Impacts of pollution and climate change on ombrotrophic Sphagnum species in the UK: analysis of uncertainties in two empirical niche models

A significant challenge in the prediction of climate change impacts on ecosystems and biodiversity is quantifying the sources of uncertainty that emerge within and between different models. Statistical species niche models have grown in popularity, yet no single best technique has been identified reflecting differing performance in different situations. Our aim was to quantify uncertainties associated with the application of 2 complimentary modelling techniques. Generalised linear mixed models (GLMM) and generalised additive mixed models (GAMM) were used to model the realised niche of ombrotrophic Sphagnum species in British peatlands. These models were then used to predict changes in Sphagnum cover between 2020 and 2050 based on projections of climate change and atmospheric deposition of nitrogen and sulphur. Over 90% of the variation in the GLMM predictions was due to niche model parameter uncertainty, dropping to 14% for the GAMM. After having covaried out other factors, average variation in predicted values of Sphagnum cover across UK peatlands was the next largest source of variation (8% for the GLMM and 86% for the GAMM). The better performance of the GAMM needs to be weighed against its tendency to overfit the training data. While our niche models are only a first approximation, we used them to undertake a preliminary evaluation of the relative importance of climate change and nitrogen and sulphur deposition and the geographic locations of the largest expected changes in Sphagnum cover. Predicted changes in cover were all small (generally <1% in an average 4 m2 unit area) but also highly uncertain. Peatlands expected to be most affected by climate change in combination with atmospheric pollution were Dartmoor, Brecon Beacons and the western Lake District.

Drivers of change in mountain farming in Slovakia: from socialist collectivisation to the Common Agricultural Policy

The transformations in Slovak agriculture from the 1950s to the present day, considering both the generic (National and EU) and site-specific (local) drivers of landscape change, were analysed in five mountain study areas in the country. An interdisciplinary approach included analysis of population trends, evaluation of land use and landscape change combined with exploration of the perceptions of local stakeholders and results of previous biodiversity studies. The generic processes active from the 1950s to 1970s were critical for all study areas with impacts lasting right up until the present day. Agricultural collectivisation, agricultural intensification and land abandonment had negative effects in all study areas. However, the precise impacts on the landscape were different in the different study areas due to site-specific attributes (e.g. population trends, geographic localisation and local attitudes and opportunities), and these played a decisive role in determining the trajectory of change. Regional contrasts in rural development between these territories have increased in the last two decades, also due to the imperfect preconditions of governmental support. The recent Common Agricultural Policy developments are focused on maintenance of intensive large-scale farming rather than direct enhancement of agro-biodiversity and rural development at the local scale. In this context, local, site-specific attributes can and must form an essential part of rural development plans, to meet the demands for management of the diversity of agricultural mountain landscapes and facilitate the multifunctional role of agriculture.

Contrastive analysis of keywords in discourses: intégration and integration in French and German discourses about migration

This article suggests a theoretical and methodological framework for a systematic contrastive discourse analysis across languages and discourse communities through keywords, constituting a lexical approach to discourse analysis which is considered to be particularly fruitful for comparative analysis. We use a corpus assisted methodology, presuming meaning to be constituted, revealed and constrained by collocation environment. We compare the use of the keyword intégration and Integration in French and German public discourses about migration on the basis of newspaper corpora built from two French and German newspapers from 1998 to 2011. We look at the frequency of these keywords over the given time span, group collocates into thematic categories and discuss indicators of discursive salience by comparing the development of collocation profiles over time in both corpora as well as the occurrence of neologisms and compounds based on intégration/Integration.

Interacting effects of change in climate, human population, land use, and water use on biodiversity and ecosystem services

Human population growth and resource use, mediated by changes in climate, land use, and water use, increasingly impact biodiversity and ecosystem services provision. However, impacts of these drivers on biodiversity and ecosystem services are rarely analyzed simultaneously and remain largely unknown. An emerging question is how science can improve the understanding of change in biodiversity and ecosystem service delivery and of potential feedback mechanisms of adaptive governance. We analyzed past and future change in drivers in south-central Sweden. We used the analysis to identify main research challenges and outline important research tasks. Since the 19th century, our study area has experienced substantial and interlinked changes; a 1.6°C temperature increase, rapid population growth, urbanization, and massive changes in land use and water use. Considerable future changes are also projected until the mid-21st century. However, little is known about the impacts on biodiversity and ecosystem services so far, and this in turn hampers future projections of such effects. Therefore, we urge scientists to explore interdisciplinary approaches designed to investigate change in multiple drivers, underlying mechanisms, and interactions over time, including assessment and analysis of matching-scale data from several disciplines. Such a perspective is needed for science to contribute to adaptive governance by constantly improving the understanding of linked change complexities and their impacts.

A comparative evaluation of functions for the analysis of growth in male broilers

Data from six studies with male broilers fed diets covering a wide range of energy and protein were used in the current two analyses. In the first analysis, five models, specifically re-parameterized for analysing energy balance data, were evaluated for their ability to determine metabolizable energy intake at maintenance and efficiency of utilization of metabolizable energy intake for producing gain. In addition to the straight line, two types of functional form were used. They were forms describing (i) diminishing returns behaviour (monomolecular and rectangular hyperbola) and (ii) sigmoidal behaviour with a fixed point of inflection (Gompertz and logistic). These models determined metabolizable energy requirement for maintenance to be in the range 437-573 kJ/kg of body weight/day depending on the model. The values determined for average net energy requirement for body weight gain varied from 7(.)9 to 11(.)2 kJ/g of body weight. These values show good agreement with previous studies. In the second analysis, three types of function were assessed as candidates for describing the relationship between body weight and cumulative metabolizable energy intake. The functions used were: (a) monomolecular (diminishing returns behaviour), (b) Gompertz (smooth sigmoidal behaviour with a fixed point of inflection) and (c) Lopez, France and Richards (diminishing returns and sigmoidal behaviour with a variable point of inflection). The results of this analysis demonstrated that equations capable of mimicking the law of diminishing returns describe accurately the relationship between body weight and cumulative metabolizable energy intake in broilers.

Recent patterns of change in vegetation structure and tree composition of British broadleaved woodland: evidence from large-scale surveys

Evidence is presented of widespread changes in structure and species composition between the 1980s and 2003–2004 from surveys of 249 British broadleaved woodlands. Structural components examined include canopy cover, vertical vegetation profiles, field-layer cover and deadwood abundance. Woods were located in 13 geographical localities and the patterns of change were examined for each locality as well as across all woods. Changes were not uniform throughout the localities; overall, there were significant decreases in canopy cover and increases in sub-canopy (2–10 m) cover. Changes in 0.5–2 m vegetation cover showed strong geographic patterns, increasing in western localities, but declining or showing no change in eastern localities. There were significant increases in canopy ash Fraxinus excelsior and decreases in oak Quercus robur/petraea. Shrub layer ash and honeysuckle Lonicera periclymenum increased while birch Betula spp. hawthorn Crataegus monogyna and hazel Corylus avellana declined. Within the field layer, both bracken Pteridium aquilinum and herbs increased. Overall, deadwood generally increased. Changes were consistent with reductions in active woodland management and changes in grazing and browsing pressure. These findings have important implications for sustainable active management of British broadleaved woodlands to meet silvicultural and biodiversity objectives.

Identification of genetic and phenotypic differences associated with prevalent and non-prevalent Salmonella Enteritidis phage types: analysis of variation in amino acid transport

In this study, differences at the genetic level of 37 Salmonella Enteritidis strains from five phage types (PTs) were compared using comparative genomic hybridization (CGH) to assess differences between PTs. There were approximately 400 genes that differentiated prevalent (4, 6, 8 and 13a) and sporadic (11) PTs, of which 35 were unique to prevalent PTs, including six plasmid-borne genes, pefA, B, C, D, srgC and rck, and four chromosomal genes encoding putative amino acid transporters. Phenotype array studies also demonstrated that strains from prevalent PTs were less susceptible to urea stress and utilized L-histidine, L-glutamine, L-proline, L-aspartic acid, gly-asn and gly-gln more efficiently than PT11 strains. Complementation of a PT11 strain with the transporter genes from PT4 resulted in a significant increase in utilization of the amino acids and reduced susceptibility to urea stress. In epithelial cell association assays, PT11 strains were less invasive than other prevalent PTs. Most strains from prevalent PTs were better biofilm formers at 37 degrees C than at 28 degrees C, whilst the converse was true for PT11 strains. Collectively, the results indicate that genetic and corresponding phenotypic differences exist between strains of the prevalent PTs 4, 6, 8 and 13a and non-prevalent PT11 strains that are likely to provide a selective advantage for strains from the former PTs and could help them to enter the food chain and cause salmonellosis.

Global networks, cities and economic performance: Observations from an analysis of cities in Europe and the USA

The network paradigm has been highly influential in spatial analysis in the globalisation era. As economies across the world have become increasingly integrated, so-called global cities have come to play a growing role as central nodes in the networked global economy. The idea that a city’s position in global networks benefits its economic performance has resulted in a competitive policy focus on promoting the economic growth of cities by improving their network connectivity. However, in spite of the attention being given to boosting city connectivity little is known about whether this directly translates to improved city economic performance and, if so, how well connected a city needs to be in order to benefit from this. In this paper we test the relationship between network connectivity and economic performance between 2000 and 2008 for cities with over 500,000 inhabitants in Europe and the USA to inform European policy.

Is there a Rhythm Of The Rain? An analysis of weather in popular music

Weather is frequently used in music to frame events and emotions, yet quantitative analyses are rare. From a collated base set of 759 weather-related songs, 419 were analysed based on listings from a karaoke database. This article analyses the 20 weather types described, frequency of occurrence, genre, keys, mimicry, lyrics and songwriters. Vocals were the principal means of communicating weather: sunshine was the most common, followed by rain, with weather depictions linked to the emotions of the song. Bob Dylan, John Lennon and Paul McCartney wrote the most weather-related songs, partly following their experiences at the time of writing.

Sodium hydroxide enhances extractability and analysis of proanthocyanidins in ensiled sainfoin (onobrychis viciifolia)

Little information exists on the effects of ensiling on condensed tannins or proanthocyanidins. The acetone–butanol–HCl assay is suitable for measuring proanthocyanidin contents in a wide range of samples, silages included, but provides limited information on proanthocyanidin composition, which is of interest for deciphering the relationships between tannins and their bioactivities in terms of animal nutrition or health. Degradation with benzyl mercaptan (thiolysis) provides information on proanthocyanidin composition, but proanthocyanidins in several sainfoin silages have proved resistant to thiolysis. We now report that a pretreatment step with sodium hydroxide prior to thiolysis was needed to enable their analysis. This alkaline treatment increased their extractability from ensiled sainfoin and facilitated especially the release of larger proanthocyanidins. Ensiling reduced assayable proanthocyanidins by 29%, but the composition of the remaining proanthocyanidins in silage resembled that of the fresh plants.

Bayesian analysis of uncertainty in the GlobCover 2009 land cover product at climate model grid scale

Land cover data derived from satellites are commonly used to prescribe inputs to models of the land surface. Since such data inevitably contains errors, quantifying how uncertainties in the data affect a model’s output is important. To do so, a spatial distribution of possible land cover values is required to propagate through the model’s simulation. However, at large scales, such as those required for climate models, such spatial modelling can be difficult. Also, computer models often require land cover proportions at sites larger than the original map scale as inputs, and it is the uncertainty in these proportions that this article discusses. This paper describes a Monte Carlo sampling scheme that generates realisations of land cover proportions from the posterior distribution as implied by a Bayesian analysis that combines spatial information in the land cover map and its associated confusion matrix. The technique is computationally simple and has been applied previously to the Land Cover Map 2000 for the region of England and Wales. This article demonstrates the ability of the technique to scale up to large (global) satellite derived land cover maps and reports its application to the GlobCover 2009 data product. The results show that, in general, the GlobCover data possesses only small biases, with the largest belonging to non–vegetated surfaces. In vegetated surfaces, the most prominent area of uncertainty is Southern Africa, which represents a complex heterogeneous landscape. It is also clear from this study that greater resources need to be devoted to the construction of comprehensive confusion matrices.

Changes in fire regimes since the Last Glacial Maximum: an assessment based on a global synthesis and analysis of charcoal data

Fire activity has varied globally and continuously since the last glacial maximum (LGM) in response to long-term changes in global climate and shorter-term regional changes in climate, vegetation, and human land use. We have synthesized sedimentary charcoal records of biomass burning since the LGM and present global maps showing changes in fire activity for time slices during the past 21,000 years (as differences in charcoal accumulation values compared to pre-industrial). There is strong broad-scale coherence in fire activity after the LGM, but spatial heterogeneity in the signals increases thereafter. In North America, Europe and southern South America, charcoal records indicate less-than-present fire activity during the deglacial period, from 21,000 to ∼11,000 cal yr BP. In contrast, the tropical latitudes of South America and Africa show greater-than-present fire activity from ∼19,000 to ∼17,000 cal yr BP and most sites from Indochina and Australia show greater-than-present fire activity from 16,000 to ∼13,000 cal yr BP. Many sites indicate greater-than-present or near-present activity during the Holocene with the exception of eastern North America and eastern Asia from 8,000 to ∼3,000 cal yr BP, Indonesia and Australia from 11,000 to 4,000 cal yr BP, and southern South America from 6,000 to 3,000 cal yr BP where fire activity was less than present. Regional coherence in the patterns of change in fire activity was evident throughout the post-glacial period. These complex patterns can largely be explained in terms of large-scale climate controls modulated by local changes in vegetation and fuel load

Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription

BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a powerful tool for genome-wide transcription studies. Unlike microarrays, it has the ability to detect novel forms of RNA such as alternatively spliced and antisense transcripts, without the need for prior knowledge of their existence. One limitation of using SAGE on an organism with a complex genome and lacking detailed sequence information, such as the hexaploid bread wheat Triticum aestivum, is accurate annotation of the tags generated. Without accurate annotation it is impossible to fully understand the dynamic processes involved in such complex polyploid organisms. Hence we have developed and utilised novel procedures to characterise, in detail, SAGE tags generated from the whole grain transcriptome of hexaploid wheat. RESULTS: Examination of 71,930 Long SAGE tags generated from six libraries derived from two wheat genotypes grown under two different conditions suggested that SAGE is a reliable and reproducible technique for use in studying the hexaploid wheat transcriptome. However, our results also showed that in poorly annotated and/or poorly sequenced genomes, such as hexaploid wheat, considerably more information can be extracted from SAGE data by carrying out a systematic analysis of both perfect and "fuzzy" (partially matched) tags. This detailed analysis of the SAGE data shows first that while there is evidence of alternative polyadenylation this appears to occur exclusively within the 3' untranslated regions. Secondly, we found no strong evidence for widespread alternative splicing in the developing wheat grain transcriptome. However, analysis of our SAGE data shows that antisense transcripts are probably widespread within the transcriptome and appear to be derived from numerous locations within the genome. Examination of antisense transcripts showing sequence similarity to the Puroindoline a and Puroindoline b genes suggests that such antisense transcripts might have a role in the regulation of gene expression. CONCLUSION: Our results indicate that the detailed analysis of transcriptome data, such as SAGE tags, is essential to understand fully the factors that regulate gene expression and that such analysis of the wheat grain transcriptome reveals that antisense transcripts maybe widespread and hence probably play a significant role in the regulation of gene expression during grain development.

Duration from vine emergence to flowering suggests a long-day or rate of change of photoperiod response in white yam (Dioscorea rotundata Poir.)

The objective of this study was to quantify the effect of photoperiod on the duration from vine (shoot) emergence to flowering in white or Guinea yam (Dioscorea rotundata). The duration from vine emergence to flowering in two clonal varieties of yam (TDr 131 and TDr 99-9) was recorded at 10 different sowing dates/locations in Nigeria. Durations to flowering varied from 40 to > 88 days. Mean daily temperature and photoperiod between vine emergence and flowering varied from 25 to 27 degrees C and 13.1 to 13.4 h day(-1), respectively. Both clones had similar responses to temperature, with base and optimum temperatures of 12 and 25-27 degrees C, respectively. Thermal durations to flowering were strongly related (r(2) > 0.75-0.83) to absolute photoperiod (h) at vine emergence as well as to rate of change of photoperiod (s day(-1)) at vine emergence. The response to absolute photoperiod suggests that white yams are quantitative LDPs, flowering sooner in long than short days. Yams also flowered earlier when the rate of change of photoperiod was positive but small, or was negative. It is suggested that yams may use a combination of photoperiod and rate of change in order to fine tune flowering time. (c) 2006 Elsevier B.V. All rights reserved.

Duration from vine emergence to flowering suggests a long-day or rate of change of photoperiod response in white yam (Dioscorea rotundata Poir.)

The objective of this study was to quantify the effect of photoperiod on the duration from vine (shoot) emergence to flowering in white or Guinea yam (Dioscorea rotundata). The duration from vine emergence to flowering in two clonal varieties of yam (TDr 131 and TDr 99-9) was recorded at 10 different sowing dates/locations in Nigeria. Durations to flowering varied from 40 to > 88 days. Mean daily temperature and photoperiod between vine emergence and flowering varied from 25 to 27 degrees C and 13.1 to 13.4 h day(-1), respectively. Both clones had similar responses to temperature, with base and optimum temperatures of 12 and 25-27 degrees C, respectively. Thermal durations to flowering were strongly related (r(2) > 0.75-0.83) to absolute photoperiod (h) at vine emergence as well as to rate of change of photoperiod (s day(-1)) at vine emergence. The response to absolute photoperiod suggests that white yams are quantitative LDPs, flowering sooner in long than short days. Yams also flowered earlier when the rate of change of photoperiod was positive but small, or was negative. It is suggested that yams may use a combination of photoperiod and rate of change in order to fine tune flowering time. (c) 2006 Elsevier B.V. All rights reserved.