Four rural cemeteries in central western NSW: Islands of Australiana in a European sea?

Vascular plants present in groundstoreys of variously–managed areas in four cemeteries in central western NSW – two on the Central Western Slopes (Garra and Toogong) and two on the Central Tablelands (Lyndhurst and Carcoar) – were recorded over periods of 6–10 years. It was hypothesised that (a) areas of the cemeteries with a history of nil or low disturbance would represent high quality remnant vegetation (i.e. contain a diversity of native species but few naturalised species), and (b) that clearing of woody vegetation, together with similar management (e.g. regular mowing) would result in homogenisation of the groundstoreys such that many species, native and naturalised, would be common to all sites. 344 species (176 native, 154 naturalised and 14 non–naturalised exotics) were recorded across the four cemeteries. Many native species that were rare in the surrounding agricultural lands were present in the cemeteries (enhancing their value as conservation areas) but no cemetery contained areas of groundstorey that would qualify as ‘pristine’. Across all management areas, the proportions of naturalised species in the native + naturalised floras of the cemeteries ranged from 46 to 55 %. Though never dominant, naturalised species also comprised high proportions (42 to 51 %) of the floras of the least disturbed (nil or infrequently mown) areas within each cemetery. Many (40 %) of the species recorded occurred at only one cemetery. This partly explained why the floras of similarly– managed parts of cemeteries on the Central Western Slopes were, contrary to expectations, markedly different to those on the Central Tablelands. However, within the same botanic subdivision, floras – particularly of naturalised species in regularly mown grasslands – were more similar (‘homogenised’) than those of nil or infrequently mown grasslands

Is there a close association between "soils" and "vegetation"? : A case study from central western New South Wales

The assumption that ‘soils’ and ‘vegetation’ are closely associated was tested by describing soils and vegetation along a Travelling Stock Reserve west of Grenfell, New South Wales (lat 33° 55’S, long 147° 45’E). The transect was selected on the basis of (a) minimising the effects of non-soil factors (human interference, climate and relief) on vegetation and (b) the presence of various soil and vegetation types as indicated by previous mapping. ‘Soils’ were considered at three levels: soil landscapes (a broad mapping unit widely used in central western NSW), soil types (according to a range of classifications) and soil properties (depth, pH, etc.). ‘Vegetation’ was considered in three ways: vegetation type (in various classifications), density/floristic indices (density of woody species, abundance of native species, etc.) and presence/absence of individual species. Sites along the transect were grouped according to soil landscapes or soil types and compared to vegetation types or indices recorded at the sites. Various measures indicated low associations between vegetation types and soil landscapes or soil types. Except for infrequent occurrences of a soil type or landscape, any one soil type or landscape was commonly associated with a number of vegetation types and any one vegetation type was associated with a number of soil landscapes or soil types. However, significant associations between some vegetation indices, mainly density or numbers of woody species, and some soil landscapes and soil types were evident. Although many species were relatively ubiquitous, some groups of species that were restricted to one or two soil types were identified. Canonical Correspondence Analysis provided some suggestions as to which properties (e.g. texture) of these soils were associated with the presence of particular species

Quartet compatibility and the quartet graph

A collection P of leaf-labelled trees is compatible if there exists a single leaf-labelled tree that displays each of the trees in P. Despite its difficulty, determining the compatibility of P is a fundamental task in evolutionary biology. Attractive characterizations in terms of chordal graphs have been previously given for this problem as well as for the problems of (i) determining if there is a unique tree that displays each of the trees in P, that is 'P is definitive and (ii) determining if there is a tree that displays P and has the property that every other tree that displays P is a refinement of it, that is 'P identifies a leaf-labelled tree. In this paper, we describe new characterizations of each of these problems in terms of edge colourings. Furthermore, for an arbitrary leaf-labelled tree 'T, we also determine the minimum number of 'quartets' required to identify 'T, thus correcting a previously published result

Sushi gets serious:the draft genome sequence of the pufferfish Fugu rubripes

The publication of the Fugu rubripes draft genome sequence will take this fish from culinary delicacy to potent tool in deciphering the mysteries of human genome function

Analyzing and reconstructing reticulation networks under timing constraints

Reticulation networks are now frequently used to model the history of life for various groups of organisms whose evolutionary past is likely to include reticulation events like horizontal gene transfer or hybridization. However, the reconstructed networks are rarely guaranteed to be temporal. If a reticulation network is temporal, then it satisfies the two biologically motivated timing constraints of instantaneously occurring reticulation events and successively occurring speciation events. On the other hand, if a reticulation network is not temporal, it is always possible to resolve this issue by adding a number of additional unsampled or extinct taxa. In the first half of the paper, we show that deciding whether a given number of additional taxa is sufficient to transform a non-temporal reticulation network into a temporal one is an NP-complete problem. As one is often given a set of gene trees instead of a network in the context of hybridization, this motivates the second half of the paper which provides an algorithm for reconstructing a temporal hybridization network that simultaneously explains the ancestral history of two trees or indicates that no such network exists. We highlight two practical applications of this algorithm and illustrate the second application on a grass data set

Cognitive bias in a non-human primate: husbandry procedures influence cognitive indicators of psychological well-being in captive rhesus macaques

The measurement of 'cognitive bias' has recently emerged as a powerful tool for assessing animal welfare. Cognitive bias was initially, and widely, studied in humans, and describes the way in which particular emotions are associated with biases in information processing. People suffering from clinical levels of anxiety or depression, for example, interpret ambiguous events more negatively than do non-anxious or non-depressed people. Development of methods for use with non-human animals has revealed similar biases in several species of mammals and birds, and one invertebrate. However, cognitive bias has not been previously explored in any species of non-human primate, despite specific concerns raised about the welfare of these animals in captivity. Here, we describe a touchscreen-based cognitive-bias task developed for use with captive rhesus macaques (Macaca mulatta). Monkeys were initially trained on a 'Go/No-Go' operant task, in which they learned to touch one of two lines that differed in size in order to receive a reward (food), and to desist from touching the other line to avoid a mildly aversive stimulus (delay to the next trial and white noise). In testing sessions, the monkeys were presented with lines of intermediate size. We measured whether touchscreen responses to these ambiguous stimuli were affected by husbandry procedures (environmental enrichment, and a statutory health check involving restraint and ketamine hydrochloride injection) presumed to induce positive and negative shifts in affective state, respectively. Monkeys made fewer responses to ambiguous stimuli post health check compared to during the phase of enrichment suggesting greater expectation of negative outcomes following the health check compared to during enrichment. Shifts in affective state following standard husbandry procedures may therefore be associated with changes in information processing similar to those demonstrated in anxious and depressed humans, and in a number of other taxa

Emotion evaluation and response slowing in a non-human primate: New directions for cognitive bias measures of animal welfare

The cognitive bias model of animal welfare assessment is informed by studies with humans demonstrating that the interaction between emotion and cognition can be detected using laboratory tasks. A limitation of cognitive bias tasks is the amount of training required by animals prior to testing. A potential solution is to use biologically relevant stimuli that trigger innate emotional responses. Here; we develop a new method to assess emotion in rhesus macaques; informed byparadigms used with humans: emotional Stroop; visual cueing and; in particular; response slowing. In humans; performance on a simple cognitive task can become impaired when emotional distractor content is displayed. Importantly; responses become slower in anxious individuals in the presence of mild threat; a pattern not seen in non-anxious individuals; who are able to effectively process and disengage from the distractor. Here; we present a proof-of-concept study; demonstrating that rhesus macaques show slowing of responses in a simple touch-screen task when emotional content is introduced; but only when they had recently experienced a presumably stressful veterinary inspection. Our results indicate the presence of a subtle “cognitive freeze” response; the measurement of which may provide a means of identifying negative shifts in emotion in animals

The genomic signature of trait-associated variants

BACKGROUND: Genome-wide association studies have identified thousands of SNP variants associated with hundreds of phenotypes. For most associations the causal variants and the molecular mechanisms underlying pathogenesis remain unknown. Exploration of the underlying functional annotations of trait-associated loci has thrown some light on their potential roles in pathogenesis. However, there are some shortcomings of the methods used to date, which may undermine efforts to prioritize variants for further analyses. Here, we introduce and apply novel methods to rigorously identify annotation classes showing enrichment or depletion of trait-associated variants taking into account the underlying associations due to co-location of different functional annotations and linkage disequilibrium. RESULTS: We assessed enrichment and depletion of variants in publicly available annotation classes such as genic regions, regulatory features, measures of conservation, and patterns of histone modifications. We used logistic regression to build a multivariate model that identified the most influential functional annotations for trait-association status of genome-wide significant variants. SNPs associated with all of the enriched annotations were 8 times more likely to be trait-associated variants than SNPs annotated with none of them. Annotations associated with chromatin state together with prior knowledge of the existence of a local expression QTL (eQTL) were the most important factors in the final logistic regression model. Surprisingly, despite the widespread use of evolutionary conservation to prioritize variants for study we find only modest enrichment of trait-associated SNPs in conserved regions. CONCLUSION: We established odds ratios of functional annotations that are more likely to contain significantly trait-associated SNPs, for the purpose of prioritizing GWAS hits for further studies. Additionally, we estimated the relative and combined influence of the different genomic annotations, which may facilitate future prioritization methods by adding substantial information

The relationship between workers' self-reported changes in health and their attitudes towards a workplace intervention: lessons from smoke-free legislation across the UK hospitality industry

Background: The evaluation of smoke-free legislation (SFL) in the UK examined the impacts on exposure to second-hand smoke, workers’ attitudes and changes in respiratory health. Studies that investigate changes in the health of groups of people often use self-reported symptoms. Due to the subjective nature it is of interest to determine whether workers’ attitudes towards the change in their working conditions may be linked to the change in health they report. Methods: Bar workers were recruited before the introduction of the SFL in Scotland and England with the aim of investigating their changes to health, attitudes and exposure as a result of the SFL. They were asked about their attitudes towards SFL and the presence of respiratory and sensory symptoms both before SFL and one year later. Here we examine the possibility of a relationship between initial attitudes and changes in reported symptoms, through the use of regression analyses. Results: There was no difference in the initial attitudes towards SFL between those working in Scotland and England. Bar workers who were educated to a higher level tended to be more positive towards SFL. Attitude towards SFL was not found to be related to change in reported symptoms for bar workers in England (Respiratory, p = 0.755; Sensory, p = 0.910). In Scotland there was suggestion of a relationship with reporting of respiratory symptoms (p = 0.042), where those who were initially more negative to SFL experienced a greater improvement in self-reported health. Conclusions: There was no evidence that workers who were more positive towards SFL reported greater improvements in respiratory and sensory symptoms. This may not be the case in all interventions and we recommend examining subjects’ attitudes towards the proposed intervention when evaluating possible health benefits using self-reported methods. Keywords: ‘Self-Reported Health’, Attitudes, ‘Workplace Intervention’, ‘Public Health Intervention

The comparative clinical course of pregnant and non-pregnant women hospitalised with influenza A(H1N1)pdm09 infection

Introduction: The Influenza Clinical Information Network (FLU-CIN) was established to gather detailed clinical and epidemiological information about patients with laboratory confirmed A(H1N1)pdm09 infection in UK hospitals. This report focuses on the clinical course and outcomes of infection in pregnancy.Methods: A standardised data extraction form was used to obtain detailed clinical information from hospital case notes and electronic records, for patients with PCR-confirmed A(H1N1)pdm09 infection admitted to 13 sentinel hospitals in five clinical 'hubs' and a further 62 non-sentinel hospitals, between 11th May 2009 and 31st January 2010.Outcomes were compared for pregnant and non-pregnant women aged 15-44 years, using univariate and multivariable techniques.Results: Of the 395 women aged 15-44 years, 82 (21%) were pregnant; 73 (89%) in the second or third trimester. Pregnant women were significantly less likely to exhibit severe respiratory distress at initial assessment (OR?=?0.49 (95% CI: 0.30-0.82)), require supplemental oxygen on admission (OR?=?0.40 (95% CI: 0.20-0.80)), or have underlying co-morbidities (p-trend <0.001). However, they were equally likely to be admitted to high dependency (Level 2) or intensive care (Level 3) and/or to die, after adjustment for potential confounders (adj. OR?=?0.93 (95% CI: 0.46-1.92). Of 11 pregnant women needing Level 2/3 care, 10 required mechanical ventilation and three died.Conclusions: Since the expected prevalence of pregnancy in the source population was 6%, our data suggest that pregnancy greatly increased the likelihood of hospital admission with A(H1N1)pdm09. Pregnant women were less likely than non-pregnant women to have respiratory distress on admission, but severe outcomes were equally likely in both groups