Epialleles in plant evolution

Heritable phenotypic differences caused by epigenetic modifications, rather than DNA sequence mutations, pose a challenge to our understanding of natural variation. Here, we review what is known about plant epialleles and the role of epigenetics in evolution.     

Post-dispersal seed predation: consequences for plant demography and evolution

Post-dispersal seed predation is only one of many factors underlying plant demography and evolution. Nevertheless, the generalist feeding habits of many post-dispersal seed predators and the limited ability of plants either to compensate for or to respond to post-dispersal seed losses directly suggest that post-dispersal seed predation may have a considerable impact on plant populations. Seed predators probably have little direct influence on the demography of plants that regenerate exclusively by vegetative means or are buffered by a large active seed bank, but such species are only a minority in most plant communities.In general, ants are significant post-dispersal seed predators in arid and semi-arid ecosystems while they act mainly as seed dispersers rather than as predators in temperate ecosystems. Although studies have probably underestimated the importance of invertebrates and birds as seed predators, rodents appear to have greater potential to influence seed dynamics, and are particularly important in temperate ecosystems. For example, production of mast seed crops is more effective at satiating specialist invertebrate seed predators than generalist vertebrates, and recruitment may be limited by post-dispersal seed predation even during mast years.Both spatial variation in post-dispersal seed predation and differences in predation between species are important elements which facilitate the coexistence of different plant species. Where microsites are limiting, selective post-dispersal seed predators can influence pre-emptive competition for these microsites. Seed size determines the extent of density-dependent predation and the exploitation of buried seed. This suggests that post-dispersal seed predators may also play a role in the evolution of seed characteristics. However, conclusions regarding the ecological and evolutionary impact of post-dispersal seed predators will remain speculative without a more substantial empirical base.     

DNA cytosine methylation in plant development

Cytosine bases of the nuclear genome in higher plants are often extensively methylated.Cytosine methylation has been implicated in the silencing of both transposable elements (TEs) and endogenous genes,and loss of methylation may have severe functional consequences.The recent methylation profiling of the entire Arabidopsis genome has provided novel insights into the extent and pattern of cytosine methylation and its relationships with gene activity.In addition,the fresh studies also revealed the more dynami...     

iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition

Predominantly occurring on cytosine, DNA methylation is a process by which cells can modify their DNAs to change the expression of gene products. It plays very important roles in life development but also in forming nearly all types of cancer. Therefore, knowledge of DNA methylation sites is significant for both basic research and drug development. Given an uncharacterized DNA sequence containing many cytosine residues, which one can be methylated and which one cannot? With the avalanche of DNA sequences generated during the postgenomic age, it is highly desired to develop computational methods for accurately identifying the methylation sites in DNA. Using the trinucleotide composition, pseudo amino acid components, and a dataset-optimizing technique, we have developed a new predictor called “iDNA-Methyl” that has achieved remarkably higher success rates in identifying the DNA methylation sites than the existing predictors. A user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/iDNA-Methyl, where users can easily get their desired results. We anticipate that the web-server predictor will become a very useful high-throughput tool for basic research and drug development and that the novel approach and technique can also be used to investigate many other DNA-related problems and genome analysis.     

Developmental consequences of imprinting of parental chromosomes by DNA methylation

Genomic imprinting by epigenetic modifications, such as DNA methylation, confers functional differences on parental chromosomes during development so that neither the male nor the female genome is by itself totipotential. We propose that maternal chromosomes are needed at the time when embryonic cells are totipotential or pluripotential, but paternal chromosomes are probably required for the proliferation of progenitor cells of differentiated tissues. Selective elimination or proliferation of embryonic cells may occur if there is an imbalance in the parental origin of some alleles. The inheritance of repressed and derepressed chromatin structures probably constitutes the initial germ-line-dependent 'imprints'. The subsequent modifications, such as changes in DNA methylation during early development, will be affected by the initial inheritance of epigenetic modifications and by the genotype-specific modifier genes. A significant number of transgene inserts are prone to reversible methylation imprinting so that paternally transmitted transgenes are undermethylated, whereas maternal transmission results in hypermethylation. Hence, allelic differences in epigenetic modifications can affect their potential for expression. The germ line evidently reverses the previously acquired epigenetic modifications before the introduction of new modifications. Errors in the reversal process could result in the transmission of epigenetic modifications to subsequent generation(s) with consequent cumulative phenotypic and grandparental effects.     

Polyploidy: its consequences and enabling role in plant diversification and evolution

BackgroundMost, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility.ScopeWorld-wide interest in how green plants have evolved under different conditions – whether in small, isolated populations, or globally – suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany, consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids.ConclusionChromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy – generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses.     

Arbuscular mycorrhizal fungi change host plant DNA methylation systemically

• DNA methylation is an important epigenetic mechanism regulating gene expression in plants. DNA methylation has been shown to vary among species and also among plant tissues. However, no study has evaluated whether arbuscular mycorrhizal (AM) fungi affect DNA methylation levels in a tissue‐specific manner.
• We investigated whether symbiosis with AM fungi affects DNA methylation in the host, focusing on different plant tissues (roots versus leaves) and across time. We carried out a 6‐month pot experiment using Geranium robertianum in symbiosis with the AM fungus Funneliformis mosseae.
• Our results show that the pattern of total DNA methylation differed between leaves and roots and was related to when plants were harvested, confirming that DNA methylation is a process that occurs dynamically throughout an organism's lifetime. More importantly, the presence of AM fungus in roots of our experimental plants had a positive effect on total DNA methylation in both tissues.
• This study shows that colonisation by AM fungi can affect DNA methylation levels in their hosts and that plant DNA methylation varies in an age‐ and tissue‐specific manner.

     

Ecological consequences of evolution in plant defenses in a metacommunity

Dispersal can affect the assembly of local communities in a metacommunity as well as evolution of local populations in a metapopulation. These two processes may also affect each other in ways that have not yet been well studied and that may have novel effects on community structure. Here, we illustrate the interaction of these two processes on community structure with a model of adaptive evolutionary dynamics of plant defenses in a metacommunity food web involving multiple patches along a productivity gradient. We find an enhanced suite of adaptive plant types in our metacommunity model than is predicted in the absence of dispersal. We also find that this, and the movement of nutrients among patches via dispersal, alters patterns of food web architecture, trophic structure and diversity along the productivity gradient. Overall, our model illustrates that evolutionary and metacommunity dynamics may influence communities in complex interactive ways that may not be predicted by models that ignore either of these types of processes.     

Complex interactions between a plant pathogen and insect parasitoid via the shared vector-host: consequences for host plant infection

Plant viruses modify the development of their aphid vectors by inducing physiological changes in the shared host plant. The performance of hymenopterous parasitoids exploiting these aphids can also be modified by the presence of the plant pathogen. We used laboratory and glasshouse microcosms containing beans (Vicia faba) as the host plant to examine the interactions between a plant virus (pea enation mosaic virus; PEMV) and a hymenopterous parasitoid (Aphidius ervi) that share the aphid vector/host Acyrthosiphon pisum. Neither PEMV-infection of V. faba, nor the carriage of PEMV virions by A. pisum, affected the growth or morphology of the aphid, or the oviposition behaviour and development of A. ervi. The presence of developing Aphidius ervi larvae within Acyrthosiphon pisum did not affect the ability of the aphids to transmit PEMV. However, by reducing their longevity, parasitism ultimately decreased the time viruliferous aphids were able to inoculate plants. In terms of virus dispersal, parasitized aphids exhibited more movement around experimental arenas than unparasitized controls, causing a slight increase in the proportion of beans infected with PEMV. Exposure to adult Aphidius ervi caused Acyrthosiphon pisum to rapidly drop off bean plants and disperse to new hosts, resulting in considerably higher plant infection rates (70%) than that seen in control arenas (25%). The results of this investigation demonstrate that when parasitoids are added to a plant-pathogen-vector system, benefits to the host plant due to reduced herbivore infestation must be balanced against the consequences of parasitoid-induced aphid dispersal and a subsequent increase in the level of plant infection.     

Stage-specific DNA methylation in a fungal plant pathogen.

Significantly more 5-methylcytosine residues were found in the DNA from the dormant sclerotia of Phymatotrichum omnivorum than in the DNA from the metabolically active mycelia of the fungus, as shown by high-pressure liquid chromatography of acid-hydrolyzed DNA digests and by restriction of the DNA with the isoschizomers MspI and HpaII. N6-Methyladenine was not detected in GATC sequences in the DNA isolated from either stage.     

Animal personalities: consequences for ecology and evolution

Personality differences are a widespread phenomenon throughout the animal kingdom. Past research has focused on the characterization of such differences and a quest for their proximate and ultimate causation. However, the consequences of these differences for ecology and evolution received much less attention. Here, we strive to fill this gap by providing a comprehensive inventory of the potential implications of personality differences, ranging from population growth and persistence to species interactions and community dynamics, and covering issues such as social evolution, the speed of evolution, evolvability, and speciation. The emerging picture strongly suggests that personality differences matter for ecological and evolutionary processes (and their interaction) and, thus, should be considered a key dimension of ecologically and evolutionarily relevant intraspecific variation.