The status of traditional Scottish animal breeds and plant varieties and the implications for biodiversity

The aim of this scoping study was to evaluate the effects on Scottish biodiversity of changes in the use of traditional breeds and varieties. The overall objectives were: a) The evaluation of the importance of genetic loss from the reduction in use of these breeds and varieties, for example, the loss of unusual characteristics that might have been of particular local use. b) An assessment of the impacts of reduction in the ability to conduct further breeding or research on rare and traditional varieties and breeds. c) Identification of the loss of certain farming techniques associated with particular varieties and breeds. d) An assessment of possible losses of biodiversity associated with reduction in the use of these breeds and varieties and the farming systems associated with them

Long-term balancing selection drives evolution of immunity genes in Capsella.

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease-related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long-term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck

An investigation of the performance portability of OpenCL

This paper reports on the development of an MPI/OpenCL implementation of LU, an application-level benchmark from the NAS Parallel Benchmark Suite. An account of the design decisions addressed during the development of this code is presented, demonstrating the importance of memory arrangement and work-item/work-group distribution strategies when applications are deployed on different device types. The resulting platform-agnostic, single source application is benchmarked on a number of different architectures, and is shown to be 1.3–1.5× slower than native FORTRAN 77 or CUDA implementations on a single node and 1.3–3.1× slower on multiple nodes. We also explore the potential performance gains of OpenCL’s device fissioning capability, demonstrating up to a 3× speed-up over our original OpenCL implementation

Diversity of Chironomidae (Diptera) breeding in the Great Stour, Kent: baseline results from the Westgate Parks non-biting midge project

Chalk rivers and streams are of conservation importance due their ecological diversity, historical relevance and economic value. With more than 200 chalk watercourses, England is considered unusual in having the most chalk rivers in the world. However, due to increasing anthropogenic activities, many English chalk rivers and streams are becoming badly degraded. The non-biting midges or chironomids (Diptera, Chironomidae) are considered key-stone taxa in aquatic food webs, and have been used as ecological indicators of freshwater quality and environmental stress. Here we determined the generic richness, diversity, and community structure of Chironomidae across six sites in the mid-section of the Great Stour in Kent, a chalk river for which concern has been expressed regarding both water and habitat quality. Based on the morphological identification of 1336 insect larvae from the six sites (four in Westgate Parks, Canterbury, and two at nearby locations upstream and downstream from Canterbury City), a total of 20 genera of Chironomidae were identified, including some taxa indicative of freshwater habitats with low levels of organic pollution. There were different levels of generic richness and diversity among sites, and while there was little variation in the community composition among the sites within Westgate Parks, there were noticeable generic differences among Westgate Parks sites compared with those upstream and downstream, showing the highest complementarity and Beta diversity values. Overall, the results were comparable with other studies on chironomids in chalk rivers and other river systems. Although spatially limited to a small stretch of river, this represents the first study on chironomids in the Great Stour and provides baseline information on the diversity and structure of this important insect group with aquatic larvae, useful for the objective interpretation of any future biological assessments and monitoring programmes on the Kentish Stour, and also for comparisons with other chalk rivers

A Resolved Ring of Debris Dust around the Solar Analog HD 107146

We present resolved images of the dust continuum emission from the debris disk around the young (80-200 Myr) solar-type star HD 107146 with CARMA at λ = 1.3 mm and the CSO at λ = 350 μ. Both images show that the dust emission extends over an approximately 10" diameter region. The high-resolution (3") CARMA image further reveals that the dust is distributed in a partial ring with significant decrease in a flux inward of 97 AU. Two prominent emission peaks appear within the ring separated by ~140° in the position angle. The morphology of the dust emission is suggestive of dust captured into a mean motion resonance, which would imply the presence of a planet at an orbital radius of ~45-75 AU

The Power-Optimised Software Envelope

Advances in processor design have delivered performance improvements for decades. As physical limits are reached, refinements to the same basic technologies are beginning to yield diminishing returns. Unsustainable increases in energy consumption are forcing hardware manufacturers to prioritise energy efficiency in their designs. Research suggests that software modifications may be needed to exploit the resulting improvements in current and future hardware. New tools are required to capitalise on this new class of optimisation. In this paper, we present the Power Optimised Software Envelope (POSE) model, which allows developers to assess the potential benefits of power optimisation for their applications. The POSE model is metric agnostic and in this paper we provide derivations using the established Energy-Delay Product metric and the novel Energy-Delay Sum and Energy-Delay Distance metrics that we believe are more appropriate for energy-aware optimisation efforts. We demonstrate POSE on three platforms by studying the optimisation characteristics of applications from the Mantevo benchmark suite. Our results show that the Pathfinder application has very little scope for power optimisation while TeaLeaf has the most, with all other applications in the benchmark suite falling between the two. Finally, we extend our POSE model with a formulation known as System Summary POSE – a meta-heuristic that allows developers to assess the scope a system has for energy-aware software optimisation independent of the code being run

Metrics for energy-aware software optimisation

Energy consumption is rapidly becoming a limiting factor in scientific computing. As a result, hardware manufacturers increasingly prioritise energy efficiency in their processor designs. Performance engineers are also beginning to explore software optimisation and hardware/software co-design as a means to reduce energy consumption. Energy efficiency metrics developed by the hardware community are often re-purposed to guide these software optimisation efforts. In this paper we argue that established metrics, and in particular those in the Energy Delay Product (Etn) family, are unsuitable for energyaware software optimisation. A good metric should provide meaningful values for a single experiment, allow fair comparison between experiments, and drive optimisation in a sensible direction. We show that Etn metrics are unable to fulfil these basic requirements and present suitable alternatives for guiding energy-aware software optimisation. We finish with a practical demonstration of the utility of our proposed metrics

Secondary literacy across the curriculum: Challenges and possibilities

This paper discusses the challenges and possibilities attendant upon successfully implementing literacy across the curriculum initiatives – or ‘school language policies’ as they have come to be known - particularly at the secondary or high school level. It provides a theoretical background to these issues, exploring previous academic discussions of school language policies, and highlights key areas of concern as well as opportunity with respect to school implementation of such policies. As such, it provides a necessary conceptual background to the subsequent papers in this special issue, which focus upon the Secondary Schools’ Literacy Initiative (SSLI) – a New Zealand funded programme that aims to establish cross-curricular language and literacy policies in secondary schools

High DNA sequence diversity in pericentromeric genes of the plant Arabidopsis lyrata

Differences in neutral diversity at different loci are predicted to arise due to differences in mutation rates and from the “hitchhiking” effects of natural selection. Consistent with hitchhiking models, Drosophila melanogaster chromosome regions with very low recombination have unusually low nucleotide diversity. We compared levels of diversity from five pericentromeric regions with regions of normal recombination in Arabidopsis lyrata, an outcrossing close relative of the highly selfing A. thaliana. In contrast with the accepted theoretical prediction, and the pattern in Drosophila, we found generally high diversity in pericentromeric genes, which is consistent with the observation in A. thaliana. Our data rule out balancing selection in the pericentromeric regions, suggesting that hitchhiking is more strongly reducing diversity in the chromosome arms than the pericentromere regions

Rapid weed adaptation and range expansion in response to agriculture over the past two centuries

North America has experienced a massive increase in cropland use since 1800, accompanied more recently by the intensification of agricultural practices. Through genome analysis of present-day and historical samples spanning environments over the past two centuries, we studied the effect of these changes in farming on the extent and tempo of evolution across the native range of the common waterhemp (Amaranthus tuberculatus), a now pervasive agricultural weed. Modern agriculture has imposed strengths of selection rarely observed in the wild, with notable shifts in allele frequency trajectories since agricultural intensification in the 1960s. An evolutionary response to this extreme selection was facilitated by a concurrent human-mediated range shift. By reshaping genome-wide diversity across the landscape, agriculture has driven the success of this weed in the 21st century