bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny of the Liliales (Monocotyledons) with special emphasis on data partition congruence and RNA editing
Authors: Petersen Gitte , Seberg Ole , Davis Jerrold I. 
Published: October 2012

AbstractA phylogenetic analysis of the monocot order Liliales was performed using sequence data from three mitochondrial (atp1, cob, nad5) and two plastid genes (rbcL, ndhF). The complete data matrix includes 46 terminals representing all 10 families currently included in Liliales. The two major partitions, mitochondrial and plastid data, were congruent, and parsimony analysis resulted in 50 equally parsimonious trees and a well resolved consensus tree confirming monophyly of all families. Mitochondrial genes are known to include RNA edited sites, and in some cases unprocessed genes are replaced by retro‐processed gene copies, that is processed paralogs. To test the effects on phylogeny reconstruction of predicted edited sites and potentially unintentionally sampled processed paralogs, a number of analyses were performed using subsets of the complete data matrix. In general, predicted edited sites were more homoplasious than the other characters and increased incongruence among most data partitions. The predicted edited sites have a non‐random phylogenetic signal in conflict with the signal of the non‐edited sites. The potentially misleading signal was caused partially by the apparent presence of processed paralogs in Galanthus (Amaryllidaceae), part of the outgroup, but also by a deviating evolutionary pattern of predicted edited sites in Liliaceae compared with the remainder of the Liliales. Despite the problems that processed paralogs may cause, we argue that they should not a priori be excluded from phylogenetic analysis.
Shifting thresholds and changing degradation patterns: climate change effects on the simulated long‐term response of a semi‐arid savanna to grazing
Authors: Lohmann Dirk , Tietjen Britta , Blaum Niels , Joubert David F. , Jeltsch Florian 
Published: October 2012

Summary1. The complex, nonlinear response of dryland systems to grazing and climatic variations is a challenge to management of these lands. Predicted climatic changes will impact the desertification of drylands under domestic livestock production. Consequently, there is an urgent need to understand the response of drylands to grazing under climate change.2. We enhanced and parameterized an ecohydrological savanna model to assess the impacts of a range of climate change scenarios on the response of a semi‐arid African savanna to grazing. We focused on the effects of temperature and CO2 level increase in combination with changes in inter‐ and intra‐annual precipitation patterns on the long‐term dynamics of three major plant functional types.3. We found that the capacity of the savanna to sustain livestock grazing was strongly influenced by climate change. Increased mean annual precipitation and changes in intra‐annual precipitation pattern have the potential to slightly increase carrying capacities of the system. In contrast, decreased precipitation, higher interannual variation and temperature increase are leading to a severe decline of carrying capacities owing to losses of the perennial grass biomass.4. Semi‐arid rangelands will be at lower risk of shrub encroachment and encroachment will be less intense under future climatic conditions. This finding holds in spite of elevated levels of atmospheric CO2 and irrespective of changes in precipitation pattern, because of the drought sensitivity of germination and establishment of encroaching species.5. Synthesis and applications. Changes in livestock carrying capacities, both positive and negative, mainly depend on the highly uncertain future rainfall conditions. However, independent of the specific changes, shrub encroachment becomes less likely and in many cases less severe. Thus, managers of semi‐arid rangelands should shift their focus from woody vegetation towards perennial grass species as indicators for rangeland degradation. Furthermore, the resulting reduced competition from woody vegetation has the potential to facilitate ecosystem restoration measures such as re‐introduction of desirable plant species that are only little promising or infeasible under current climatic conditions. On a global scale, the reductions in standing biomass resulting from altered degradation dynamics of semi‐arid rangelands can have negative impacts on carbon sequestration.
Implementation uncertainty when using recreational hunting to manage carnivores
Authors: Bischof Richard , Nilsen Erlend B. , Brøseth Henrik , Männil Peep , Ozoliņš Jaānis , Linnell John D. C. 
Published: October 2012

Summary1. Wildlife managers often rely on resource users, such as recreational or commercial hunters, to achieve management goals. The use of hunters to control wildlife populations is especially common for predators and ungulates, but managers cannot assume that hunters will always fill annual quotas set by the authorities. It has been advocated that resource management models should account for uncertainty in how harvest rules are realized, requiring that this implementation uncertainty be estimated.2. We used a survival analysis framework and long‐term harvest data from large carnivore management systems in three countries (Estonia, Latvia and Norway) involving four species (brown bear, grey wolf, Eurasian lynx and wolverine) to estimate the performance of hunters with respect to harvest goals set by managers.3. Variation in hunter quota‐filling performance was substantial, ranging from 40% for wolverine in Norway to nearly 100% for lynx in Latvia. Seasonal and regional variation was also high within country–species pairs. We detected a positive relationship between the instantaneous potential to fill a quota slot and the relative availability of the target species for both wolverine and lynx in Norway.4. Survivor curves and hazards – with survival time measured as the time from the start of a season until a quota slot is filled – can indicate the extent to which managers can influence harvest through adjustments of season duration and quota limits.5. Synthesis and applications. We investigated seven systems where authorities use recreational hunting to manage large carnivore populations. The variation and magnitude of deviation from harvest goals was substantial, underlining the need to incorporate implementation uncertainty into resource management models and decisions‐making. We illustrate how survival analysis can be used by managers to estimate the performance of resource users with respect to achieving harvest goals set by managers. The findings in this study come at an opportune time given the growing popularity of management strategy evaluation (MSE) models in fisheries and a push towards incorporating MSE into terrestrial harvest management.
Topography drives migratory flight altitude of golden eagles: implications for on‐shore wind energy development
Authors: Katzner Todd E. , Brandes David , Miller Tricia , Lanzone Michael , Maisonneuve Charles , Tremblay Junior A. , Mulvihill Robert , Merovich George T. 
Published: October 2012

Summary
Wind power is a fast‐growing industry with broad potential to impact volant wildlife. Flight altitude is a key determinant of the risk to wildlife from modern horizontal‐axis wind turbines, which typically have a rotor‐swept zone of 50–150 m above the ground.
We used altitudinal GPS data collected from golden eagles Aquila chrysaetos tracked using satellite telemetry to evaluate the potential impacts of wind turbines on eagles and other raptors along migratory routes. Eagle movements during migration were classified as local (1–5 km h−1) or migratory (>10 km h−1) and were characterized based on the type of terrain over which each bird was flying, and the bird's distance from wind resources preferred for energy development.
Birds engaged in local movements turned more frequently and flew at lower altitude than during active migration. This flight behaviour potentially exposes them to greater risk of collision with turbines than when engaged in longer‐distance movements.
Eagles flew at relatively lower altitude over steep slopes and cliffs (sites where orographic lift can develop) than over flats and gentle slopes (sites where thermal lift is more likely).
Eagles predominantly flew near to wind resources preferred by energy developers, and locally moving eagles flew closer to those wind resources with greater frequency than eagles in active migration.
Synthesis and applications. Our research outlines the general effects of topography on raptor flight altitude and demonstrates how topography can interact with raptor migration behaviour to drive a potential human–wildlife conflict resulting from wind energy development. Management of risk to migratory species from industrial‐scale wind turbines should consider the behavioural differences between both locally moving and actively migrating individuals. Additionally, risk assessment for wind energy–wildlife interactions should incorporate the consequences of topography on the flight altitude of potentially impacted wildlife.
Cultivar genotype, application and endophyte history affects community impact of Schedonorus arundinaceus
Authors: Yurkonis Kathryn A. , Maherali Hafiz , Bolton Kim A. , Klironomos John N. , Newman Jonathan A. 
Published: October 2012

Summary

Cultivars of several cool‐season grasses used in forage and turf applications are developed to contain low (E−) or high (E+) seed fungal endophyte presence, and these characteristics may influence their competitive ability and effects on communities.
We established a long‐term field experiment to test the predictions that Schedonorus arundinaceus (SA) tall fescue forage cultivars differ in their effects on communities from turf cultivars and that E+ cultivars differ in their effects on communities from E− cultivars. Two of the three E+ turf cultivars were low endophyte, and turf cultivars were therefore defined as ‘E+ history’ and ‘E− history’.
Forage (E−) plots contained more SA than turf (E− history) plots and differed in community structure and function from turf (E− history) plots. Cultivar identity also influenced community structure and function in pairwise comparisons between forage (E−) and turf (E− history) plots.
Within the forage cultivars, E+ plots contained more SA and were marginally less dominated by other grasses than E− plots, but these differences were not consistent in comparisons between specific E+ and E− forage cultivars. Moreover, E+ and E− forage plots were similar in other aspects of community structure and function, indicating that a cultivar's endophyte status does not consistently determine its effects.
Despite low endophyte presence in two of three cultivars, E+ history turf plots differed in measures of composition, structure and nutrient cycling from E− history turf plots, indicating that there are genetic differences between E+ and E− cultivars which can influence their effects on communities.
Synthesis and applications. Schedonorus arundinaceus cultivars vary in their competitive ability and effects on communities, and this variation may be explained by the application for which the cultivars were developed, their endophyte status and genetic differences among cultivars within application categories. We recommend preferentially selecting cultivars developed for turf applications and cultivars with low seed endophyte presence to minimize negative effects of seeding a non‐native grass on communities. However, final selections should be based on common trial performances because genetic differences between cultivars will affect their performance independently of their application category and endophyte status.
Taxonomical and functional diversity turnover in Mediterranean grasslands: interactions between grazing, habitat type and rainfall
Authors: Carmona Carlos P. , Azcárate Francisco M. , de Bello Francesco , Ollero Helios S. , Lepš Jan , Peco Begoña 
Published: October 2012

Summary
Changes in livestock grazing regimes are among the most important drivers of species loss and decrease in functional diversity world‐wide. However, taxonomic and functional diversities (TD and FD) can respond differently to changes in grazing regime or productivity.
We surveyed plant communities from 67 sites under different grazing regimes (from heavy grazing to grazing abandonment) in wet and dry habitats, in both wet and dry years. We tested the influence of grazing intensity, habitat type and rainfall on TD, FD and the relationship between them. We also partitioned diversity to examine the effects of grazing on TD and FD across scales (within communities, within grazing levels and between grazing levels).
The effect of grazing within and across communities was modulated by water availability, with grazing showing the strongest effects in dry habitats. The relationship between FD and TD varied between habitat types and years and revealed high functional similarity between species (i.e. redundancy) in dry habitats. TD was reduced in the driest conditions across all the observation levels, contrasting with the high temporal stability of FD, suggesting that FD was decoupled from TD, especially in dry habitats. However, despite the high temporal and spatial stability of FD, results show that under severely limited water availability, high grazing pressure can reduce FD, revealing a convergence in traits under the combined effect of grazing and drought conditions.
Synthesis and applications. Results highlight the dependence of functional diversity on the combined effect of water availability and grazing regime. Under severely limited water availability, grazing intensification reduced the functional diversity of these grasslands. Because of the foreseeable reduction in water availability in Mediterranean environments, we recommend the adoption of flexible grazing management schemes that take species and functional diversities into account simultaneously and adapt the level of grazing pressure to water availability.
Large carabid beetle declines in a United Kingdom monitoring network increases evidence for a widespread loss in insect biodiversity
Authors: Brooks David R. , Bater John E. , Clark Suzanne J. , Monteith Don T. , Andrews Christopher , Corbett Stuart J. , Beaumont Deborah A. , Chapman Jason W. 
Published: October 2012

SummaryCarabid beetles are important functional components of many terrestrial ecosystems. Here, we describe the first long‐term, wide‐scale and quantitative assessment of temporal changes inUKcarabid communities, to inform nationwide management aimed at their conservation.Multivariate and mixed models were used to assess temporal trends over a 15‐year period, across eleven sites in theUKEnvironmental Change Network. Sites covered pasture, field margins, chalk downland, woodland and hedgerows in the lowlands, moorland and pasture in the uplands, and grassland, heaths and bogs in montane locations.We found substantial overall declines in carabid biodiversity. Three‐quarters of the species studied declined, half of which were estimated to be undergoing population reductions of > 30%, when averaged over 10‐year periods. Declines of this magnitude are recognized to be of conservation concern. They are comparable to those reported for butterflies and moths and increase the evidence base showing that insects are undergoing serious and widespread biodiversity losses.Overall trends masked differences between regions and habitats. Carabid population declines (10‐year trend, averaged across species) were estimated to be 52% in montane sites, 31% in northern moorland sites and 28% in western pasture sites (with at least 80% of species declining in each case). Conversely, populations in our southern downland site had 10‐year increases of 48% on average. Overall, biodiversity was maintained in upland pasture, and populations were mostly stable in woodland and hedgerow sites.Synthesis and applications. Our results highlight the need to assess trends for carabids, and probably other widespread and ubiquitous taxa, across regions and habitats to fully understand losses in biodiversity. Land management should be underpinned by a consideration of how wide‐scale environmental drivers interact with habitat structure. The stability of population trends in woodlands and hedgerows of species that are declining elsewhere puts these habitats at the fore‐front of integrated landscape management aimed at preserving their ecosystem services.
Riparian field margins: can they enhance the functional structure of ground beetle (Coleoptera: Carabidae) assemblages in intensively managed grassland landscapes?
Authors: Cole Lorna J. , Brocklehurst Sarah , Elston David A. , McCracken David I. 
Published: October 2012

Summary

In Europe and North America, there is growing concern that biodiversity declines associated with agricultural intensification will adversely impact the functioning and sustainability of agricultural ecosystems. Enhancing habitat heterogeneity in agricultural landscapes promotes biodiversity and, whilst erecting fences adjacent to watercourses is widely advocated as a means of mitigating diffuse pollution, associated biodiversity benefits have been largely overlooked.
A range of riparian margins and their adjacent grassland fields were investigated to determine the effects of riparian management on the diversity and functional structure of carabid assemblages. Carabid assemblages of fields and open margins (i.e. unfenced watercourses) were more diverse and species rich than those of fenced margins.
The functional structure of carabid assemblages in fenced margins differed from grassland fields and open margins. This disparity was greater in wide margins (i.e. fences erected over 5·4 m from watercourses) than narrow margins (i.e. fences erected within 2·6 m of watercourses). Wide margins had the highest relative proportions of carabids which had pushing body forms, were flightless, very small in size and Collembola specialists. During early summer, wide margins also had the highest proportion of carabids that overwinter as adults.
The taxonomic and functional structure of carabid assemblages was more sensitive for detecting impacts of agricultural management than measurements of diversity. It is likely that this also applies to other taxa, thus emphasising the need to consider a wide range of assemblage attributes when investigating agricultural impacts on biodiversity.
Synthesis and applications. Fenced riparian margins, particularly those over 5·4 m wide, harbour carabids with poor dispersal ability which are vulnerable to habitat fragmentation. While lack of management benefits sedentary species, a wider range of taxa (e.g. pollinators, foraging birds and flowering plants) are enhanced by management to obtain a more open vegetation structure (e.g. restricted grazing or mowing). It is important that management practices are implemented at a sufficiently fine spatial scale to allow recolonisation of species with restricted dispersal from adjacent undisturbed habitats. Wide riparian margins have the potential to enhance taxonomic and functional diversity at the landscape scale. Management actions must, however, be carefully balanced to ensure that they promote a wide range of taxa without unduly interfering with the margin's ability to mitigate diffuse pollution.
Radial probe endobronchial ultrasound: Factors influencing visualization yield of peripheral pulmonary lesions
Authors: TAY JUN H. , IRVING LOUIS , ANTIPPA PHILLIP , STEINFORT DANIEL P. 
Published: October 2012

ABSTRACTBackground and objective:  Endobronchial ultrasound (EBUS) has improved the diagnostic yield of transbronchial biopsy of peripheral pulmonary lesions (PPL). While EBUS diagnostic yield has been the focus of the majority of publications, few have investigated factors associated with EBUS visualization yield. This study evaluated the factors predicting visibility of PPL using EBUS‐guided bronchoscopy.Methods:  We performed a retrospective analysis of 196 consecutive patients who underwent investigation with radial EBUS. Size and distance of the lesion from the hilum and pleura measured on computed tomography scans were correlated with malignancy status, gender and EBUS visualization yields. Final diagnosis was obtained from pathology.Results:  A definitive diagnosis was established for 109 PPL (56%) using radial EBUS. Visualized lesion by EBUS probe had a higher diagnostic yield (65%) than EBUS‐invisible lesions (20%; P = 0.0001). In multivariate analysis, lesion size, final diagnosis and distance from hilum to lesion were all found to significantly affect EBUS visualization yield. Lesions of ≥20 mm had a significantly greater visualization yield (85%) than lesions of <20 mm (63%; P = 0.0022). Malignant lesions had a higher visualization rate (85%) than benign lesions (66%; P value = 0.0025). Distance of hilum ≤50 mm to PPL was found to have a significantly higher visualization yield (91%) than lesions located >50 mm from the hilum. (66%; P = 0.0001).Conclusions:  Lesion size, malignancy status and distance from hilum to lesion are significant predictors of EBUS visualization yield. Clinicians should review these factors in patients to guide choice of optimal investigation and diagnosis of PPL.
Bread consumption in the UK: what are the main attitudinal factors affecting current intake and its place in a healthy diet?
Authors: O'Connor Á. 
Published: October 2012

SummaryDespite efforts to promote the consumption of starchy foods, UK consumers are not meeting the recommended proportion of energy from starch for the population. Awareness of the nutritional benefits of starchy foods is poor and consumers tend to have highly divergent attitudes to, and beliefs about, these foods – although starchy foods are generally viewed as good for health, they are also often described as ‘fattening’ and avoided by those trying to lose weight. Concern about wheat allergy and other gastrointestinal problems commonly associated with bread in particular are also barriers to it being perceived as a ‘healthy food’. There is therefore clearly a mismatch between consumers' perceptions of starchy foods and current nutritional guidelines. This paper considers the evidence for and against the most common consumer perceptions around the health effects of bread and the possible impact of reduced levels of consumption on the nutrient intake of individuals.
Economic value of analyst recommendations in Australia: an application of the Black–Litterman asset allocation model
Authors: He Peng W. , Grant Andrew , Fabre Joel 
Published: October 2012

AbstractThis study empirically examines the investment value of security analyst recommendations on constituent stocks of the S&P/ASX 50 index. We find that stocks with favourable (unfavourable) recommendations on average outperformed (underperformed) the benchmark index. An investment strategy using the Black–Litterman asset allocation model that incorporates consensus analyst recommendations, in conjunction with daily rebalancing, outperforms the market in terms of return and risk‐adjusted performance measures. The investment strategy involves high levels of trading, and no significant abnormal returns are achieved after transaction costs. Less frequent rebalancing, under most situations, causes a decrease in both performance and turnover. Filtering of dated recommendations causes an increase in turnover, while having mixed effects on investment returns.