Phylogeny and metabolic scaling in mammals

The scaling of metabolic rates to body size is widely considered to be of great biological and ecological importance, and much attention has been devoted to determining its theoretical and empirical value. Most debate centers on whether the underlying power law describing metabolic rates is 2/3 (as predicted by scaling of surface area/volume relationships) or 3/4 ("Kleiber's law"). Although recent evidence suggests that empirically derived exponents vary among clades with radically different metabolic strategies, such as ectotherms and endotherms, models, such as the metabolic theory of ecology, depend on the assumption that there is at least a predominant, if not universal, metabolic scaling exponent. Most analyses claimed to support the predictions of general models, however, failed to control for phylogeny. We used phylogenetic generalized least-squares models to estimate allometric slopes for both basal metabolic rate (BMR) and field metabolic rate (FMR) in mammals. Metabolic rate scaling conformed to no single theoretical prediction, but varied significantly among phylogenetic lineages. In some lineages we found a 3/4 exponent, in others a 2/3 exponent, and in yet others exponents differed significantly from both theoretical values. Analysis of the phylogenetic signal in the data indicated that the assumptions of neither species-level analysis nor independent contrasts were met. Analyses that assumed no phylogenetic signal in the data (species-level analysis) or a strong phylogenetic signal (independent contrasts), therefore, returned estimates of allometric slopes that were erroneous in 30% and 50% of cases, respectively. Hence, quantitative estimation of the phylogenetic signal is essential for determining scaling exponents. The lack of evidence for a predominant scaling exponent in these analyses suggests that general models of metabolic scaling, and macro-ecological theories that depend on them, have little explanatory power.

Resistance to the first and second generation anticoagulant rodenticides: a new perspective

Warfarin resistance was first discovered among Norway rat (Rattus norvegicus) populations in Scotland in 1958 and further reports of resistance, both in this species and in others, soon followed from other parts of Europe and the United States. Researchers quickly defined the practical impact of these resistance phenomena and developed robust methods by which to monitor their spread. These tasks were relatively simple because of the high degree of immunity to warfarin conferred by the resistance genes. Later, the second generation anticoagulants were introduced to control rodents resistant to the warfarin-like compounds, but resistance to difenacoum, bromadiolone and brodifacoum is now reported in certain localities in Europe and elsewhere. However, the adoption of test methods designed initially for use with the first generation compounds to identify resistance to compounds of the second generation has led to some practical difficulties in conducting tests and in establishing meaningful resistance baselines. In particular, the results of certain test methodologies are difficult to interpret in terms of the likely impact on practical control treatments of the resistance phenomena they seek to identify. This paper defines rodenticide resistance in the context of both first and second generation anticoagulants. It examines the advantages and disadvantages of existing laboratory and field methods used in the detection of rodent populations resistant to anticoagulants and proposes some improvements in the application of these techniques and in the interpretation of their results.

Comparison of MODIS broadband albedo over an agricultural site with ground measurements and values derived from Earth observation data at a range of spatial scales

Land surface albedo is dependent on atmospheric state and hence is difficult to validate. Over the UK persistent cloud cover and land cover heterogeneity at moderate (km-scale) spatial resolution can also complicate comparison of field-measured albedo with that derived from instruments such as the Moderate Resolution Imaging Spectrometer (MODIS). A practical method of comparing moderate resolution satellite-derived albedo with ground-based measurements over an agricultural site in the UK is presented. Point measurements of albedo made on the ground are scaled up to the MODIS resolution (1 km) through reflectance data obtained at a range of spatial scales. The point measurements of albedo agreed in magnitude with MODIS values over the test site to within a few per cent, despite problems such as persistent cloud cover and the difficulties of comparing measurements made during different years. Albedo values derived from airborne and field-measured data were generally lower than the corresponding satellite-derived values. This is thought to be due to assumptions made regarding the ratio of direct to diffuse illumination used when calculating albedo from reflectance. Measurements of albedo calculated for specific times fitted closely to the trajectories of temporal albedo derived from both Systeme pour l'Observation de la Terre (SPOT) Vegetation (VGT) and MODIS instruments.

Advances in sequential data assimilation and numerical weather forecasting: an Ensemble Transform Kalman-Bucy Filter, a study on clustering in deterministic Ensemble Square Root Filters, and a test of a new time stepping scheme in an atmospheric model

This dissertation deals with aspects of sequential data assimilation (in particular ensemble Kalman filtering) and numerical weather forecasting. In the first part, the recently formulated Ensemble Kalman-Bucy (EnKBF) filter is revisited. It is shown that the previously used numerical integration scheme fails when the magnitude of the background error covariance grows beyond that of the observational error covariance in the forecast window. Therefore, we present a suitable integration scheme that handles the stiffening of the differential equations involved and doesn’t represent further computational expense. Moreover, a transform-based alternative to the EnKBF is developed: under this scheme, the operations are performed in the ensemble space instead of in the state space. Advantages of this formulation are explained. For the first time, the EnKBF is implemented in an atmospheric model. The second part of this work deals with ensemble clustering, a phenomenon that arises when performing data assimilation using of deterministic ensemble square root filters in highly nonlinear forecast models. Namely, an M-member ensemble detaches into an outlier and a cluster of M-1 members. Previous works may suggest that this issue represents a failure of EnSRFs; this work dispels that notion. It is shown that ensemble clustering can be reverted also due to nonlinear processes, in particular the alternation between nonlinear expansion and compression of the ensemble for different regions of the attractor. Some EnSRFs that use random rotations have been developed to overcome this issue; these formulations are analyzed and their advantages and disadvantages with respect to common EnSRFs are discussed. The third and last part contains the implementation of the Robert-Asselin-Williams (RAW) filter in an atmospheric model. The RAW filter is an improvement to the widely popular Robert-Asselin filter that successfully suppresses spurious computational waves while avoiding any distortion in the mean value of the function. Using statistical significance tests both at the local and field level, it is shown that the climatology of the SPEEDY model is not modified by the changed time stepping scheme; hence, no retuning of the parameterizations is required. It is found the accuracy of the medium-term forecasts is increased by using the RAW filter.

The Natural History of Slapton Ley Nature Reserve XVIII: nitrogen and phosphorus losses from the catchment - an export coefficient modelling approach

Nitrogen and phosphorus losses from the catchment of Slapton Ley, a small coastal lake in SW England, were calculated using an adaptation of a model developed by Jorgensen (1980). A detailed survey of the catchment revealed that its land use is dominated by both permanent and temporary grassland (respectively 38 and 32% of its total area), and that the remainder is made up of the cultivation of cereals and field vegetables, and market gardening. Livestock numbers in the catchment constitute ca. 6600 head of cattle, 10,000 sheep, 590 pigs, 1700 poultry and 58 horses. The permanent human population of the area is ca. 2000, served by two small gravity-fed sewage treatment works (STWs). Inputs to, and losses from, farmland in the catchment were computed using Jorgensen’s model, and coefficients derived from the data of Cooke (1976), Gostick (1982), Rast and Lee (1983) and Vollenweider (1968). Allowing for outputs from STWs, the total annual external load of N and P upon Slapton Ley is 160 t (35 kg ha-1) a-1 N, and 4.8 t (1.05 kg ha-1) a-1 P. Accordingly to Vollenweider (1968, 1975), such loadings exceed OECD permissible level by a factor of ca. 50 in the case of N, and ca. 5 in that of P. In order to reduce nutrient loads, attention would need to be paid to both STW and agricultural sources.

Heterozygosity and diversity analysis using mapped single nucelotide polymorphisms in a faba bean inbreeding programme

The aim of this study was to convert existing faba bean (Vicia faba L.) single nucleotide polymorphism (SNP) markers from cleaved amplification polymorphic sequences and SNaPshot® formats, which are expensive and time-consuming, to the more convenient KBiosciences competitive allele‐specific PCR (KASP) assay format. Out of 80 assays designed, 75 were validated, though a core set of 67 of the most robust markers is recommended for further use. The 67 best KASP SNP assays were used across two generations of single seed descent to detect unintended outcrossing and to track and quantify loss of heterozygosity, a capability that will significantly increase the efficiency and performance of pure line production and maintenance. This same set of assays was also used to examine genetic relationships between the 67 members of the partly inbred panel, and should prove useful for line identification and diversity studies in the future.

A comparison of automated keyphrase extraction techniques and of automatic evaluation vs. human evaluation

Keyphrases are added to documents to help identify the areas of interest they contain. However, in a significant proportion of papers author selected keyphrases are not appropriate for the document they accompany: for instance, they can be classificatory rather than explanatory, or they are not updated when the focus of the paper changes. As such, automated methods for improving the use of keyphrases are needed, and various methods have been published. However, each method was evaluated using a different corpus, typically one relevant to the field of study of the method’s authors. This not only makes it difficult to incorporate the useful elements of algorithms in future work, but also makes comparing the results of each method inefficient and ineffective. This paper describes the work undertaken to compare five methods across a common baseline of corpora. The methods chosen were Term Frequency, Inverse Document Frequency, the C-Value, the NC-Value, and a Synonym based approach. These methods were analysed to evaluate performance and quality of results, and to provide a future benchmark. It is shown that Term Frequency and Inverse Document Frequency were the best algorithms, with the Synonym approach following them. Following these findings, a study was undertaken into the value of using human evaluators to judge the outputs. The Synonym method was compared to the original author keyphrases of the Reuters’ News Corpus. The findings show that authors of Reuters’ news articles provide good keyphrases but that more often than not they do not provide any keyphrases.

Winter and Summer Northern Hemisphere blocking in CMIP5 models

The frequencies of atmospheric blocking in both winter and summer and the changes in them from the 20th to the 21st centuries as simulated in twelve CMIP5 models is analysed. The RCP 8.5 high emission scenario runs are used to represent the 21st century. The analysis is based on the wave-breaking methodology of Pelly and Hoskins (2003a). It differs from the Tibaldi and Molteni (1990) index in viewing equatorward cut-off lows and poleward blocking highs in equal manner as indicating a disruption to the westerlies. 1-dimensional and 2-dimensional diagnostics are applied to identify blocking of the mid-latitude storm-track and also at higher latitudes. Winter blocking frequency is found to be generally underestimated. The models give a decrease in the European blocking maximum in the 21st century, consistent with the results in other studies. There is a mean 21st century winter poleward shift of high- latitude blocking, but little agreement between the models on the details. In summer, Eurasian blocking is also underestimated in the models, whereas it is now too large over the high-latitude ocean basins. A decrease in European blocking frequency in the 21st century model runs is again found. However in summer there is a clear eastward shift of blocking over Eastern Europe and Western Russia, in a region close to the blocking that dominated the Russian summer of 2010. While summer blocking decreases in general, the poleward shift of the storm track into the region of frequent high latitude blocking may mean that the incidence of storms being obstructed by blocks may actually increase.

Using Delboeuf's illusion to improve point and click performance for older adults

Older computer users often exhibit poorer performance in point and click tasks on a computer than younger adults. This paper reports on the first phase of research that examines whether a visual illusion that makes an object appear to be larger (Delboeuf‟s Illusion), can help to improve point and click performance for older computer users. In this first phase, we look at the effect sizes for different configurations of the Delboeuf illusion. The study finds that the target size is overestimated by 8% for both older and younger adults in one configuration, and 12% for older adults in another configuration. The results will inform the design of a second phase, in which the configurations which demonstrate the largest effects will be investigated using a Fitts‟-style study of pointing performance.

Shoot calcium and magnesium concentrations differ between subtaxa, are highly heritable, and associate with potentially pleiotropic loci in Brassica oleracea

Calcium (Ca) and magnesium (Mg) are the most abundant group II elements in both plants and animals. Genetic variation in shoot Ca and shoot Mg concentration (shoot Ca and Mg) in plants can be exploited to biofortify food crops and thereby increase dietary Ca and Mg intake for humans and livestock. We present a comprehensive analysis of within-species genetic variation for shoot Ca and Mg, demonstrating that shoot mineral concentration differs significantly between subtaxa (varietas). We established a structured diversity foundation set of 376 accessions to capture a high proportion of species-wide allelic diversity within domesticated Brassica oleracea, including representation of wild relatives (C genome, 1n = 9) from natural populations. These accessions and 74 modern F-1 hybrid cultivars were grown in glasshouse and field environments. Shoot Ca and Mg varied 2- and 2.3-fold, respectively, and was typically not inversely correlated with shoot biomass, within most subtaxa. The closely related capitata (cabbage) and sabauda (Savoy cabbage) subtaxa consistently had the highest mean shoot Ca and Mg. Shoot Ca and Mg in glasshouse-grown plants was highly correlated with data from the field. To understand and dissect the genetic basis of variation in shoot Ca and Mg, we studied homozygous lines from a segregating B. oleracea mapping population. Shoot Ca and Mg was highly heritable (up to 40). Quantitative trait loci (QTL) for shoot Ca and Mg were detected on chromosomes C2, C6, C7, C8, and, in particular, C9, where QTL accounted for 14 to 55 of the total genetic variance. The presence of QTL on C9 was substantiated by scoring recurrent backcross substitution lines, derived from the same parents. This also greatly increased the map resolution, with strong evidence that a 4-cM region on C9 influences shoot Ca. This region corresponds to a 0.41-Mb region on Arabidopsis (Arabidopsis thaliana) chromosome 5 that includes 106 genes. There is also evidence that pleiotropic loci on C8 and C9 affect shoot Ca and Mg. Map-based cloning of these loci will reveal how shoot-level phenotypes relate to Ca 21 and Mg 21 uptake and homeostasis at the molecular level.

Shoot zinc (Zn) concentration varies widely within Brassica oleracea L. and is affected by soil Zn and phosphorus (P) levels

The low availability of zinc (Zn) in soils and crops affects dietary Zn intake worldwide. This study sought to determine if the natural genetic variation in shoot Zn concentrations (Zn(shoot)) is sufficient to pursue a crop improvement breeding strategy in a leafy vegetable crop. The gene-pool of Brassica oleracea L. was sampled using a large (n = 376) diversity foundation set (DFS), representing almost all species-wide common allelic variation, and 74 commercial varieties (mostly F(1)). The DFS genotypes were grown at low and high soil phosphorus (P) levels under glasshouse and field conditions, and also in a Zn-deficient soil, with or without Zn-fertilisation, in a glasshouse. Despite the large variation in Zn(shoot) among genotypes, environment had a profound effect on Zn(shoot) The heritability of Zn(shoot) was significant, but relatively low, among 90 doubled-haploid (DH) lines from a mapping population. While several quantitative trait loci (QTL) associated with Zn(shoot) occurred on chromosomes C2, C3, C5, C7, and C9, these were generally weak and conditional upon growth conditions. Breeding for Zn(shoot) in B. oleracea is therefore likely to be challenging. Shoot P concentrations increased substantially in all genotypes under low soil Zn conditions. Conversely, only some genotypes had increased Zn(shoot) at low soil P levels. Sufficient natural genetic variation may therefore exist to study some of the interactions between Zn and P nutrition.

Simple uncertainty frameworks for selecting weighting schemes and interpreting multimodel ensemble climate change experiments

Future climate change projections are often derived from ensembles of simulations from multiple global circulation models using heuristic weighting schemes. This study provides a more rigorous justification for this by introducing a nested family of three simple analysis of variance frameworks. Statistical frameworks are essential in order to quantify the uncertainty associated with the estimate of the mean climate change response. The most general framework yields the “one model, one vote” weighting scheme often used in climate projection. However, a simpler additive framework is found to be preferable when the climate change response is not strongly model dependent. In such situations, the weighted multimodel mean may be interpreted as an estimate of the actual climate response, even in the presence of shared model biases. Statistical significance tests are derived to choose the most appropriate framework for specific multimodel ensemble data. The framework assumptions are explicit and can be checked using simple tests and graphical techniques. The frameworks can be used to test for evidence of nonzero climate response and to construct confidence intervals for the size of the response. The methodology is illustrated by application to North Atlantic storm track data from the Coupled Model Intercomparison Project phase 5 (CMIP5) multimodel ensemble. Despite large variations in the historical storm tracks, the cyclone frequency climate change response is not found to be model dependent over most of the region. This gives high confidence in the response estimates. Statistically significant decreases in cyclone frequency are found on the flanks of the North Atlantic storm track and in the Mediterranean basin.

Regional climate change mitigation with crops: context and assessment

The intention of this review is to place crop albedo biogeoengineering in the wider picture of climate manipulation. Crop biogeoengineering is considered within the context of the long-term modification of the land surface for agriculture over several thousand years. Biogeoengineering is also critiqued in relation to other geoengineering schemes in terms of mitigation power and adherence to social principles for geoengineering. Although its impact is small and regional, crop biogeoengineering could be a useful and inexpensive component of an ensemble of geoengineering schemes to provide temperature mitigation. The method should not detrimentally affect food security and there may even be positive impacts on crop productivity, although more laboratory and field research is required in this area to understand the underlying mechanisms.

The lifecycle of the North Atlantic storm track

The North Atlantic eddy-driven jet exhibits latitudinal variability, with evidence of three preferred latitudinal locations: south, middle and north. Here we examine the drivers of this variability and the variability of the associated storm track. We investigate the changes in the storm track characteristics for the three jet locations, and propose a mechanism by which enhanced storm track activity, as measured by upstream heat flux, is responsible for cyclical downstream latitudinal shifts in the jet. This mechanism is based on a nonlinear oscillator relationship between the enhanced meridional temperature gradient (and thus baroclinicity) and the meridional high-frequency (periods of shorter than 10 days) eddy heat flux. Such oscillations in baroclinicity and heat flux induce variability in eddy anisotropy which is associated with the changes in the dominant type of wave breaking and a different latitudinal deflection of the jet. Our results suggest that high heat flux is conducive to a northward deflection of the jet, whereas low heat flux is conducive to a more zonal jet. This jet deflecting effect was found to operate most prominently downstream of the storm track maximum, while the storm track and the jet remain anchored at a fixed latitudinal location at the beginning of the storm track. These cyclical changes in storm track characteristics can be viewed as different stages of the storm track’s spatio-temporal lifecycle.