonal plants. Evol. Ecol. 24:1537–1543. Levy, S. F., N. Ziv, and M. L. Siegal. 2012. Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant. Plos Biol. 10:e1001325. Lushai, G., H. D. Loxdale, and J. A. Allen. 2003. The dynamic clonal genome and its adaptive potential. Biol. J. Linn. Soc. 79:193–208. Lynch, M. 1984. Destabilizing hybridization, general-purpose genotypes and geographic parthenogenesis. Q. Rev. Biol. 59:257–290. Lynch, M., R. Burger, D. Butcher, and W. Gabriel. 1993. The mutational meltdown in asexual populations. J. Hered. 84:339–344. Manning, K., M. Tor, M. Poole, Y. Hong, A. J. Thompson, G. J. King, J. J. Giovannoni, and G. B. Seymour. 2006. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 38:948–952. Martinez, G., and R. K. Slotkin. 2012. Developmental relaxation of transposable element silencing in plants: functional or byproduct? Curr. Opin. Plant Biol. 15:496–502. Massicotte, R., and B. Angers. 2012. General-purpose genotype or how epigenetics extend the flexibility of a genotype. Genet. Res. Int. 2012:317175. doi: 10.1155/2012/317175. Massicotte, R., E. Whitelaw, and B. Angers. 2011. DNA methylation A source of random variation in natural populations. Epigenetics 6:422–428. Muller, H. J. 1964. The relation of recombination to mutational advance. Mutat. Res. 1:2–9. Pal, C., and I. Miklos. 1999. Epigenetic inheritance, genetic assimilation and speciation. J. Theor. Biol. 200:19–37. Paszkowski, J., and U. Grossniklaus. 2011. Selected aspects of transgenerational epigenetic inheritance and resetting in plants. Curr. Opin. Plant Biol. 14:195–203. Prach, K., and P. Pysek. 1994. Clonal plants—what is their role in succession? Folia Geobot. 29:307–320. Raj, S., K. Brautigam, E. T. Hamanishi, O. Wilkins, B. R. Thomas, W. Schroeder, S. D. Mansfield, A. L. Plant, and M. M. Campbell. 2011. Clone history shapes Populus drought responses. Proc. Natl. Acad. Sci. USA 108:12521–12526. Ram, Y., and L. Hadany. 2012. The evolution of stress-induced hypermutation in asexual populations. Evolution 66:2315–2328.

654

EVOLUTION MARCH 2014

Rando, O. J., and K. J. Verstrepen. 2007. Timescales of genetic and epigenetic inheritance. Cell 128:655–668. Rapp, R. A., and J. F. Wendel. 2005. Epigenetics and plant evolution. New Phytol. 168:81–91. Reiss, D., Y. Zhang, A. Rouhi, M. Reuter, and D. L. Mager. 2010. Variable DNA methylation of transposable elements: the case study of mouse Early Transposons. Epigenetics 5:68–79. Richards, A. 1989. A comparison of within-plant karyological heterogeneity between agamospermous and sexual Taraxacum (Compositae) as assessed by the nucleolar organiser chromosome. Plant Syst. Evol. 163:177–185. Richards, C. L., O. Bossdorf, N. Z. Muth, J. Gurevitch, and M. Pigliucci. 2006. Jack of all trades, master of some? On the role of phenotypic plasticity in plant invasions. Ecol. Lett. 9:981–993. Richards, C. L., O. Bossdorf, and K. J. F. Verhoeven. 2010. Understanding natural epigenetic variation. New Phytol. 187:562–564. Richards, C. L., A. W. Schrey, and M. Pigliucci. 2012. Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation. Ecol. Lett. 15:1016–1025. Richards, C. L., R. L. Walls, J. P. Bailey, R. Parameswaran, T. George, and M. Pigliucci. 2008. Plasticity in salt tolerance traits allows for invasion of novel habitat by Japanese knotweed s. l. (Fallopia japonica and Fbohemica, Polygonaceae). Am. J. Bot. 95:931–942. Richards, E. J. 2006. Inherited epigenetic variation–revisiting soft inheritance. Nature reviews. Genetics 7:395–401. Salathe, M., J. Van Cleve, and M. W. Feldman. 2009. Evolution of stochastic switching rates in asymmetric fitness landscapes. Genetics 182:1159– 1164. Satory, D., A. J. E. Gordon, J. A. Halliday, and C. Herman. 2011. Epigenetic switches: can infidelity govern fate in microbes? Curr. Opin. Microbiol. 14:212–217. Schmid, B., and F. Bazzaz. 1990. Plasticity in plant size and architecture in rhizome-derived vs. seed-derived Solidago and Aster. Ecology 71:523– 535. Schmitz, R. J., and J. R. Ecker. 2012. Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends Plant Sci. 17:149–154. Schmitz, R. J., M. D. Schultz, M. G. Lewsey, R. C. O’Malley, M. A. Urich, O. Libiger, N. J. Schork, and J. R. Ecker. 2011. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334:369–373. Schrey, A., M. Alvarez, C. Foust, H. Kilvitis, J. Lee, A. Liebl, L. Martin, C. Richards, and M. Robertson. 2013. Ecological epigenetics: beyond MS-AFLP. Integr. Comp. Biol. 53:340–350. Schwaegerle, K. E., H. McIintyre, and C. Swingley. 2000. Quantitative genetics and the persistence of environmental effects in clonally propagated organisms. Evolution 54:452–461. Seisenberger, S., S. Andrews, F. Krueger, J. Arand, J. Walter, F. Santos, C. Popp, B. Thienpont, W. Dean, and W. Reik. 2012. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell 48:849–862. Shea, N., I. Pen, and T. Uller. 2011. Three epigenetic information channels and their different roles in evolution. J. Evol. Biol. 24:1178–1187. Sheldon, C. C., D. T. Rouse, E. J. Finnegan, W. J. Peacock, and E. S. Dennis. 2000. The molecular basis of vernalization: the central role of flowering locus C (FLC). Proc. Natl. Acad. Sci. USA 97:3753–3758. Slatkin, M. 2009. Epigenetic inheritance and the missing heritability problem. Genetics 182:845–850. Slotkin, R. K., and R. Martienssen. 2007. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8: 272–285.

SPECIAL SECTION

Sniegowski, P. D., P. J. Gerrish, T. Johnson, and A. Shaver. 2000. The evolution of mutation rates: separating causes from consequences. Bioessays 22:1057–1066. Sniegowski, P. D., P. J. Gerrish, and R. E. Lenski. 1997. Evolution of high mutation rates in experimental populations of E. coli. Nature 387:703– 705. Srinivasan, D. G., and J. A. Brisson. 2012. Aphids: a model for polyphenism and epigenetics. Genet. Res. Int. 2012:431531. Strand, D. J., and J. F. McDonald. 1985. Copia is transcriptionally responsive to environmental stress. Nucl. Acids Res. 13:4401–4410. Teixeira, F. K., F. Heredia, A. Sarazin, F. Roudier, M. Boccara, C. Ciaudo, C. Cruaud, J. Poulain, M. Berdasco, M. F. Fraga, O. Voinnet, P. Wincker, M. Esteller, and V. Colot. 2009. A role for RNAi in the selective correction of DNA methylation defects. Science 323:1600–1604. Tittel-Elmer, M., E. Bucher, L. Broger, O. Mathieu, J. Paszkowski, and I. Vaillant. 2010. Stress-induced activation of heterochromatic transcription. PLoS Genet. 6:e1001175. True, H. L., I. Berlin, and S. L. Lindquist. 2004. Epigenetic regulation of translation reveals hidden genetic variation to produce complex traits. Nature 431:184–187. van der Woude, M. W. 2011. Phase variation: how to create and coordinate population diversity. Curr. Opin. Microbiol. 14:205–211. van Dijk, P. J. 2003. Ecological and evolutionary opportunities of apomixis: insights from Taraxacum and Chondrilla. Philos. Trans. R. Soc. Lond. 358:1113–1121. Van Groenendael, J. M. and H. De Kroon, eds. 1990. Clonal growth in plants: regulation and function. SPB Academic Publishing, The Hague.

Verhoeven, K. J. F., J. J. Jansen, P. J. van Dijk, and A. Biere. 2010a. Stressinduced DNA methylation changes and their heritability in asexual dandelions. New Phytol. 185:1108–1118. Verhoeven, K. J. F., P. J. Van Dijk, and A. Biere. 2010b. Changes in genomic methylation patterns during the formation of triploid asexual dandelion lineages. Mol. Ecol. 19:315–324. Verhoeven, K. J. F., and T. P. van Gurp. 2012. Transgenerational effects of stress exposure on offspring phenotypes in apomictic dandelion. Plos One 7:e38605. Vrijenhoek, R. C. 1979. Factors affecting clonal diversity and coexistence. Am. Zool. 19:787–797. Vrijenhoek, R. C. 1998. Animal clones and diversity. BioScience 48:617–628. Wellensiek, S. J. 1964. Dividing cells as the prerequisite for vernalization. Plant Physiol. 39:832–835. Yoder, J. A., C. P. Walsh, and T. H. Bestor. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13: 335–340. Zhang, Y. Y., M. Fischer, V. Colot, and O. Bossdorf. 2013. Epigenetic variation creates potential for evolution of plant phenotypic plasticity. New Phytol. 197:314–322. Zhang, Y. Y., D. Y. Zhang, and S. C. H. Barrett. 2010. Genetic uniformity characterizes the invasive spread of water hyacinth (Eichhornia crassipes), a clonal aquatic plant. Mol. Ecol. 19:1774–1786.

Associate Editor: K. Donohue

EVOLUTION MARCH 2014

655