Genetic variability of Sesamum indicum1 against damage caused by three Diabrotica2 species in Guerrero, Mexico

A synthesis is underway between ecology and evolution, partly brought about by the realization that evolutionary change can take place on ecological timescales (Hairston et al., 2005; Whitham et al., 2006; Carroll et al., 2007). This synthesis attempts to understand the dynamic interplay of ecological and evolutionary processes that results from natural or anthropogenic selective forces (Lankau & Strauss, 2007). Moreover, this synthesis represents an integration of several ‘genes to ecosystems’ approaches, including ‘ecological stochiometry’, ‘community genetics’ (Whitham et al., 2006) and ‘niche construction’. United under the framework of ‘eco-evolutionary dynamics’, these ideas seek to link genetic and phenotypic variation to population dynamics, biodiversity and ecosystem function, and place these disciplines in a dynamic evolutionary framework (i.e. understanding the ecological consequences of evolutionary processes and the evolutionary consequences of ecological interactions). This is not an easy endeavor because any such synthesis needs to be broadly multidisciplinary and integrative (Whitham et al., 2006). And yet the potential pay offs are large given that genetic variation across plant and animal systems can have extended consequences at the population, community and ecosystem levels. These consequences can come in the form of the vital rates of survival, reproduction and migration, as well as arthropod and aquatic macroinvertebrate diversity, soil microbial communities, trophic interactions, carbon storage, soil nitrogen availability, dissolved organic nitrogen and production of primary producers (Whitham et al., 2006; Bailey et al., 2009; Ezard et al., 2009; Harmon et al., 2009; Johnson et al., 2009; Palkovacs et al., 2009; Post & Palkovacs, 2009). The effects of genetic or phenotypic variation are not limited to single systems or to ecologically important species (i.e. keystone species, dominant species, foundation species, ecosystem engineers), although these are excellent places to start looking. Instead, genetic variation seems to have effects that are broadly distributed across plant and animal systems - and these effects can be similar in magnitude to those of nonevolutionary ecological variables, such as climate, species invasion and habitat quality (Hairston et al., 2005; Bailey et al., 2009; Ezard et al., 2009; Palkovacs et al., 2009; Post & Palkovacs, 2009).

Measuring stress-induced DNA methylation in apomictic Dandelions

Problematic Use of Greenberg's Linguistic Classification of the Americas in Studies of Native American Genetic Variation

Polyploidization (whole genome duplication – WGD) is a recurrent process in plants and provides greater potential for diversification. Neopolyploids in natural populations should go under substantial structural changes in their genetics, reproductive mode (e.g. apomixis – asexual reproduction via seeds), and ecological preferences to ensure their successful establishment. Apomixis in plants provides reproductive assurance, and superior colonizing abilities respect to sexuals, but it also constrains genetic variation and clonal plants are expected to have restricted adaptive capabilities. These complex rearrangement processes and adaptations in polyploid complexes are well reflected by their genetic variation. However, there is a lack of non-model systems that exhibit successful changes with pronounced reflection for studies. Paspalum intermedium is a grass species with diverging genetic systems (diploidy vs. autopolyploidy, allogamy vs. autogamy and sexuality vs. apomixis) with substantial ecological differentiation between cytotypes occurring in allopatry, sympatry and parapatry, hence provides an ideal platform to study polyploidization, apomixis and their ecological and genetic importance in plant evolution. Therefore, in this thesis, I used P. intermedium as a model system to recognize the causality of biogeographic patterns, adaptation and ecological flexibility of cytotypes, to study variations in the expression of sexuality and apomixis, to analyze developmental competition between reproductive modes, and their effects on reproductive fitness, and to study genetic variation and its significance in polyploid complexes. I used chromosome counts, flow cytometry, and embryological analyses to characterize within-species genetic systems diversity. Environmental niche modelling was performed to evaluate intraspecific ecological attributes and to assess correlations among ploidy, and ecological conditions ruling species’ population dynamics, range expansion, adaptation and evolutionary history. Proportions of sexuality and apomixis in situ were analyzed against local climatic conditions to study the influence of environmental factors on reproductive modes. Total seed set and germinability analyses were used to estimate the reproductive fitness. Analysis of genetic markers AFLPs was used to assess the genetic variation between and within cytotypes and within and among populations. To get insights into the genetic structure variation depending on the reproductive mode and how it explains the niche variation between cytotypes, the results were compared with the geographical distribution patterns and different ecological preferences of the cytotypes. My results show that the two dominant cytotypes of P. intermedium are non-randomly distributed along local and regional geographical scales and displayed niche differentiation. Polyploidy and contrasting reproductive traits between cytotypes have promoted shifts in niche optima, and increased ecological tolerance and niche divergence. Ecologically specialized diploids maintain cytotype stability in core areas by displacing tetraploids, while broader ecological preferences and a shift from sexuality to apomixis favored polyploid colonization in peripheral areas promoting range expansion. The expression of sex and apomixis in tetraploid populations shows high variation both within and among populations. Even though ovule and seed analyses show apomictic development has higher competitive ability, fitness of apomictic individuals is depleted compared to sexual individuals and populations, indicating asexuality suffering higher seed abortion. Environmental modulation of reproduction was evident at population level where sex increased with higher mean diurnal range (MDR) while apomixis decreased. Thus, a Tug of War situation was identified between factors intrinsic to apomixis and environmental stressors promoting sex, suggesting a crucial role of local ecological conditions in sexual expression and adaptation of apomictic populations. Population structure analyses show that apomictic autotetraploids are of multiple independent origin. Although diploids show higher genetic variation, within and among population genetic variation equally make up the observed variation in all cytotypes. All individuals fall into three genetic clusters with substantial genetic admixture, and geographical distribution of genetic variation is in accordance with niche differentiation. The contact zone of the two cytotypes is primary in origin where tetraploids may frequently occur in mix ploidy populations. Polyploidization in P. interemedium is a recurring phenomenon and the newly arisen polyploids successfully establish themselves by acquiring enough genetic variation that allows them to adapt to new environments. Genetic variation analysis points to a slight deviation from the known General Purpose Ghenotype and the Frozen Niche Variation concepts as there is neither a common genotype nor are the diploids occupying a part of diploid sexuals’ niche.

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients.

Central European grasslands, such as calcareous grasslands and oat-grass meadows, are characterized by diverse environmental conditions and management regimes. Therefore, we aimed to determine potential differences in genetic and epigenetic variation patterns between the contrasting habitats and to identify the drivers of genetic and epigenetic variation. We investigated the genetic and epigenetic variation of the ecologically variable plant species Trifolium pratense L. applying amplified fragment length polymorphism and methylation-sensitive amplification polymorphism analyses. We observed low levels of genetic and epigenetic differentiation among populations and between habitat types. Genetic and epigenetic variations were not interdependent. Thus, genetic variation was significantly isolated by habitat dissimilarity, whereas epigenetic variation was affected by environment. More specifically, we observed a significant correlation of epigenetic diversity with soil moisture and soil pH (the latter potentially resulting in phosphorus limitation). Genetic variation was, therefore, affected more strongly by habitat-specific environmental conditions induced by land use-related disturbance and gene flow patterns, while epigenetic variation was driven by challenging environmental conditions.

BackgroundPast events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites.ResultsUsing outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations.ConclusionOur results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.

Habitat fragmentation, i.e., fragment size and isolation, can differentially alter patterns of neutral and quantitative genetic variation, fitness and phenotypic plasticity of plant populations, but their effects have rarely been tested simultaneously. We assessed the combined effects of size and connectivity on these aspects of genetic and phenotypic variation in populations of Centaurea hyssopifolia, a narrow endemic gypsophile that previously showed performance differences associated with fragmentation. We grew 111 maternal families sampled from 10 populations that differed in their fragment size and connectivity in a common garden, and characterized quantitative genetic variation, phenotypic plasticity to drought for key functional traits, and plant survival, as a measure of population fitness. We also assessed neutral genetic variation within and among populations using eight microsatellite markers. Although C. hyssopifolia is a narrow endemic gypsophile, we found substantial neutral genetic variation and quantitative variation for key functional traits. The partition of genetic variance indicated that a higher proportion of variation was found within populations, which is also consistent with low population differentiation in molecular markers, functional traits and their plasticity. This, combined with the generally small effect of habitat fragmentation suggests that gene flow among populations is not restricted, despite large differences in fragment size and isolation. Importantly, population’s similarities in genetic variation and plasticity did not reflect the lower survival observed in isolated populations. Overall, our results indicate that, although the species consists of genetically variable populations able to express functional plasticity, such aspects of adaptive potential may not always reflect populations’ survival. Given the differential effects of habitat connectivity on functional traits, genetic variation and fitness, our study highlights the need to shift the focus of fragmentation studies to the mechanisms that regulate connectivity effects, and call for caution on the use of genetic variation and plasticity to forecast population performance.

The aim of this research was to evaluate the genetic and morphological variation among the three populations of Donax spp . along the Gulf of Thailand. Samples were collected from Bangsean, Cha-Am and Suansonsandy beaches, and analyzed to reveal genetic and morphological variation by using 4 loci based on Inter-Simple Sequence Repeats markers and 5 morphological variables, respectively. The discriminant function analysis of morphology presented a clear separation among three populations. Polymorphisms were detected at 4 loci across all three populations. The mean number of alleles ranged from 1.65±0.48 to 1.90±0.30 and the effective number of alleles ranged from 1.18±0.27 to 1.29±0.30. Donax spp . from Suanson beach showed the lowest level of genetic variation which Nei’s (1973) gene diversity was 0.16±0.17. While Nei’s (1973) gene diversity of Donax spp . from Bangsean and Cha-Am beaches were 0.18±0.15 and 0.19±0.16, respectively. Percentage of polymorphic loci ranged from 66.22 to 89.86%. Overall results from this research based on genetic variation were in the range of most other marine bivalves, which allows for potential adaptation to environmental changes. Furthermore, the results can be indicated that population of Donax spp . from Suanson beach should be treated as separated units for conservation management.

In contrast to many other species examined in Wallacea, the patterns of genetic (allozyme) and morphological variation of two skink species revealed only moderate concordance with their geograph- ical arrangements. Initial analyses of genetic and morphometric variation in Lamprolepis smaragdina re- vealed the taxonomic separateness of islands in the northeast (Bandaneira, Kai Besar, and Ambon) from those in the south and southwest The relationship between these two taxa and L. smaragdina, sensu stricto has yet to be determined. Genetic variation in the southern species revealed two clusters of populations, corresponding, with one exception, to the Inner and Outer Banda Arcs. No such arrangement is seen in morphological variation, with poor discrimination of islands evidenced by substantial overlap of island ranges in canonical space. Nonetheless, there are three associations between canonical variates and island location (latitude and longitude) revealing the existence of some underlying, but weak, geographic pattern- ing. In Mabuya multifasciata, genetic variation within islands tends to decline from west to east, a trend seen in several other species in this region. Ordination of a genetic distance matrix revealed an association between the third axis and longitude. There was little morphological differentiation, with large overlaps in island ranges in canonical space and no geographic-associated patterning. There is no evidence of concor- dance between genetic and morphometric patterning within either Lamprolepis or M. multifasciata over their extensive ranges. The islands of the Banda Arc in southeastern Indonesia have long held a fascination for biol- ogists as the area of overlap between two of the world's major biogeographic regions, Asia and

Heritable epigenetic modifications may occur in response to environmental variation, further altering phenotypes through gene regulation, without genome sequence changes. However, epigenetic variation in wild plant populations and their correlations with genetic and phenotypic variation remain largely unknown, especially for clonal plants. We investigated genetic, epigenetic and phenotypic variation of ten populations of an introduced clonal herb Hydrocotyle vulgaris in China. Populations of H. vulgaris exhibited extremely low genetic diversity with one genotype exclusively dominant, but significantly higher epigenetic diversity. Both intra- and inter-population epigenetic variation were related to genetic variation. But there was no correlation between intra-/inter-population genetic variation and phenotypic variation. When genetic variation was controlled, intra-population epigenetic diversity was related to petiole length, specific leaf area, and leaf area variation, while inter-population epigenetic distance was correlated with leaf area differentiation. Our study provides empirical evidence that even though epigenetic variation is partly under genetic control, it could also independently play a role in shaping plant phenotypes, possibly serving as a pathway to accelerate evolution of clonal plant populations.

Duckweeds have emerged as frontier plants in research, food, and bioenergy applications. Consistency in genetic and morphological traits within species is therefore crucial for their effective use. Thailand hosts diverse duckweed populations with representatives from four of the five genera and at least four species recorded. However, the extent of genetic and morphological variation within these species in Thailand remains unclear. Here, we investigated the genetic and morphological variation in four duckweed species—Landoltia punctata, Lemna aequinoctialis, Spirodela polyrhiza, and Wolffia globosa—collected from 26 sites across Thailand. Using the multilocus sequence typing approach based on three chloroplast genes (rbcL, atpF–atpH, and psbK–psbI), we show that genetic variation in duckweed is distinct at both inter-species and intra-species levels. Among these four species, Lemna aequinoctialis exhibits the highest genetic variation, forming four distinct phylogenetic clusters. This is followed by Spirodela polyrhiza, Wolffia globosa, and Landoltia punctata. In addition, we observe that morphological variation, particularly frond aspect ratio, varies significantly among clusters but remains consistent within each cluster of each species. These findings suggest that duckweed populations in Thailand exhibit substantial genetic variation at the intraspecific level, which is closely associated with frond morphological variation.

The immune system protects the body from infection. Key to this protection is the ability to mount an immune response that is sufficient to deal with the threat, but is not so large that the damage it causes to the body exceeds its immediate benefit. Immune cells called regulatory T cells (or Treg cells for short) help to shut down the immune response after a threat has been successfully destroyed. They also prevent the immune system from attacking the body's own cells, a phenomenon known as autoimmunity. All cells in the body carry the same set of genes, but the activity of these genes varies between cell types to enable the cells to perform their different jobs. This is possible because our DNA contains regions called regulatory elements that can control the expression of particular genes. These regions can be activated in specific types of cells, which results in specific chemical modifications to DNA that only affect gene activity in those cells. The DNA sequences of these regulatory elements vary between individuals. This ‘genetic variation’ can lead to differences in the chemical modifications that occur to DNA, which is known as epigenetic variation. This means that Treg cells in one person may work in a different way to those in another individual, which could make some individuals more susceptible to autoimmune diseases than others. However, it was not clear how much genetic and epigenetic variation exists in Treg cells. Here, Arvey et al. examined Treg and other immune cells from human and mouse donors. The experiments show that some of the epigenetic modifications present in many individuals only in Treg cells, which indicates that they may be important for the activity of the Treg cells. Unexpectedly, most of the epigenetic modifications were specific to either mice or humans, but Arvey et al. identified a core set of genes that had been modified only in Treg cells in both species. In the human cells, Arvey et al. also identified genetic differences in regulatory elements that are associated with autoimmune diseases. Arvey et al.'s findings suggest that a small set of regulatory elements are crucial to the role of Treg cells in the immune system. Furthermore, genetic variation in these elements can lead to epigenetic changes in Treg cells that contribute to autoimmune diseases in humans. Further study may lead to the development of new treatments for these diseases.

Understanding the interaction between genetic and epigenetic variation remains a challenge due to confounding environmental factors. We propose that human induced Pluripotent Stem Cells (iPSCs) are an excellent model to study the relationship between genetic and epigenetic variation while controlling for environmental factors. In this study, we have created a comprehensive resource of high-quality genomic, epigenomic, and transcriptomic data from iPSC lines and three iPSC-derived cell types (neural stem cell (NSC), motor neuron, monocyte) from three healthy donors. We find that epigenetic variation is most strongly associated with genetic variation at the iPSC stage, and that relationship weakens as epigenetic variation increases in differentiated cells. Additionally, cell type is a stronger source of epigenetic variation than genetic variation. Further, we elucidate a utility of studying epigenetic variation in iPSCs and their derivatives for identifying important loci for GWAS studies and the cell types in which they may be acting.

Epigenetic variation may contribute to traits that are important in domestication, but how patterns of genetic and epigenetic variation differ between cultivated and wild plants remains poorly understood. In particular, we know little about how selection may shape epigenetic variation in natural and cultivated populations. In this study, we investigated 11 natural populations and 6 major cultivated populations using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MS-AFLP or MSAP) markers to identify patterns of genetic and epigenetic diversity among Corydalis yanhusuo populations. We further explored correlations among genetic, epigenetic, alkaloidal, and climatic factors in natural and cultivated C. yanhusuo. We found support for a single origin for all cultivated populations, from a natural population which was differentiated from the other natural populations. The magnitude of F ST based on AFLP was significantly correlated with that for MSAP in pairwise comparisons in both natural and cultivated populations, suggesting a relationship between genetic and epigenetic variation in C. yanhusuo. This relationship was further supported by dbRDA (distance-based redundancy analyses) where some of the epigenetic variation could be explained by genetic variation in natural and cultivated populations. Genetic variation was slightly higher in natural than cultivated populations, and exceeded epigenetic variation in both types of populations. However, epigenetic differentiation exceeded that of genetic differentiation among cultivated populations, while the reverse was observed among natural populations. The differences between wild and cultivated plants may be partly due to processes inherent to cultivation and in particular the differences in mode of reproduction. The importance of epigenetic compared to genetic modifications is thought to vary depending on reproductive strategies, and C. yanhusuo usually reproduces sexually in natural environments, while the cultivated C. yanhusuo are propagated clonally. In addition, alkaloid content of C. yanhusuo varied across cultivated populations, and alkaloid content was significantly correlated to climatic variation, but also to genetic (6.89%) and even more so to epigenetic (14.09%) variation in cultivated populations. Our study demonstrates that epigenetic variation could be important in cultivation of C. yanhusuo and serve as a source of variation for response to environmental conditions.