Genetic structure and linkage disequilibrium in landrace populations of barley in Sardinia

Multilocus digenic linkage disequilibria (LD) and their population structure were investigated in eleven landrace populations of barley (Hordeum vulgare ssp. vulgare L.) in Sardinia, using 134 dominant simple-sequence amplified polymorphism markers. The analysis of molecular variance for these markers indicated that the populations were partially differentiated (F ST = 0.18), and clustered into three geographic areas. Consistent with this population pattern, STRUCTURE analysis allocated individuals from a bulk of all populations into four genetic groups, and these groups also showed geographic patterns. In agreement with other molecular studies in barley, the general level of LD was low (13 % of locus pairs, with P < 0.01) in the bulk of 337 lines, and decayed steeply with map distance between markers. The partitioning of multilocus associations into various components indicated that genetic drift and founder effects played a major role in determining the overall genetic makeup of the diversity in these landrace populations, but that epistatic homogenising or diversifying selection was also present. Notably, the variance of the disequilibrium component was relatively high, which implies caution in the pooling of barley lines for association studies. Finally, we compared the analyses of multilocus structure in barley landrace populations with parallel analyses in both composite crosses of barley on the one hand and in natural populations of wild barley on the other. Neither of these serves as suitable mimics of landraces in barley, which require their own study. Overall, the results suggest that these populations can be exploited for LD mapping if population structure is controlled.

Microbial−mammalian cometabolites dominate the age-associated urinary metabolic phenotype in Taiwanese and American populations

Understanding the metabolic processes associated with aging is key to developing effective management and treatment strategies for age-related diseases. We investigated the metabolic profiles associated with age in a Taiwanese and an American population. 1H NMR spectral profiles were generated for urine specimens collected from the Taiwanese Social Environment and Biomarkers of Aging Study (SEBAS; n = 857; age 54–91 years) and the Mid-Life in the USA study (MIDUS II; n = 1148; age 35–86 years). Multivariate and univariate linear projection methods revealed some common age-related characteristics in urinary metabolite profiles in the American and Taiwanese populations, as well as some distinctive features. In both cases, two metabolites—4-cresyl sulfate (4CS) and phenylacetylglutamine (PAG)—were positively associated with age. In addition, creatine and β-hydroxy-β-methylbutyrate (HMB) were negatively correlated with age in both populations (p < 4 × 10–6). These age-associated gradients in creatine and HMB reflect decreasing muscle mass with age. The systematic increase in PAG and 4CS was confirmed using ultraperformance liquid chromatography–mass spectrometry (UPLC–MS). Both are products of concerted microbial–mammalian host cometabolism and indicate an age-related association with the balance of host–microbiome metabolism.

A molecular, morphological and cytological investigation of the identity of non-native Ludwigia (Onagraceae) populations in Britain

A combined molecular, morphological and cytological analysis was used to study the identity and number of species of Ludwigia section Oligospermum occurring in British waterways. Only one taxon was identified for which the name L. grandiflora subsp. hexapetala (Hook. & Arn.) G.L. Nesom & Kartesz is preferred. A chromosome count of 2n = 80 was made for all plants tested and DNA evidence demonstrates that at least two clones are present in Britain. Morphological characters to differentiate L.grandiflora subsp. hexapetala and L. peploides subsp. montevidensis (Spreng.) P.H. Raven are provided. Though the production of fruit in Britain by apparently isolated populations is noted, repeated introduction into the wild from gardens is judged to be primarily responsible for the British distribution of the taxon. Legislative implications are considered and an amendment to Schedule 9 of the UK Wildlife and Countryside Act (1981) is strongly advocated.

Use of batch culture and a two-stage continuous culture system to study the effect of supplemental a-lactalbumin and glycomacropeptide on mixed populations of human gut bacteria

Certain milk factors can promote the growth of a host-friendly gastrointestinal microflora. This may explain why breast-fed infants experience fewer intestinal infections than their formula-fed counterparts. The effect of formula supplementation with two such factors was investigated in this study. Infant faecal specimens were used to ferment formulas supplemented with glycomacropeptide and α-lactalbumin in a two-stage compound continuous culture model. Bacteriology was determined by fluorescence in situ hybridisation. Vessels that contained breast milk as well as α-lactalbumin and glycomacropeptide had stable counts of bifidobacteria while lactobacilli increased significantly only in vessels with breast milk. Bacteroides, clostridia and Escherichia coli decreased significantly in all runs. Acetate was the principal acid found along with high amounts of propionate and lactate. Supplementation of infant formulas with appropriate milk proteins may be useful in simulating the beneficial bacteriological effects of breast milk.

Supplementary feeding of wild birds indirectly affects ground beetle populations in suburban gardens

Supplementary feeding of wild birds by domestic garden-holders is a globally widespread and popular form of human–wildlife interaction, particularly in urban areas. Vast amounts of energy are thus being added to garden ecosystems. However, the potential indirect effects of this activity on non-avian species have been little studied to date, with the only two previous studies taking place under experimentally manipulated conditions. Here we present the first evidence of a localised depletive effect of wild bird feeding on ground beetles (Coleoptera: Carabidae) in suburban gardens under the usual feeding patterns of the garden-holders. We trapped significantly fewer ground beetles directly under bird-feeding stations than in matched areas of habitat away from feeders. Video analysis also revealed significantly higher activity by ground-foraging birds under the feeding stations than in the control areas. Small mammal trapping revealed no evidence that these species differ in abundance between gardens with and without bird feeders. We therefore suggest that local increases in ground-foraging activity by bird species whose diets encompass arthropods as well as seed material are responsible for the reduction in ground beetle numbers. Our work therefore illustrates that providing food for wild birds can have indirect negative effects on palatable prey species under typical conditions.

Competing effects of toxin-producing phytoplankton on overall plankton populations in the Bay of Bengal

The coexistence of a large number of phytoplankton species on a seemingly limited variety of resources is a classical problem in ecology, known as ‘the paradox of the plankton’. Strong fluctuations in species abundance due to the external factors or competitive interactions leading to oscillations, chaos and short-term equilibria have been cited so far to explain multi-species coexistence and biodiversity of phytoplankton. However, none of the explanations has been universally accepted. The qualitative view and statistical analysis of our field data establish two distinct roles of toxin-producing phytoplankton (TPP): toxin allelopathy weakens the interspecific competition among phytoplankton groups and the inhibition due to ingestion of toxic substances reduces the abundance of the grazer zooplankton. Structuring the overall plankton population as a combination of nontoxic phytoplankton (NTP), toxic phytoplankton, and zooplankton, here we offer a novel solution to the plankton paradox governed by the activity of TPP. We demonstrate our findings through qualitative analysis of our sample data followed by analysis of a mathematical model.

Landscape structure mediates the effects of a stressor on field vole populations

Spatio-temporal landscape heterogeneity has rarely been considered in population-level impact assessments. Here we test whether landscape heterogeneity is important by examining the case of a pesticide applied seasonally to orchards which may affect non-target vole populations, using a validated ecologically realistic and spatially explicit agent-based model. Voles thrive in unmanaged grasslands and untreated orchards but are particularly exposed to applied pesticide treatments during dispersal between optimal habitats. We therefore hypothesised that vole populations do better (1) in landscapes containing more grassland and (2) where areas of grassland are closer to orchards, but (3) do worse if larger areas of orchards are treated with pesticide. To test these hyposeses we made appropriate manipulations to a model landscape occupied by field voles. Pesticide application reduced model population sizes in all three experiments, but populations subsequently wholly or partly recovered. Population depressions were, as predicted, lower in landscapes containing more unmanaged grassland, in landscapes with reduced distance between grassland and orchards, and in landscapes with fewer treated orchards. Population recovery followed a similar pattern except for an unexpected improvement in recovery when the area of treated orchards was increased. Outside the period of pesticide application, orchards increase landscape connectivity and facilitate vole dispersal and so speed population recovery. Overall our results show that accurate prediction of population impact cannot be achieved without taking account of landscape structure. The specifics of landscape structure and habitat connectivity are likely always important in mediating the effects of stressors.

An energy budget agent-based model of earthworm populations and its application to study the effects of pesticides

Earthworms are important organisms in soil communities and so are used as model organisms in environmental risk assessments of chemicals. However current risk assessments of soil invertebrates are based on short-term laboratory studies, of limited ecological relevance, supplemented if necessary by site-specific field trials, which sometimes are challenging to apply across the whole agricultural landscape. Here, we investigate whether population responses to environmental stressors and pesticide exposure can be accurately predicted by combining energy budget and agent-based models (ABMs), based on knowledge of how individuals respond to their local circumstances. A simple energy budget model was implemented within each earthworm Eisenia fetida in the ABM, based on a priori parameter estimates. From broadly accepted physiological principles, simple algorithms specify how energy acquisition and expenditure drive life cycle processes. Each individual allocates energy between maintenance, growth and/or reproduction under varying conditions of food density, soil temperature and soil moisture. When simulating published experiments, good model fits were obtained to experimental data on individual growth, reproduction and starvation. Using the energy budget model as a platform we developed methods to identify which of the physiological parameters in the energy budget model (rates of ingestion, maintenance, growth or reproduction) are primarily affected by pesticide applications, producing four hypotheses about how toxicity acts. We tested these hypotheses by comparing model outputs with published toxicity data on the effects of copper oxychloride and chlorpyrifos on E. fetida. Both growth and reproduction were directly affected in experiments in which sufficient food was provided, whilst maintenance was targeted under food limitation. Although we only incorporate toxic effects at the individual level we show how ABMs can readily extrapolate to larger scales by providing good model fits to field population data. The ability of the presented model to fit the available field and laboratory data for E. fetida demonstrates the promise of the agent-based approach in ecology, by showing how biological knowledge can be used to make ecological inferences. Further work is required to extend the approach to populations of more ecologically relevant species studied at the field scale. Such a model could help extrapolate from laboratory to field conditions and from one set of field conditions to another or from species to species.

Ionospheric ion and electron heating at the poleward boundary of a poleward expanding substorm-disturbed region

We present observations of a poleward propagating substorm-disturbed region which was observed by the European Incoherent SCATter (EISCAT) radar and the Svalbard International Monitor for Auroral Geomagnetic Effects (IMAGE) magnetometers in the postmidnight sector. The expansion of the disturbance was launched by a substorm intensification which started similar to 25 min after the initial onset, and similar to 10 min before the disturbance arrived over Svalbard. In association with the magnetic disturbance, a poleward expanding enduring enhancement in the F region electron temperature was observed, indicative of soft electron precipitation, with a narrow band of enhanced ion temperature straddling its poleward edge, indicative of fast ion flows and ion-neutral collisional heating. This electron temperature boundary was coincident with the poleward propagating electrojet current system detected by the high-latitude IMAGE magnetometer stations and is taken to be a proxy for the observation of a substorm auroral bulge. The electron temperature boundary is inferred to have a width comparable or less than one radar range gate (similar to 60 km transverse to the magnetic field), while the region of high ion temperature was found to be approximately three gates wide, extending approximately two gates (similar to 120 km) poleward of the electron temperature boundary, and approximately one gate (similar to 60 km) equatorward. The two-beam radar line-of-sight velocity data are found to be consistent with the existence of a layer of high-speed flow in the boundary, peaking at values similar to1.5-3 km s(-1), roughly consistent with the ion temperature data. The flow is directed either east or west along the boundary depending on the direction of the flow in the poleward region. We infer that the flow is deflected along and around the boundary of the substorm-disturbed region due to the high conductivity of the latter. Variations in the flow poleward of the boundary produced no discernible magnetic effects on the ground, confirming the low conductivity of the preboundary ionosphere.

Ion populations on open field lines within the dayside low-latitude boundary layer: theory and observations during a transient event

We analyze of ion populations observed by the NOAA-12 satellite within dayside auroral transients. The data are matched with an open magnetopause model which allows for the transmission of magnetosheath ions across one or both of the two Alfvén waves which emanate from the magnetopause reconnection site. It also allows for reflection and acceleration of ions of magnetospheric origin by these waves. From the good agreement found between the model and the observations, we propose that the events and the low-latitude boundary precipitation are both on open field lines.