Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array

Background A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNPbased linkage map of an apple rootstock progeny. Results Of the 7,867 Malus SNP markers on the array, 1,823 (23.2 %) were heterozygous in one of the two parents of the progeny, 1,007 (12.8 %) were heterozygous in both parental genotypes, whilst just 2.8 % of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the ‘Golden Delicious’ genome sequence. A total of 311 markers (13.7 % of all mapped markers) mapped to positions that conflicted with their predicted positions on the ‘Golden Delicious’ pseudo-chromosomes, indicating the presence of paralogous genomic regions or misassignments of genome sequence contigs during the assembly and anchoring of the genome sequence. Conclusions We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the ‘Golden Delicious’ reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.

Institutional capacity and implementation issues in farmers' rights

Armed with the ‘equity’ and ‘conservation’ arguments that have a deep resonance with farming communities, developing countries are crafting a range of measures designed to protect farmers’ access to innovations, reward their contributions to the conservation and enhancement of plant genetic resources and provide incentives for sustained on-farm conservation. These measures range from the commericialization of farmers’ varieties to the conferment of a set of legally enforceable rights on farming communities – the exercise of which is expected to provide economic rewards to those responsible for on-farm conservation and innovation. The rights-based approach has been the cornerstone of legislative provision for implementing farmers’ rights in most developing countries. In drawing up these measures, developing countries do not appear to have systematically examined or provided for the substantial institutional capacity required for the effective implementation of farmers’ rights provisions. The lack of institutional capacity threatens to undermine any prospect of serious implementation of these provisions. More importantly, the expectation that significant incentives for on-farm conservation and innovation will flow from these ‘rights’ may be based on a flawed understanding of the economics of intellectual property rights. While farmers’ rights may provide only limited rewards for conservation, they may still have the effect of diluting the incentives for innovative institutional breeding programs – with the private sector increasingly relying on non-IPR instruments to profit from innovation. The focus on a rights-based approach may also draw attention away from alternative stewardship-based approaches to the realization of farmers’ rights objectives.

Mobilising community action towards a low-carbon future: Opportunities and challenges for local government in the UK

Over the last decade the important role that local authorities can play in catalyzing communityaction on climate change has been repeatedly emphasised by the UK Government. The paper examines this policy context and explores the options available to local authorities in terms of reaching and engaging their communities. The type of progressive response shown by some UKlocal authorities is illustrated with empirical evidence gathered through a study conducted in the London Borough of Islington focusing on their recently established ‘Green Living Centre’. The results confirm interest in this major council-led community initiative, with positive attitudes expressed by the majority of those questioned in terms of the advice and information available. However, it is also clear that many participants had preexisting pro-environmental attitudes and behavioural routines. Results from a broader sample of Islington residents indicate a substantial challenge in reaching the wider community, where enthusiasm for sustainability change and interest in this type of scheme were more mixed. The prospect for local government in addressing this challenge – and their ability to trigger and capitalize upon concepts of social change at the community level towardsalowercarbon future – is discussed in the final part of the paper.

Control without deception

Lying to participants offers an experimenter the enticing prospect of making “others' behaviour” a controlled variable, but is eschewed by experimental economists because it may pollute the pool of subjects. This paper proposes and implements a new experimental design, the Conditional Information Lottery, which offers all the benefits of deception without actually deceiving anyone. The design should be suitable for most economics experiments, and works by a modification of an already standard device, the Random Lottery incentive system. The deceptive scenarios of designs which use deceit are replaced with fictitious scenarios, each of which, from a subject's viewpoint, has a chance of being true. The design is implemented in a sequential play public good experiment prompted by Weimann's (1994) result, from a deceptive design, that subjects are more sensitive to freeriding than cooperation on the part of others. The experiment provides similar results to Weimann's, in that subjects are at least as cooperative when uninformed about others' behaviour as they are if reacting to high contributions. No deception is used and the data cohere well both internally and with other public goods experiments. In addition, simultaneous play is found to be more efficient than sequential play, and subjects contribute less at the end of a sequence than at the start. The results suggest pronounced elements of overconfidence, egoism and (biased) reciprocity in behaviour, which may explain decay in contributions in repeated play designs. The experiment shows there is a workable alternative to deception.

The Marlborough mound, Wiltshire. A further Neolithic monumental mound by the River Kennet.

Recent radiocarbon dates obtained from two soil cores taken through the Marlborough Castle mound, Wiltshire, show the main body of it to be a contemporaneous monument to Silbury Hill, dating to the second half of the 3rd millennium cal bc. In light of these dates, this paper considers the sequence identified within the cores, which includes two possible flood events early in the construction of the mound. It also describes four cores taken through the surrounding ditch, as well as small-scale work to the north-east of the mound. The topographic location of the mound in a low-lying area and close to rivers and springs is discussed, and the potential for Late Neolithic sites nearby is set out, with the land to the south of the mound identified as an area for future research. The paper ends with the prospect that other apparent mottes in Wiltshire and beyond may well also have prehistoric origins

Quantification of UV-B flux through time using UV-B-absorbing compounds contained in fossil Pinus sporopollenin

• UV-B radiation currently represents c. 1.5% of incoming solar radiation. However, significant changes are known to have occurred in the amount of incoming radiation both on recent and on geological timescales. Until now it has not been possible to reconstruct a detailed measure of UV-B radiation beyond c. 150 yr ago. • Here, we studied the suitability of fossil Pinus spp. pollen to record variations in UV-B flux through time. In view of the large size of the grain and its long fossil history, we hypothesized that this grain could provide a good proxy for recording past variations in UV-B flux. • Two key objectives were addressed: to determine whether there was, similar to other studied species, a clear relationship between UV-B-absorbing compounds in the sporopollenin of extant pollen and the magnitude of UV-B radiation to which it had been exposed; and to determine whether these compounds could be extracted from a small enough sample size of fossil pollen to make reconstruction of a continuous record through time a realistic prospect. • Preliminary results indicate the excellent potential of this species for providing a quantitative record of UV-B through time. Using this technique, we present the first record of UV-B flux during the last 9500 yr from a site near Bergen, Norway.

Fire in the Earth System

Fire is an important component of the Earth System that is tightly coupled with climate, vegetation, biogeochemical cycles, and human activities. Observations of how fire regimes change on seasonal to millennial timescales are providing an improved understanding of the hierarchy of controls on fire regimes. Climate is the principal control on fire regimes, although human activities have had an increasing influence on the distribution and incidence of fire in recent centuries. Understanding of the controls and variability of fire also underpins the development of models, both conceptual and numerical, that allow us to predict how future climate and land-use changes might influence fire regimes. Although fires in fire-adapted ecosystems can be important for biodiversity and ecosystem function, positive effects are being increasingly outweighed by losses of ecosystem services. As humans encroach further into the natural habitat of fire, social and economic costs are also escalating. The prospect of near-term rapid and large climate changes, and the escalating costs of large wildfires, necessitates a radical re-thinking and the development of approaches to fire management that promote the more harmonious co-existence of fire and people.

Predictability of large interannual Arctic sea-ice anomalies

In projections of twenty-first century climate, Arctic sea ice declines and at the same time exhibits strong interannual anomalies. Here, we investigate the potential to predict these strong sea-ice anomalies under a perfect-model assumption, using the Max-Planck-Institute Earth System Model in the same setup as in the Coupled Model Intercomparison Project Phase 5 (CMIP5). We study two cases of strong negative sea-ice anomalies: a 5-year-long anomaly for present-day conditions, and a 10-year-long anomaly for conditions projected for the middle of the twenty-first century. We treat these anomalies in the CMIP5 projections as the truth, and use exactly the same model configuration for predictions of this synthetic truth. We start ensemble predictions at different times during the anomalies, considering lagged-perfect and sea-ice-assimilated initial conditions. We find that the onset and amplitude of the interannual anomalies are not predictable. However, the further deepening of the anomaly can be predicted for typically 1 year lead time if predictions start after the onset but before the maximal amplitude of the anomaly. The magnitude of an extremely low summer sea-ice minimum is hard to predict: the skill of the prediction ensemble is not better than a damped-persistence forecast for lead times of more than a few months, and is not better than a climatology forecast for lead times of two or more years. Predictions of the present-day anomaly are more skillful than predictions of the mid-century anomaly. Predictions using sea-ice-assimilated initial conditions are competitive with those using lagged-perfect initial conditions for lead times of a year or less, but yield degraded skill for longer lead times. The results presented here suggest that there is limited prospect of predicting the large interannual sea-ice anomalies expected to occur throughout the twenty-first century.

The invisible hand guiding technology: crossing the boundary of technology

This paper examines attitudes towards Radio Frequency Identification (RFID) technology and explores the wider concerns of the ever increasing prospect of social tagging. Capturing vignettes and narratives from a sample of study participants, the paper highlights concerns about adopting RFID implements now and in the future. The views captured through qualitative methodology act as the platform for a wider argument concerning the human rights and privacy intrusion concerns over IT applications. Intended as an insight into the reality of technology impact, this paper lists a series of questions for leaders to consider over matters of human rights specifically concerning RFID adoption. The authors conclude that caution, naivety and fear are the underlying reasons for society accepting RFIDs without question and that RFIDs will be a part of everyday working and domestic life in the near future.

Numerical analyses of Runge–Kutta implicit–explicit schemes for horizontally explicit, vertically implicit solutions of atmospheric models

With the prospect of exascale computing, computational methods requiring only local data become especially attractive. Consequently, the typical domain decomposition of atmospheric models means horizontally-explicit vertically-implicit (HEVI) time-stepping schemes warrant further attention. In this analysis, Runge-Kutta implicit-explicit schemes from the literature are analysed for their stability and accuracy using a von Neumann stability analysis of two linear systems. Attention is paid to the numerical phase to indicate the behaviour of phase and group velocities. Where the analysis is tractable, analytically derived expressions are considered. For more complicated cases, amplification factors have been numerically generated and the associated amplitudes and phase diagnosed. Analysis of a system describing acoustic waves has necessitated attributing the three resultant eigenvalues to the three physical modes of the system. To do so, a series of algorithms has been devised to track the eigenvalues across the frequency space. The result enables analysis of whether the schemes exactly preserve the non-divergent mode; and whether there is evidence of spurious reversal in the direction of group velocities or asymmetry in the damping for the pair of acoustic modes. Frequency ranges that span next-generation high-resolution weather models to coarse-resolution climate models are considered; and a comparison is made of errors accumulated from multiple stability-constrained shorter time-steps from the HEVI scheme with a single integration from a fully implicit scheme over the same time interval. Two schemes, “Trap2(2,3,2)” and “UJ3(1,3,2)”, both already used in atmospheric models, are identified as offering consistently good stability and representation of phase across all the analyses. Furthermore, according to a simple measure of computational cost, “Trap2(2,3,2)” is the least expensive.

Thin place

This publication is a full colour bi-lingual catalogue for the exhibition Thin Place, curated by Ciara Healy for Oriel Myrddin. It includes artwork by five interdisciplinary artists based in West Wales, the West of Ireland and London. The exhibition, symposium and education programme, funded by the Arts Council of Wales aims to show how the fields of art, literature, science and theology are interconnected, especially when considering the nature of reality, the concept of an otherworld and the prospect of an afterlife. Included in the catalogue are texts especially commissioned for the exhibition by professionals who work in disciplines outside of the art world. It also includes an introductory essay by Ciara Healy.

Thermal remote sensing of sea surface temperature

Sea surface temperature has been an important application of remote sensing from space for three decades. This chapter first describes well-established methods that have delivered valuable routine observations of sea surface temperature for meteorology and oceanography. Increasingly demanding requirements, often related to climate science, have highlighted some limitations of these ap-proaches. Practitioners have had to revisit techniques of estimation, of characterising uncertainty, and of validating observations—and even to reconsider the meaning(s) of “sea surface temperature”. The current understanding of these issues is reviewed, drawing attention to ongoing questions. Lastly, the prospect for thermal remote sens-ing of sea surface temperature over coming years is discussed.

Parametric preference functionals under risk in the gain domain: a Bayesian analysis

The performance of rank dependent preference functionals under risk is comprehensively evaluated using Bayesian model averaging. Model comparisons are made at three levels of heterogeneity plus three ways of linking deterministic and stochastic models: the differences in utilities, the differences in certainty equivalents and contextualutility. Overall, the"bestmodel", which is conditional on the form of heterogeneity is a form of Rank Dependent Utility or Prospect Theory that cap tures the majority of behaviour at both the representative agent and individual level. However, the curvature of the probability weighting function for many individuals is S-shaped, or ostensibly concave or convex rather than the inverse S-shape commonly employed. Also contextual utility is broadly supported across all levels of heterogeneity. Finally, the Priority Heuristic model, previously examined within a deterministic setting, is estimated within a stochastic framework, and allowing for endogenous thresholds does improve model performance although it does not compete well with the other specications considered.

Dyspnea-related cues engage the prefrontal cortex - evidence from functional brain imaging in COPD

Dyspnea is the major source of disability in chronic obstructive pulmonary disease (COPD). In COPD, environmental cues (e.g. the prospect of having to climb stairs) become associated with dyspnea, and may trigger dyspnea even before physical activity commences. We hypothesised that brain activation relating to such cues would be different between COPD patients and healthy controls, reflecting greater engagement of emotional mechanisms in patients. Methods: Using FMRI, we investigated brain responses to dyspnea-related word cues in 41 COPD patients and 40 healthy age-matched controls. We combined these findings with scores of self-report questionnaires thus linking the FMRI task with clinically relevant measures. This approach was adapted from studies in pain that enables identification of brain networks responsible for pain processing despite absence of a physical challenge. Results: COPD patients demonstrate activation in the medial prefrontal cortex (mPFC), and anterior cingulate cortex (ACC) which correlated with the visual analogue scale (VAS) response to word cues. This activity independently correlated with patient-reported questionnaires of depression, fatigue and dyspnea vigilance. Activation in the anterior insula, lateral prefrontal cortex (lPFC) and precuneus correlated with the VAS dyspnea scale but not the questionnaires. Conclusions: Our findings suggest that engagement of the brain's emotional circuitry is important for interpretation of dyspnea-related cues in COPD, and is influenced by depression, fatigue, and vigilance. A heightened response to salient cues is associated with increased symptom perception in chronic pain and asthma, and our findings suggest such mechanisms may be relevant in COPD.

Responsibility effects in decision making under risk

We systematically explore decision situations in which a decision maker bears responsibility for somebody else's outcomes as well as for her own in situations of payoff equality. In the gain domain we confirm the intuition that being responsible for somebody else's payoffs increases risk aversion. This is however not attributable to a 'cautious shift' as often thought. Indeed, looking at risk attitudes in the loss domain, we find an increase in risk seeking under responsibility. This raises issues about the nature of various decision biases under risk, and to what extent changed behavior under responsibility may depend on a social norm of caution in situations of responsibility versus naive corrections from perceived biases. To further explore this issue, we designed a second experiment to explore risk-taking behavior for gain prospects offering very small or very large probabilities of winning. For large probabilities, we find increased risk aversion, thus confirming our earlier finding. For small probabilities however, we find an increase of risk seeking under conditions of responsibility. The latter finding thus discredits hypotheses of a social rule dictating caution under responsibility, and can be explained through flexible self-correction models predicting an accentuation of the fourfold pattern of risk attitudes predicted by prospect theory. An additional accountability mechanism does not change risk behavior, except for mixed prospects, in which it reduces loss aversion. This indicates that loss aversion is of a fundamentally different nature than probability weighting or utility curvature. Implications for debiasing are discussed.