Genetic structure and systematic relationships within the Ophrys fuciflora aggregate (Orchidaceae: Orchidinae): high diversity in Kent and a wind-induced discontinuity bisecting the Adriatic

A recent phylogenetic study based on multiple datasets is used as the framework for a more detailed examination of one of the ten molecularly circumscribed groups identified, the Ophrys fuciflora aggregate. The group is highly morphologically variable, prone to phenotypic convergence, shows low levels of sequence divergence and contains an unusually large proportion of threatened taxa, including the rarest Ophrys species in the UK. The aims of this study were to (a) circumscribe minimum resolvable genetically distinct entities within the O. fuciflora aggregate, and (b) assess the likelihood of gene flow between genetically and geographically distinct entities at the species and population levels. Fifty-five accessions sampled in Europe and Asia Minor from the O. fuciflora aggregate were studied using the AFLP genetic fingerprinting technique to evaluate levels of infraspecific and interspecific genetic variation and to assess genetic relationships between UK populations of O. fuciflora s.s. in Kent and in their continental European and Mediterranean counterparts. The two genetically and geographically distinct groups recovered, one located in England and central Europe and one in south-eastern Europe, are incongruent with current species delimitation within the aggregate as a whole and also within O. fuciflora s.s. Genetic diversity is higher in Kent than in the rest of western and central Europe. Gene flow is more likely to occur between populations in closer geographical proximity than those that are morphologically more similar. Little if any gene flow occurs between populations located in the south-eastern Mediterranean and those dispersed throughout the remainder of the distribution, revealing a genetic discontinuity that runs north-south through the Adriatic. This discontinuity is also evident in other clades of Ophrys and is tentatively attributed to the long-term influence of prevailing winds on the long-distance distribution of pollinia and especially seeds. A cline of gene flow connects populations from Kent and central and southern Europe; these individuals should therefore be considered part of an extensive meta-population. Gene flow is also evident among populations from Kent, which appear to constitute a single metapopulation. They show some evidence of hybridization, and possibly also introgression, with O. apifera.

Long-term effectiveness of sowing high and low diversity seed mixtures to enhance plant community development on ex-arable fields

Questions: How is succession on ex-arable land affected by sowing high and low diversity mixtures of grassland species as compared to natural succession? How long do effects persist? Location: Experimental plots installed in the Czech Republic, The Netherlands, Spain, Sweden and the United Kingdom. Methods: The experiment was established on ex-arable land, with five blocks, each containing three 10 m x 10 m experiment tal plots: natural colonization, a low- (four species) and high-diversity (15 species) seed mixture. Species composition and biomass was followed for eight years. Results: The sown plants considerably affected the whole successional pathway and the effects persisted during the whole eight year period. Whilst the proportion of sown species (characterized by their cover) increased during the study period, the number of sown species started to decrease from the third season onwards. Sowing caused suppression of natural colonizing species, and the sown plots had more biomass. These effects were on average larger in the high diversity mixtures. However, the low diversity replicate sown with the mixture that produced the largest biomass or largest suppression of natural colonizers fell within the range recorded at the five replicates of the high diversity plots. The natural colonization plots usually had the highest total species richness and lowest productivity at the end of the observation period. Conclusions: The effect of sowing demonstrated dispersal limitation as a factor controlling the rate of early secondary succession. Diversity was important primarily for its 'insurance effect': the high diversity mixtures were always able to compensate for the failure of some species.

The role of weeds in supporting biological diversity within crop fields

Weeds are major constraints on crop production, yet as part of the primary producers within farming systems, they may be important components of the agroecosystem. Using published literature, the role of weeds in arable systems for other above-ground trophic levels are examined. In the UK, there is evidence that weed flora have changed over the past century, with some species declining in abundance, whereas others have increased. There is also some evidence for a decline in the size of arable weed seedbanks. Some of these changes reflect improved agricultural efficiency, changes to more winter-sown crops in arable rotations and the use of more broad-spectrum herbicide combinations. Interrogation of a database of records of phytophagous insects associated with plant species in the UK reveals that many arable weed species support a high diversity of insect species. Reductions in abundances of host plants may affect associated insects and other taxa. A number of insect groups and farmland birds have shown marked population declines over the past 30 years. Correlational studies indicate that many of these declines are associated with changes in agricultural practices. Certainly reductions in food availability in winter and for nestling birds in spring are implicated in the declines of several bird species, notably the grey partridge, Perdix perdix . Thus weeds have a role within agroecosystems in supporting biodiversity more generally. An understanding of weed competitivity and the importance of weeds for insects and birds may allow the identification of the most important weed species. This may form the first step in balancing the needs for weed control with the requirements for biodiversity and more sustainable production methods.

Importance of allelopathy as peudo-mixotrophy for the dynamics and diversity of phytoplankton

Understanding the dynamics and diversity of marine phytoplankton is essential for predicting oceanic primary production, oxygen generation and carbon sequestration. Several top-down and bottom-up factors lead to complex phytoplankton dynamics. Complexities further arise from inter-species interactions within phytoplankton communities. Consequently, some of the basic questions on phytoplankton diversity, identified long ago, still puzzle the ecologists: for example, what regulates the diversity in simple systems where species compete for limiting resources? In this context, allelopathic interaction among phytoplankton species has been identified as a potential driver of their dynamics and regulator of their diversity. This chapter deals with the importance of allelopathy in regulating the outcome of nutrient competition among phytoplankton species, through analysis of a resource-competition model. It demonstrates that, through the mechanism of pseudo-mixotrophy - proposed earlier by the author - allelopathy provides essential growth advantage to weaker competitors, and stabilizes resource competition, which ensures the coexistence of two phytoplankton on a single nutrient. In simple nutrient-phytoplankton interactions where higher-trophic influences are negligible, this mechanism theoretically promotes phytoplankton diversity, and can potentially support high diversity in natural phytoplankton communities.

Genetic diversity at the Dhn3 locus in Turkish Hordeum spontaneum populations with comparative structural analyses

We analysed Hordeum spontaneum accessions from 21 different locations to understand the genetic diversity of HsDhn3 alleles and effects of single base mutations on the intrinsically disordered structure of the resulting polypeptide (HsDHN3). HsDHN3 was found to be YSK2-type with a low-frequency 6-aa deletion in the beginning of Exon 1. There is relatively high diversity in the intron region of HsDhn3 compared to the two exon regions. We have found subtle differences in K segments led to changes in amino acids chemical properties. Predictions for protein interaction profiles suggest the presence of a protein-binding site in HsDHN3 that coincides with the K1 segment. Comparison of DHN3 to closely related cereals showed that all of them contain a nuclear localization signal sequence flanking to the K1 segment and a novel conserved region located between the S and K1 segments [E(D/T)DGMGGR]. We found that H. vulgare, H. spontaneum, and Triticum urartu DHN3s have a greater number of phosphorylation sites for protein kinase C than other cereal species, which may be related to stress adaptation. Our results show that the nature and extent of mutations in the conserved segments of K1 and K2 are likely to be key factors in protection of cells.

Forensic acarology: an introduction

Mites can be found in all imaginable terrestrial habitats, in freshwater, and in salt water. Mites can be found in our houses and furnishings, on our clothes, and even in the pores of our skin-almost every single person carries mites. Most of the time, we are unaware of them because they are small and easily overlooked, and-most of the time-they do not cause trouble. In fact, they may even proof useful, for instance in forensics. The first arthropod scavengers colonising a dead body will be flies with phoretic mites. The flies will complete their life cycle in and around the corpse, while the mites may feed on the immature stages of the flies. The mites will reproduce much faster than their carriers, offering themselves as valuable timeline markers. There are environments where insects are absent or rare or the environmental conditions impede their access to the corpse. Here, mites that are already present and mites that arrive walking, through air currents or material transfer become important. At the end of the ninetieth century, the work of Jean Pierre M,gnin became the starting point of forensic acarology. M,gnin documented his observations in 'La Faune des Cadavres' [The Fauna of Carcasses]. He was the first to list eight distinct waves of arthropods colonising human carcasses. The first wave included flies and mites, the sixth wave was composed of mites exclusively. The scope of forensic acarology goes further than mites as indicators of time of death. Mites are micro-habitat specific and might provide evidential data on movement or relocation of bodies, or locating a suspect at the scene of a crime. Because of their high diversity, wide occurrence, and abundance, mites may be of great value in the analysis of trace evidence.

Comparative analysis of performance and stability among composite cross populations, variety mixtures and pure lines of winter wheat in organic and conventional cropping systems

This study investigated the effects of increased genetic diversity in winter wheat (Triticum aestivum L.), either from hybridization across genotypes or from physical mixing of lines, on grain yield, grain quality, and yield stability in different cropping environments. Sets of pure lines (no diversity), chosen for high yielding ability or high quality, were compared with line mixtures (intermediate level of diversity), and lines crossed with each other in composite cross populations (CCPn, high diversity). Additional populations containing male sterility genes (CCPms) to increase outcrossing rates were also tested. Grain yield, grain protein content, and protein yield were measured at four sites (two organically-managed and two conventionally-managed) over three years, using seed harvested locally in each preceding year. CCPn and mixtures out-yielded the mean of the parents by 2.4% and 3.6%, respectively. These yield differences were consistent across genetic backgrounds but partly inconsistent across cropping environments and years. Yield stability measured by environmental variance was higher in CCPn and CCPms than the mean of the parents. An index of yield reliability tended to be higher in CCPn, CCPms and mixtures than the mean of the parents. Lin and Binns’ superiority values of yield and protein yield were consistently and significantly lower (i.e. better) in the CCPs than in the mean of the parents, but not different between CCPs and mixtures. However, CCPs showed greater early ground cover and plant height than mixtures. When compared with the (locally non-predictable) best-yielding pure line, CCPs and mixtures exhibited lower mean yield and somewhat lower yield reliability but comparable superiority values. Thus, establishing CCPs from smaller sets of high-performing parent lines might optimize their yielding ability. On the whole, the results demonstrate that using increased within-crop genetic diversity can produce wheat crops with improved yield stability and good yield reliability across variable and unpredictable cropping environments.

Inter-simple sequence repeat and aggressiveness analyses revealed high genetic diversity, recombination and long-range dispersal in Fusarium culmorum

Inter-simple sequence repeat (ISSR) analysis and aggressiveness assays were used to investigate genetic variability within a global collection of Fusarium culmorum isolates. A set of four ISSR primers were tested, of which three primers amplified a total of 37 bands out of which 30 (81%) were polymorphic. The intraspecific diversity was high, ranging from four to 28 different ISSR genotypes for F. culmorum depending on the primer. The combined analysis of ISSR data revealed 59 different genotypes clustered into seven distinct clades amongst 75 isolates of F. culmorum examined. All the isolates were assayed to test their aggressiveness on a winter wheat cv. 'Armada'. A significant quantitative variation for aggressiveness was found among the isolates. The ISSR and aggressiveness variation existed on a macro- as well as micro-geographical scale. The data suggested a long-range dispersal of F. culmorum and indicated that this fungus may have been introduced into Canada from Europe. In addition to the high level of intraspecific diversity observed in F. culmorum, the index of multilocus association calculated using ISSR data indicated that reproduction in F. culmorum cannot be exclusively clonal and recombination is likely to occur.

Restricting microbial exposure in early life negates the immune benefits associated with gut colonization in environments of high microbial diversity

Background: Acquisition of the intestinal microbiota in early life corresponds with the development of the mucosal immune system. Recent work on caesarean-delivered infants revealed that early microbial composition is influenced by birthing method and environment. Furthermore, we have confirmed that early-life environment strongly influences both the adult gut microbiota and development of the gut immune system. Here, we address the impact of limiting microbial exposure after initial colonization on the development of adult gut immunity. Methodology/Principal Findings: Piglets were born in indoor or outdoor rearing units, allowing natural colonization in the immediate period after birth, prior to transfer to high-health status isolators. Strikingly, gut closure and morphological development were strongly affected by isolator-rearing, independent of indoor or outdoor origins of piglets. Isolator-reared animals showed extensive vacuolation and disorganization of the gut epithelium, inferring that normal gut closure requires maturation factors present in maternal milk. Although morphological maturation and gut closure were delayed in isolatorreared animals, these hard-wired events occurred later in development. Type I IFN, IL-22, IL-23 and Th17 pathways were increased in indoor-isolator compared to outdoor-isolator animals during early life, indicating greater immune activation in pigs originating from indoor environments reflecting differences in the early microbiota. This difference was less apparent later in development due to enhanced immune activation and convergence of the microbiota in all isolator-reared animals. This correlated with elevation of Type I IFN pathways in both groups, although T cell pathways were still more affected in indoor-reared animals. Conclusions/Significance: Environmental factors, in particular microbial exposure, influence expression of a large number of immune-related genes. However, the homeostatic effects of microbial colonization in outdoor environments require sustained microbial exposure throughout development. Gut development in high-hygiene environments negatively impacts on normal succession of the gut microbiota and promotes innate immune activation which may impair immune homeostasis.

High prevalence of undernutrition and low dietary diversity in institutionalised elderly living in Sri Lanka

This research received no specific grant from any funding agency in the public, commercial and not-for-profit sectors. The authors wish to thank the participants, administrators and caregivers of the homes for elders for their enthusiastic cooperation and also the Nutrition Research Team of the Department of Applied Nutrition, Wayamba University of Sri Lanka, for their valuable assistance during the course of the study. The authors also wish to thank Mr. S. Rahanan for coordination and the assistance given in data collection especially in Tamil speaking participants. K.M.R designed and managed the study, interpreted the data and drafted the manuscript. M.P.P.M contributed to the data collection, data analysis and coordination of the study. M.W, K.G.J and J.A.L assisted in data interpretation and critical revision of the manuscript. The authors declare that there is no conflict of interest of any kind involved in this study or this publication. Ethical clearance for this study was obtained from the Ethical Review Committee of the Sri Lanka Medical Association (ERC/13-037).

High-throughput monitoring of wild bee diversity and abundance via mitogenomics

1. Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline. 2. We show that the metagenomic mining and resequencing of mitochondrial genomes (mitogenomics) can be applied successfully to bulk samples of wild bees. We assembled the mitogenomes of 48 UK bee species and then shotgun-sequenced total DNA extracted from 204 whole bees that had been collected in 10 pan-trap samples from farms in England and been identified morphologically to 33 species. Each sample data set was mapped against the 48 reference mitogenomes. 3. The morphological and mitogenomic data sets were highly congruent. Out of 63 total species detections in the morphological data set, the mitogenomic data set made 59 correct detections (93�7% detection rate) and detected six more species (putative false positives). Direct inspection and an analysis with species-specific primers suggested that these putative false positives were most likely due to incorrect morphological IDs. Read frequency significantly predicted species biomass frequency (R2 = 24�9%). Species lists, biomass frequencies, extrapolated species richness and community structure were recovered with less error than in a metabarcoding pipeline. 4. Mitogenomics automates the onerous task of taxonomic identification, even for cryptic species, allowing the tracking of changes in species richness and istributions. A mitogenomic pipeline should thus be able to contain costs, maintain consistently high-quality data over long time series, incorporate retrospective taxonomic revisions and provide an auditable evidence trail. Mitogenomic data sets also provide estimates of species counts within samples and thus have potential for tracking population trajectories.

The high-water mark. The siting of megalithic tombs on the Swedish island of Tjorn

In 1977 Grahame Clark suggested that the siting of megalithic tombs along the west coast of Scandinavia reflected the distribution of productive fishing grounds. Unlike the situation in other parts of Europe, these monuments were not associated with agriculture. Opinions have varied over the last quarter century, but enough is now known about changes of sea-level for his interpretation to be investigated on the ground. There seems to have been considerable diversity. On the large island of Örust some of the tombs located near to the sea appear to be associated with small natural enclosures defined by rock outcrops and may have been associated with grazing land. On the neighbouring island of Tjörn, however, the tombs were associated with small islands and important sea channels. During the Bronze Age the same areas included carvings of ships. Recent fieldwork in western Norway suggests that such locations were especially important in a maritime economy.

Vascular plant diversity and climate change in the alpine zone of the Lefka Ori, Crete

The aim of this study is to analyse the vascular flora and the local climate along an altitudinal gradient in the Lefka Ori massif Crete and to evaluate the potential effects of climate change on the plant diversity of the sub-alpine and alpine zones. It provides a quantitative/qualitative analysis of vegetation-environment relationships for four summits along an altitude gradient on the Lefka Ori massif Crete (1664-2339 m). The GLORIA multi-summit approach was used to provide vegetation and floristic data together with temperature records for every summit. Species richness and species turnover was calculated together with floristic similarity between the summits. 70 species were recorded, 20 of which were endemic, belonging to 23 different families. Cretan endemics dominate at these high altitudes. Species richness and turnover decreased with altitude. The two highest summits showed greater floristic similarity. Only 20% of the total flora recorded reaches the highest summit while 10% is common among summits. Overall there was a 4.96 degrees C decrease in temperature along the 675 m gradient. Given a scenario of temperature increase the ecotone between the sub-alpine and alpine zone would be likely to have the greatest species turnover. Southern exposures are likely to be invaded first by thermophilous species while northern exposures are likely to be more resistant to changes. Species distribution shifts will also depend on habitat availability. Many, already threatened, local endemic species will be affected first.

Response of plant-pollinator communities to fire: changes in diversity, abundance and floral reward structure

Globally, plant-pollinator communities are subject to a diverse array of perturbations and in many temperate and semi-arid systems fire is a dominant structuring force. We present a novel and highly integrated approach, which quantifies, in parallel, the response to fire of pollinator communities, floral communities and floral reward structure. Mt Carmel, Israel is a recognised bee-flower biodiversity hotspot, and using a chronosequence of habitats with differing post-fire ages, we follow the changes in plant-pollinator community organisation from immediately following a burn until full regeneration of vegetation. Initially, fire has a catastrophic effect on these communities, however, recovery is rapid with a peak in diversity of both flowers and bees in the first 2 years post-fire, followed by a steady decline over the next 50 years. The regeneration of floral communities is closely matched by that of their principal pollinators. At the community level we quantify, per unit area of habitat, key parameters of nectar and pollen forage known to be of importance in structuring pollinator communities. Nectar Volume, nectar water content, nectar concentration and the diversity of nectar foraging niches are all greatest immediately following fire with a steady decrease as regeneration proceeds. Temporal changes in energy availability for nectar, pollen, total energy (nectar + pollen) and relative importance of pollen to nectar energy show a similar general decline with site age, however, the pattern is less clear owing to the highly patchy distribution of floral resources. Changes in floral reward structure reflect the general shift from annuals (generally low-reward open access flowers) to perennials (mostly high-reward and restricted access flowers) as post-fire regeneration ensues. The impact of fire on floral communities and their associated rewards have clear implications for pollinator community structure and we discuss this and the role of other disturbance factors on these systems.

Nectar resource diversity organises flower-visitor community structure

Communities of nectar-producing plants show high spatio-temporal variation in the patterns of volume and concentration presentation. We illustrate a novel approach for quantifying nectar reward structures in complex communities, demonstrating that nectar resource diversity (defined as the variety of nectar volume-concentration combinations available) may be a fundamental factor organising nectarivore communities. In a series of diverse bee and entomophilous flower communities in Israel, our measure of nectar resource diversity alone explains the majority of variation in bee species richness, while other nectar variables (volume, concentration, energy value, and water content) have little predictive value per se. The new measure of nectar resource diversity is highly correlated with floral species richness and particularly with the species richness of annuals, yet it is additive in its effect on bee diversity. We conclude that relying solely upon measurements of mean nectar volume and mean nectar concentration overlooks a key characteristic of community-level reward structure, nectar resource diversity, so that previous studies may have failed to identify an important determinant of flower-visitor community structure.