Twisted trees and inconsistency of tree estimation when gaps are treated as missing data -- the impact of model mis-specification in distance corrections

Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004) reported some strikingly broad results about the forms of inconsistency in tree estimation that can arise if corrected distances are not proportional to the true distances. They showed that if the corrected distance is a concave function of the true distance, then inconsistency due to long branch attraction will occur. If these functions are convex, then two "long branch repulsion" trees will be preferred over the true tree -- though these two incorrect trees are expected to be tied as the preferred true. Here we extend their results, and demonstrate the existence of a tree shape (which we refer to as a "twisted Farris-zone" tree) for which a single incorrect tree topology will be guaranteed to be preferred if the corrected distance function is convex. We also report that the standard practice of treating gaps in sequence alignments as missing data is sufficient to produce non-linear corrected distance functions if the substitution process is not independent of the insertion/deletion process. Taken together, these results imply inconsistent tree inference under mild conditions. For example, if some positions in a sequence are constrained to be free of substitutions and insertion/deletion events while the remaining sites evolve with independent substitutions and insertion/deletion events, then the distances obtained by treating gaps as missing data can support an incorrect tree topology even given an unlimited amount of data.Comment: 29 pages, 3 figure

Little and often makes much: identifying the time-reinforced toxicity of pesticides and their impacts on bees

Bees provide important pollination services for crops and wild flowers, estimated to be valued at £120 billion to the global economy. However, declining bee populations have put these services in jeopardy. Pesticides are widely blamed, at least in part, for declines in both wild and managed bee species. Bees are exposed to dietary residues of pesticides when foraging on the nectar and pollen of treated bee-attractive crops. However, these residues are generally found at such low levels that it would not be feasible for a bee to ingest an acute lethal dose. Pesticides which exhibit time-reinforced toxicity could cause mortality to bees over an extended exposure period, though, as the damage they cause can increase exponentially over time. Currently, there is no test for time-reinforced toxicity included in bee risk assessments of pesticides. The overall aims of this thesis were to identify pesticides that exhibit time-reinforced toxicity and determine their effects on a range of demographically important sublethal endpoints in bees. Using a bioassay based on Haber’s Law, I identified fipronil as a pesticide exhibiting time-reinforced toxicity (TRT) in both the honey bee (Apis mellifera) and bumble bee (Bombus terrestris), from four widely-used candidate pesticides. Fipronil at field-relevant levels was found to significantly reduce the longevity and feeding of individual worker bumble bees and those in microcolonies. This nutrient limitation was postulated to be the cause of reduced fecundity of bumble bee microcolonies exposed to dietary fipronil at concentrations of 1 part per billion and less. The toxic effect of fipronil was dramatically increased when microcolonies were placed outside to forage for food, an effect documented by several other studies, and potentially due to an increase in metabolic rate from the need to fly. However, these effects were not observed in queenright Bombus terrestris colonies in the field. This disparity in effects may have been due to problems with exposure to fipronil rather than any possible resilience of colonies. The thesis findings highlight the need for time-reinforced toxicity testing in bees to be integrated into current risk assessment protocols for pesticides. My work in this thesis has provided validation for the use of the TRT bioassay in future risk assessments of pesticides. Current-use pesticides that exhibit TRT, in this case fipronil, pose a serious threat to both wild and managed bees, impacting on demographically important endpoints including feeding and reproduction. Further research, continuing on from the work in this thesis, is needed to ascertain the impacts of TRT pesticides at both colony and population levels. Determining the mechanisms of TRT pesticides will also be key to protecting bees from the danger they pose.NER

Bringing environmental justice to the centre of environmental law research: developing a collective case study methodology

Drawing on classic studies of environmental justice, as well as our smaller scale experience of using case studies to research environmental assessment and the protection of open green spaces, we suggest that collective case studies (also known as multisite or multiple case studies) offer an opportunity to map out and realise common concerns and losses and the similar experiences of legal hurdles and challenges on the part of geographically disparate local communities. The collective nature of these studies helps to build up a picture of environmental injustices across different, but related, cases and are capable of revealing broad discriminatory and unfair practices in environmental decision making which may form part of a pattern of experiencing discrimination and lack of influence and participation in decision making extending beyond the specifics of a particular site, environmental conflict or legal dispute. In this respect, the development of collective case studies provides a method of research practice but may also contribute to the generation or development of theories of environmental justice, crossing the line between specificity/context of experience in a locality and generality/unity of theory

Recognising an ecological ethic of care in the law of everyday shared spaces

Law plays a vital role in the life and loss of open shared spaces, used and enjoyed on an everyday basis by local people. In this article, we adopt an analytical framework based on an ethic of care to critique the registration of land as a ‘town or village green’, using the example of an inquiry into the greens status of an ancient woodland. Analysing written and oral witness statements in this inquiry makes clear the centrality of such places in many people’s lives, giving rise to community-based, and forward-looking, interests. However, the legal focus upon quantitative assessments of individuals’ use of land in the recent past means that the prospective consequences of losing such valued areas are currently poorly acknowledged, and accounted for, in the registration process. This leads to the question whether an ethic of care towards everyday shared spaces may be better recognised via more deliberative plan-making regimes

An analysis of Council Directive 85/337 on the assessment of the effects of certain public and private projects on the environment and the development of environmental law in the United Kingdom

From an historical perspective, environmental law is an assembly of common law principles and regulatory techniques derived from public health and planning legislation. Until recently, it lacked a distinct, recognisable identity, and status. A separate discipline of ‘environmental law’ now exists which appears to have an internal coherence and to operate within a settled conceptual framework, anchored by a number of guiding principles. This development is not, though, a one-way process. There is an equally dynamic contraflow of legal disciplines claiming environmental concerns as their own, notably property and tort, company and insurance law. In a similar vein, at both European Union and national levels of government, there is a sense that the very nature of environmental problems means that environmental protection must form part of a wider range of policies and law. This thesis takes account of these recent developments by considering the contribution of environmental assessment to the development of environmental law. It examines the implementation of Council Directive 85/337 on the Assessment of the Effects of Certain Public and Private Projects on the Environment' in the United Kingdom and thus the integration of a European Community method of environmental assessment alongside indigenous’ methods of environmental appraisal in the planning system. Some explanation is required, both as to the choice of subject matter, and to the methodology chosen to write this thesis

The influence of carbon morphologies and concentrations on the rheology and electrical performance of screen-printed carbon pastes

Screen-printing inks containing various morphologies of carbon are used in the production of a variety of printed electronics applications. Particle morphology influences the rheology of the ink which will affect the deposition and therefore the electrical performance of a printed component. To assess the effect of both carbon morphology and concentration on print topography and conductivity, screen printable carbon inks with differing loading concentrations of graphite, carbon black and graphite nanoplatelets (GNPs) were formulated, printed and characterised, with rheological and novel print visualisation techniques used to elucidate the mechanisms responsible. Carbon morphology had significant effects on the packing of particles. The smaller carbon black particles had more interparticle interactions leading to better conductivities, but also higher ink viscosities and elasticities than the other morphologies. Increases in carbon concentration led to increases in film thickness and roughness for all morphologies. However, beyond a critical point further increases in carbon concentration led to agglomerations of particles, mesh marking and increases in surface roughness, preventing further improvements in the print conductivity. The optimal loading concentrations were identifiable using a custom-made screen-printing apparatus used with high speed imaging for all morphologies. Notable increases in filamentation during ink separation were found to occur with further increases in carbon concentration beyond the optimum. As this point could not be identified using shear rheology alone, this method combined with shear rheology could be used to optimise the carbon concentration of screen-printing inks, preventing the use of excess material which has no benefit on print quality and conductivity

Soil N2O emissions with different reduced tillage methods during the establishment of Miscanthus in temperate grassland

An increase in renewable energy and the planting of perennial bioenergy crops is expected in order to meet global greenhouse gas (GHG) targets. Nitrous oxide (N2O) is a potent greenhouse gas, and this paper addresses a knowledge gap concerning soil N2O emissions over the possible “hot spot” of land use conversion from established pasture to the biofuel crop Miscanthus. The work aims to quantify the impacts of this land use change on N2O fluxes using three different cultivation methods. Three replicates of four treatments were established: Miscanthus x giganteus (Mxg) planted without tillage; Mxg planted with light tillage; a novel seed‐based Miscanthus hybrid planted with light tillage under bio‐degradable mulch film; and a control of uncultivated established grass pasture with sheep grazing. Soil N2O fluxes were recorded every 2 weeks using static chambers starting from preconversion in April 2016 and continuing until the end of October 2017. Monthly soil samples were also taken and analysed for nitrate and ammonium. There was no significant difference in N2O emissions between the different cultivation methods. However, in comparison with the uncultivated pasture, N2O emissions from the cultivated Miscanthus plots were 550%–819% higher in the first year (April to December 2016) and 469%–485% higher in the second year (January to October 2017). When added to an estimated carbon cost for production over a 10 year crop lifetime (including crop management, harvest, and transportation), the measured N2O conversion cost of 4.13 Mg CO2‐eq./ha represents a 44% increase in emission compared to the base case. This paper clearly shows the need to incorporate N2O fluxes during Miscanthus establishment into assessments of GHG balances and life cycle analysis and provides vital knowledge needed for this process. This work therefore also helps to support policy decisions regarding the costs and benefits of land use change to Miscanthus

The Iowa Homemaker vol.33, no.7

It’s an Old Custom, Betty Holder, page 5 She Emphasizes Good Fun, Doris Jirsa, page 6 Celebrate, Plan a Buffet, Dorothy Will, page 7 Candle-Making, Jane Hammerly, page 8 Blue Ribbon Designs, Gwen Olson, page 10 Here’s An Idea, page 12 Laugh at Yourself, Len Green, page 14 Recipe for Perfume, Mary Jean Stoddard, page 15 Small Talk, Ruth Anderson, page 16 Translate That Menu, Joanne Ryals, page 17 Trends, Jane Montgomery, page 1

Characterization of the repertoire diversity of the Plasmodium falciparum stevor multigene family in laboratory and field isolates

BACKGROUND: The evasion of host immune response by the human malaria parasite Plasmodium falciparum has been linked to expression of a range of variable antigens on the infected erythrocyte surface. Several genes are potentially involved in this process with the var, rif and stevor multigene families being the most likely candidates and coding for rapidly evolving proteins. The high sequence diversity of proteins encoded by these gene families may have evolved as an immune evasion strategy that enables the parasite to establish long lasting chronic infections. Previous findings have shown that the hypervariable region (HVR) of STEVOR has significant sequence diversity both within as well as across different P. falciparum lines. However, these studies did not address whether or not there are ancestral stevor that can be found in different parasites. METHODS: DNA and RNA sequences analysis as well as phylogenetic approaches were used to analyse the stevor sequence repertoire and diversity in laboratory lines and Kilifi (Kenya) fresh isolates. RESULTS: Conserved stevor genes were identified in different P. falciparum isolates from different global locations. Consistent with previous studies, the HVR of the stevor gene family was found to be highly divergent both within and between isolates. Importantly phylogenetic analysis shows some clustering of stevor sequences both within a single parasite clone as well as across different parasite isolates. CONCLUSION: This indicates that the ancestral P. falciparum parasite genome already contained multiple stevor genes that have subsequently diversified further within the different P. falciparum populations. It also confirms that STEVOR is under strong selection pressure