Epigenetic differentiation persists after male gametogenesis in natural populations of the perennial herb Helleborus foetidus (Ranunculaceae)

Despite the importance of assessing the stability of epigenetic variation in non-model organisms living in real-world scenarios, no studies have been conducted on the transgenerational persistence of epigenetic structure in wild plant populations. This gap in knowledge is hindering progress in the interpretation of natural epigenetic variation. By applying the methylation-sensitive amplified fragment length polymorphism (MSAP) technique to paired plant-pollen (i.e., sporophyte-male gametophyte) DNA samples, and then comparing methylation patterns and epigenetic population differentiation in sporophytes and their descendant gametophytes, we investigated transgenerational constancy of epigenetic structure in three populations of the perennial herb Helleborus foetidus (Ranunculaceae). Single-locus and multilocus analyses revealed extensive epigenetic differentiation between sporophyte populations. Locus-by-locus comparisons of methylation status in individual sporophytes and descendant gametophytes showed that ~75% of epigenetic markers persisted unchanged through gametogenesis. In spite of some epigenetic reorganization taking place during gametogenesis, multilocus epigenetic differentiation between sporophyte populations was preserved in the subsequent gametophyte stage. In addition to illustrating the efficacy of applying the MSAP technique to paired plant-pollen DNA samples to investigate epigenetic gametic inheritance in wild plants, this paper suggests that epigenetic differentiation between adult plant populations of H. foetidus is likely to persist across generations.

Microorganisms transported by ants induce changes in floral nectar composition of an ant-pollinated plant

PREMISE OF THE STUDY

Interactions between plants and ants abound in nature and have significant consequences for ecosystem functioning. Recently, it has been suggested that nectar-foraging ants transport microorganisms to flowers; more specifically, they transport yeasts, which can potentially consume sugars and alter nectar composition. Therefore, ants could indirectly change nectar sugar profile, an important floral feature involved in the plant-pollinator mutualism. But this novel role for ants has never been tested. We here investigate the effects of nectarivorous ants and their associated yeasts on the floral nectar sugar composition of an ant-pollinated plant.

METHODS

Differences in the nectar sugar composition of ant-excluded and ant-visited flowers were examined in 278 samples by using high-performance liquid-chromatography. The importance of the genetic identity and density of ant-transported basidiomycetous and ascomycetous yeasts on the variation of nectar traits was also evaluated.

KEY RESULTS

Ant visitation had significant effects on nectar sugar composition. The nectar of ant-visited flowers contained significantly more fructose, more glucose, and less sucrose than the nectar of ant-excluded flowers, but these effects were context dependent. Nectar changes were correlated with the density of yeast cells in nectar. The magnitude of the effects of ant-transported ascomycetes was much higher than that of basiodiomycetes.

CONCLUSIONS

Ants and their associated yeasts induce changes in nectar sugar traits, reducing the chemical control of the plant over this important floral trait. The potential relevance of this new role for ants as indirect nectar modifiers is a rich topic for future research into the ecology of ant-flower interactions.

Acinetobacter nectaris sp. nov. and Acinetobacter boissieri sp. nov., isolated from floral nectar of wild Mediterranean insect-pollinated plants

The taxonomic status of 14 strains of members of the genus Acinetobacter isolated from floral nectar of wild Mediterranean insect-pollinated plants, which did not belong to any previously described species within this genus, was investigated following a polyphasic approach. Confirmation that these strains formed two separate lineages within the genus Acinetobacter was obtained from comparative analysis of the partial sequences of the 16S rRNA gene and the gene encoding the β-subunit of RNA polymerase (rpoB), DNA–DNA reassociation data, determination of the DNA G+C content and physiological tests. The names Acinetobacter nectaris sp. nov. and Acinetobacter boissieri sp. nov. are proposed. The type strain of A. nectaris sp. nov. is SAP 763.2T ( = LMG 26958T = CECT 8127T) and that of A. boissieri sp. nov. is SAP 284.1T ( = LMG 26959T = CECT 8128T).

Permanent genetic resources added to molecular ecology resources database 1 October 2012-30 November 2012

This article documents the addition of 153 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brassica oleracea, Brycon amazonicus, Dimorphandra wilsonii, Eupallasella percnurus, Helleborus foetidus, Ipomoea purpurea, Phrynops geoffroanus, Prochilodus argenteus, Pyura sp., Sylvia atricapilla, Teratosphaeria suttonii, Trialeurodes vaporariorum and Trypanosoma brucei. These loci were cross-tested on the following species: Dimorphandra coccicinea, Dimorphandra cuprea, Dimorphandra gardneriana, Dimorphandra jorgei, Dimorphandra macrostachya, Dimorphandra mollis, Dimorphandra parviflora and Dimorphandra pennigera.

Herkogamy and mate diversity in the wild daffodil Narcissus longispathus: beyond the selfing-outcrossing paradigm in the evolution of mixed mating

Spatial separation of male and female reproductive structures (herkogamy) is a widespread floral trait that has traditionally been viewed as an adaptation that reduces the likelihood of self-pollination. Here we propose that increased herkogamy may also influence another important aspect of plant mating: the diversity of pollen donors siring seeds within fruits. We test this hypothesis in Narcissus longispathus, a wild daffodil species with extensive variation in anther-stigma separation. To study the morphological basis of variation in herkogamy, floral measurements were undertaken in 16 populations of N. longispathus. We then quantified multilocus outcrossing rates and the correlation of outcrossed paternity in three of these populations sampled over several years. Mating system estimates were calculated for each population and year, and also separately for groups of plants that differed markedly in herkogamy within each population and year. In N.  longispathus herkogamy was much more variable than other floral traits, and was more closely related to style length than to anther position. Averaged across populations and years, plants with high herkogamy had similar outcrossing rates (0.683) to plants with intermediate (0.648) or low herkogamy (0.590). However, a significant linear trend was found for correlation of outcrossed paternity, which increased monotonically from high herkogamy (0.221), through intermediate herkogamy (0.303) to low herkogamy (0.463) plants. The diversity of pollen donors siring seeds of high herkogamy Narcissus flowers was thus consistently greater than the diversity of pollen donors siring seeds of low herkogamy flowers. Results of this study contribute to the emerging consensus that floral traits can simultaneously influence several aspects of plant mating system in complex ways, thus extending the traditional focus centred exclusively on patterns and relative importance of self- and cross-fertilisation.

Zooming-in on floral nectar: a first exploration of nectar-associated bacteria in wild plant communities

Floral nectar of some animal-pollinated plants usually harbours highly adapted yeast communities which can profoundly alter nectar characteristics and, therefore, potentially have significant impacts on plant reproduction through their effects on insect foraging behaviour. Bacteria have also been occasionally observed in floral nectar, but their prevalence, phylogenetic diversity and ecological role within plant-pollinator-yeast systems remains unclear. Here we present the first reported survey of bacteria in floral nectar from a natural plant community. Culturable bacteria occurring in a total of 71 nectar samples collected from 27 South African plant species were isolated and identified by 16S rRNA gene sequencing. Rarefaction-based analyses were used to assess operational taxonomic units (OTUs) richness at the plant community level using nectar drops as sampling units. Our results showed that bacteria are common inhabitants of floral nectar of South African plants (53.5% of samples yielded growth), and their communities are characterized by low species richness (18 OTUs at a 16S rRNA gene sequence dissimilarity cut-off of 3%) and moderate phylogenetic diversity, with most isolates belonging to the Gammaproteobacteria. Furthermore, isolates showed osmotolerance, catalase activity and the ability to grow under microaerobiosis, three traits that might help bacteria to overcome important factors limiting their survival and/or growth in nectar.

Genetic structure of the shrub Daphne laureola across the Baetic Ranges, a Mediterranean glacial refugium and biodiversity hotspot

Distribution margins constitute areas particularly prone to random and/or adaptive intraspecific differentiation in plants. This trend may be particularly marked in species discontinuously distributed across mountain ranges, where sharp geographic isolation gradients and habitat boundaries will enhance genetic isolation among populations. In this study, we analysed the level of neutral genetic differentiation among populations of the long-lived shrub Daphne laureola (Thymelaeaceae) across the Baetic Ranges, a glacial refugium and biodiversity hotspot in the western Mediterranean Basin. Within this area, core and marginal populations of D. laureola were compared with regard to their spatial isolation, size, genetic diversity and differentiation. A spatially explicit analysis conducted on the vast majority of the species' known populations in the study area (N = 111) showed that marginal populations (western and eastern) present larger spatial isolation than core populations, but are not smaller. We compared genetic diversity and differentiation between core and marginal populations using a subsample of 15 populations and 225 amplified fragment length polymorphism (AFLP) markers. Core and marginal populations did not differ in genetic diversity, probably because of the occurrence of large populations on the local margins. Western populations were strongly differentiated from the other populations. In addition, spatial and genetic differentiation among populations was larger on the western margin. Eastern populations constituted a genetically homogeneous group closely related to core populations, despite their greater spatial isolation. Results suggest that studies on phenotypic differentiation between core and marginal populations of D. laureola, and presumably other species having discontinuous distributions across the Baetic ranges, should take into account geographical differences in levels of genetic differentiation between the different distribution borders.

Nectar yeasts of two southern Spanish plants: the roles of immigration and physiological traits in community assembly

Recent studies have shown that dense yeast populations often occurring in floral nectar are numerically dominated by a few species from the flower–insect interface specialized genus Metschnikowia, while generalist yeast species commonly occurring on leaf surfaces, soil, freshwater, and air were rarely isolated from nectar samples. This study was designed to understand the main factors responsible for the assembly of nectar yeast communities, by combining field experiments with laboratory tests characterizing the physiological abilities of all yeast species forming the pool of potential colonizers for two Spanish flowering plants (Digitalis obscura and Atropa baetica). Yeast frequency and species richness were assessed in external sources (bee glossae, air, plant phylloplane) as well as in pollinator rewards (pollen, nectar). Yeasts were most frequent in external sources (air, flower-visiting insects), less so in the proximate floral environment (phylloplane), and least in pollen and nectar. Nectar communities appeared to be considerably impoverished versions of those in insect glossae and phylloplane. Nectar, pollen, and insect yeast assemblages differed in physiological characteristics from those in other substrates. Nectarivorous Metschnikowia were not more resistant than other yeast species to plant secondary compounds and high sugar concentrations typical of nectar, but their higher growth rates may be decisive for their dominance in ephemeral nectar communities.

Metschnikowia proteae sp. nov., a nectarivorous insect-associated yeast species from Africa

A collection of yeasts isolated from nectar of flowers of Protea caffra (Proteaceae) and associated scarab beetles (Atrichelaphinis tigrina, Cyrtothyrea marginalis, Trichostetha fascicularis and Heterochelus sp.) and drosophilid flies in South Africa, contained 28 isolates that could not be assigned to known species. Comparisons of the D1/D2 domains of the large subunit rRNA gene demonstrated the existence of three separate phylotypes with an affinity to the genus Metschnikowia and more specifically to the beetle-associated large-spored Metschnikowia clade. Twenty-six strains that had similar D1/D2 sequences were mixed in all pairwise combinations. They were found to mate and give rise to large asci typical of those in the clade. The name Metschnikowia proteae sp. nov. (type strain EBDT1Y1(T) = CBS 12522(T) = NRRL Y-48784(T); allotype strain EBDC2Y2 = CBS 12521 = NRRL Y-48785) is proposed to accommodate this novel species. The ecology of this novel yeast species is discussed in relation to its potential plant and insect host species. The additional two single strains isolated from Heterochelus sp. represent two novel undescribed species (Candida sp. 1 EBDM2Y3 and Candida sp. 2 EBDM8Y1). As these single strains are probably haploid mating types of Metschnikowia species, their description is deferred until the species are sufficiently well sampled to permit meaningful descriptions.

Zooming-in on floral nectar: a first exploration of nectar-associated bacteria in wild plant communities

Floral nectar of some animal-pollinated plants usually harbours highly adapted yeast communities which can profoundly alter nectar characteristics and, therefore, potentially have significant impacts on plant reproduction through their effects on insect foraging behaviour. Bacteria have also been occasionally observed in floral nectar, but their prevalence, phylogenetic diversity and ecological role within plant-pollinator-yeast systems remains unclear. Here we present the first reported survey of bacteria in floral nectar from a natural plant community. Culturable bacteria occurring in a total of 71 nectar samples collected from 27 South African plant species were isolated and identified by 16S rRNA gene sequencing. Rarefaction-based analyses were used to assess operational taxonomic units (OTUs) richness at the plant community level using nectar drops as sampling units. Our results showed that bacteria are common inhabitants of floral nectar of South African plants (53.5% of samples yielded growth), and their communities are characterized by low species richness (18 OTUs at a 16S rRNA gene sequence dissimilarity cut-off of 3%) and moderate phylogenetic diversity, with most isolates belonging to the Gammaproteobacteria. Furthermore, isolates showed osmotolerance, catalase activity and the ability to grow under microaerobiosis, three traits that might help bacteria to overcome important factors limiting their survival and/or growth in nectar.

Genomic scan as a tool for assessing the genetic component of phenotypic variance in wild populations

Methods for estimating quantitative trait heritability in wild populations have been developed in recent years which take advantage of the increased availability of genetic markers to reconstruct pedigrees or estimate relatedness between individuals, but their application to real-world data is not exempt from difficulties. This chapter describes a recent marker-based technique which, by adopting a genomic scan approach and focusing on the relationship between phenotypes and genotypes at the individual level, avoids the problems inherent to marker-based estimators of relatedness. This method allows the quantification of the genetic component of phenotypic variance ("degree of genetic determination" or "heritability in the broad sense") in wild populations and is applicable whenever phenotypic trait values and multilocus data for a large number of genetic markers (e.g., amplified fragment length polymorphisms, AFLPs) are simultaneously available for a sample of individuals from the same population. The method proceeds by first identifying those markers whose variation across individuals is significantly correlated with individual phenotypic differences ("adaptive loci"). The proportion of phenotypic variance in the sample that is statistically accounted for by individual differences in adaptive loci is then estimated by fitting a linear model to the data, with trait value as the dependent variable and scores of adaptive loci as independent ones. The method can be easily extended to accommodate quantitative or qualitative information on biologically relevant features of the environment experienced by each sampled individual, in which case estimates of the environmental and genotype × environment components of phenotypic variance can also be obtained.

A piece of the puzzle: a method for comparing pollination quality and quantity across multiple species and reproductive events

• Understanding how pollination affects plant reproductive success and how changes in pollination service affect plant populations, communities and ecosystems is of increasing concern. Yet supplemental hand-pollination traditionally used to assess pollen limitation is prohibitive for large-scale comparative work. Moreover, it does not differentiate between quality and quantity aspects of pollen limitation, and it may suffer from confounds of post-pollination processes such as resource availability to fill seeds. • Here, we highlight pollen tubes as the functional link between pollen arrival and seed production and suggest that consideration of pollen tubes leads to a better depiction of limitation at the pre-zygotic (pollination) phase of sexual reproduction. • We assessed the rigor of piecewise regression to analyze the relationship between the numbers of pollen grains and pollen tubes observed in nonmanipulated wilted flowers. We illustrate how parameters obtained from this analysis provide quantitative insight into the relative relevance of the quantity and quality of pollen receipt in limiting natural pollination success, and can facilitate comparisons among data sets. • This nonmanipulative method opens up new opportunities for rigorous assessment of the relative importance of the quantity and quality of pollination in limiting plant reproduction, especially from a community-wide perspective.

Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast

In addition to genetic differences between individuals as a result of nucleotide sequence variation, epigenetic changes that occur as a result of DNA methylation may also contribute to population niche width by enhancing phenotypic plasticity, although this intriguing possibility remains essentially untested. Using the nectar-living yeast Metschnikowia reukaufii as study subject, we examine the hypothesis that changes in genome-wide DNA methylation patterns underlie the ability of this fugitive species to exploit a broad resource range in its heterogeneous and patchy environment. Data on floral nectar characteristics and their use by M. reukaufii in the wild were combined with laboratory experiments and methylation-sensitive amplified polymorphism (MSAP) analyses designed to detect epigenetic responses of single genotypes to variations in sugar environment that mimicked those occurring naturally in nectar. M. reukaufii exploited a broad range of resources, occurring in nectar of 48% of species and 52% of families surveyed, and its host plants exhibited broad intra- and interspecific variation in sugar-related nectar features. Under experimental conditions, sugar composition, sugar concentration and their interaction significantly influenced the mean probability of MSAP markers experiencing a transition from unmethylated to methylated state. Alterations in methylation status were not random but predictably associated with certain markers. The methylation inhibitor 5-azacytidine (5-AzaC) had strong inhibitory effects on M. reukaufii proliferation in sugar-containing media, and a direct relationship existed across sugar × concentration experimental levels linking inhibitory effect of 5-AzaC and mean per-marker probability of genome-wide methylation. Environmentally induced DNA methylation polymorphisms allowed genotypes to grow successfully in extreme sugar environments, and the broad population niche width of M. reukaufii was largely made possible by epigenetic changes enabling genotype plasticity in resource use.

Complex implications around a simple trait: ecological context determines the fecundity effects of corolla marcescence

PREMISE OF THE STUDY

Post-anthesis functionality of persistent perianth parts has rarely been investigated, but available evidence suggests that perianth persistence may not always have an adaptive value. Given the high occurrence of the trait, that it may sometimes be maladaptive is an intriguing possibility and deserves exploration. This paper tests the hypothesis that the fitness value of corolla persistence after anthesis depends on ecological context, specifically the abundance of fruit predators and pollinators.

METHODS

The study was conducted on Narcissus longispathus, a species in which corolla marcescence is apparently maladaptive because withered corollas provide a shelter for fruit-predatory lepidopteran larvae. By experimentally manipulating corolla persistence, presence of fruit predators, and pollination, I tested whether variation in ecological scenario led to concomitant variation in the sign and magnitude of the effects of corolla marcescence on fecundity.

KEY RESULTS

Persistent corollas were detrimental to fecundity when plants were exposed to larvae, but not when larvae were excluded. Pollination and herbivory had nonadditive effects on the fecundity consequences of corolla marcescence, the strongest detrimental effects of corolla persistence occurring for the "exposed to larvae + supplementary pollination" treatment combination.

CONCLUSIONS

The hypothesis that ecological context is a major determinant of the fitness value of corolla marcescence was supported. In N. longispathus, corolla marcescence will be a maladaptive trait in situations in which pollinators and fruit predators are simultaneously abundant, but will be a neutral character in the absence of fruit predators, irrespective of pollinator service.

Endozoochory by beetles: a novel seed dispersal mechanism

BACKGROUND AND AIMS

Due in part to biophysical sized-related constraints, insects unlike vertebrates are seldom expected to act as primary seed dispersers via ingestion of fruits and seeds (endozoochory). The Mediterranean parasitic plant Cytinus hypocistis, however, possesses some characteristics that may facilitate endozoochory by beetles. By combining a long-term field study with experimental manipulation, we tested whether C. hypocistis seeds are endozoochorously dispersed by beetles.

METHODS

Field studies were carried out over 4 years on six populations in southern Spain. We recorded the rate of natural fruit consumption by beetles, the extent of beetle movement, beetle behaviour and the relative importance of C. hypocistis fruits in beetle diet.

KEY RESULTS

The tenebrionid beetle Pimelia costata was an important disperser of C. hypocistis seeds, consuming up to 17·5 % of fruits per population. Forty-six per cent of beetles captured in the field consumed C. hypocistis fruits, with up to 31 seeds found in individual beetle frass. An assessment of seeds following passage through the gut of beetles indicated that seeds remained intact and viable and that the proportion of viable seeds from beetle frass was not significantly different from that of seeds collected directly from fruits.

CONCLUSIONS

A novel plant-animal interaction is revealed; endozoochory by beetles may facilitate the dispersal of viable seeds after passage through the gut away from the parent plant to potentially favourable underground sites offering a high probability of germination and establishment success. Such an ecological role has until now been attributed only to vertebrates. Future studies should consider more widely the putative role of fruit and seed ingestion by invertebrates as a dispersal mechanism, particularly for those plant species that possess small seeds.

Back-and-forth hermaphroditism: phylogenetic context of reproductive system evolution in subdioecious Daphne laureola

Recent phylogenetic analyses of sexual reproductive systems supported the evolutionary pathway from hermaphroditism to dioecy via gynodioecy in different groups of angiosperms. In this study, we explore the evolution of sexual reproductive systems in Daphne laureola L. (Thymelaeaceae), a species with variation in reproductive system among population. Sequences from the ITS region of the nuclear ribosomal cistron and two plastid markers (psbA-trnH and ndhF) were analyzed and used to map the population reproductive system along the molecular phylogeny. Our results support D. laureola as a monophyletic lineage with three different clades within the Iberian Peninsula. The hermaphroditic populations belong to two different clades, whereas gynodioecy is ubiquitous but characteristic of the third clade, which grouped together all the North-Western Iberian populations sampled, including the apparently oldest haplotype sampled. Gynodioecy appears as the most likely basal condition of the 13 analyzed populations, but different evolutionary transitions in reproductive sexual system were traced within each D. laureola clade. Both ecological conditions and (meta)population dynamics may help explain plant reproductive system evolution at the microevolutionary scale. Phylogenetic studies in which the historical relationships between populations differing in reproductive system can be ascertained will help to clarify the process.

Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory

Individual variation in ecologically important features of organisms is a crucial element in ecology and evolution, yet disentangling its underlying causes is difficult in natural populations. We applied a genomic scan approach using amplified fragment length polymorphism (AFLP) markers to quantify the genetic basis of long-term individual differences in herbivory by mammals at a wild population of the violet Viola cazorlensis monitored for two decades. In addition, methylation-sensitive amplified polymorphism (MSAP) analyses were used to investigate the association between browsing damage and epigenetic characteristics of individuals, an aspect that has been not previously explored for any wild plant. Structural equation modelling was used to identify likely causal structures linking genotypes, epigenotypes and herbivory. Individuals of V. cazorlensis differed widely in the incidence of browsing mammals over the 20-year study period. Six AFLP markers (1.6% of total) were significantly related to herbivory, accounting altogether for 44% of population-wide variance in herbivory levels. MSAP analyses revealed considerable epigenetic variation among individuals, and differential browsing damage was significantly related to variation in multilocus epigenotypes. In addition, variation across plants in epigenetic characteristics was related to variation in several herbivory-related AFLP markers. Statistical comparison of alternative causal models suggested that individual differences in herbivory are the outcome of a complex causal structure where genotypes and epigenotypes are interconnected and have direct and indirect effects on herbivory. Insofar as methylation states of MSAP markers influential on herbivory are transgenerationally heritable, herbivore-driven evolutionary changes at the study population will involve correlated changes in genotypic and epigenotypic distributions.

Species richness of yeast communities in floral nectar of southern Spanish plants

Floral nectar of insect-pollinated plants often contains dense yeast populations, yet little quantitative information exists on patterns and magnitude of species richness of nectar-dwelling yeasts in natural plant communities. This study evaluates yeast species richness at both the plant community and plant species levels in a montane forest area in southern Spain, and also explores possible correlations between the incidence of different yeast species in nectar and their reported tolerance to high sugar concentrations, and between yeast diversity and pollinator composition. Yeast species occurring in a total of 128 field-collected nectar samples from 24 plant species were identified by sequencing the D1/D2 domain of the large subunit rDNA, and rarefaction-based analyses were used to estimate yeast species richness at the plant community and plant species levels, using nectar drops as elemental sampling units. Individual nectar samples were generally characterized by very low species richness (1.2 yeast species/sample, on average), with the ascomycetous Metschnikowia reukaufii and Metschnikowia gruessii accounting altogether for 84.7% of the 216 isolates identified. Other yeasts recorded included species in the genera Aureobasidium, Rhodotorula, Cryptococcus, Sporobolomyces, and Lecythophora. The shapes and slopes of observed richness accumulation curves were quite similar for the nectar drop and plant species approaches, but the two approaches yielded different expected richness estimates. Expected richness was higher for plant species-based than for nectar drop-based analyses, showing that the coverage of nectar yeast species occurring in the region would be improved by sampling additional host plant species. A significant correlation was found between incidence of yeast species in nectar and their reported ability to grow in a medium containing 50% glucose. Neither diversity nor incidence of yeasts was correlated with pollinator composition across plant species.