The use of agricultural, open and forest habitats by juvenile Mauritius Kestrels Falco punctatus

Knowledge of tropical raptor habitat use is limited and yet a thorough understanding is vital when trying to conserve endangered species. We used a well studied, reintroduced population of the vulnerable Mauritius Kestrel Falco punctatus to investigate habitat preferences in a modified landscape. We constructed a high resolution digital habitat map and radiotracked 13 juvenile Kestrels to quantify habitat preferences. We distinguished seven habitat types in our study area and tracked Kestrels from 71 to 130 days old during which they dispersed from their natal territory and settled within a home-range after reaching independence. Mean home-range size was 0.95 km(2) characterized by a bimodal pattern of intensity around the natal site and post-independence home-range. Compositional analysis showed that home-ranges were located non-randomly with respect to habitat but there was no evidence to suggest differential use of habitats within home-ranges. Native and semi-invaded forest and grassland were consistently preferred, whereas agriculture was used significantly less than other habitats. No difference was found between the available length of edge dividing native forest and grassland within a home-range when compared to that available within a 2.35-km buffer around their nest-site, based on the maximum distance a juvenile was found to disperse. Repeating the analysis in three dimensions gave very similar results. Our results suggest that Mauritius Kestrels are not obligate forest dwellers as was once thought but can also exploit open habitats such as grassland. Kestrels may be using isolated mature trees within grassland as vantage points for hunting in the same way as they use the natural stratified forest structure. We suggest that the avoidance of agriculture is partly due to a lack of such vantage points. The conservation importance of forest degradation and agricultural encroachment is highlighted and comparisons with the habitat preferences of other tropical falcons are discussed.

Mining, grievance and conflict in rural Tanzania

This paper provides an extended analysis of the tensions that have surfaced between large-scale mine operators and artisanal miners in gold-rich areas of rural Tanzania. The literature on grievance is used to contextualise, these disputes, the underlying cause of which is artisanal miners' mounting frustration over not being able to secure viable concessions to work. Newly implemented legislation has, for the most part, empowered foreign large-scale mine operators, while simultaneously disempowering indigenous small-scale miners. In many cases, the former have addressed mounting security and community problems on their own. Until the country's major mine operators extend assistance to marginalised small-scale mining groups, the likelihood of violent conflict unfolding between these parties will increase.

Climate change and coastal waterbird populations – past declines and future impacts

Considerable attention has been given to the impact of climate change on avian populations over the last decade. In this paper we examine two issues with respect to coastal bird populations in the UK: (1) is there any evidence that current populations are declining due to climate change, and (2) how might we predict the response of populations in the future? We review the cause of population decline in two species associated with saltmarsh habitats. The abundance of Common Redshank Tringa totanus breeding on saltmarsh declined by about 23% between the mid-1980s and mid-1990s, but the decline appears to have been caused by an increase in grazing pressure. The number of Twite Carduelis flavirostris wintering on the coast of East Anglia has declined dramatically over recent decades; there is evidence linking this decline with habitat loss but a causal role for climate change is unclear. These examples illustrate that climate change could be having population-level impacts now, but also show that it is dangerous to become too narrowly focused on single issues affecting coastal birds. Making predictions about how populations might respond to future climate change depends on an adequate understanding of important ecological processes at an appropriate spatial scale. We illustrate this with recent work conducted on the Icelandic population of Black-tailed Godwits Limosa limosa islandica that shows large-scale regulatory processes. Most predictive models to date have focused on local populations (single estuary or a group of neighbouring estuaries). We discuss the role such models might play in risk assessment, and the need for them to be linked to larger-scale ecological processes. We argue that future work needs to focus on spatial scale issues and on linking physical models of coastal environments with important ecological processes.

Use of remote sensing to measure change in the extent of habitat for the critically endangered Jerdon's Courser Rhinoptilus bitorquatus in India

Jerdon's Courser Rhinoptilus bitorquatus is one of the most endangered and least understood birds in the world. It is endemic to scrub habitats in southeast India which have been lost and degraded because of human land use. We used satellite images from 1991 and 2000 and two methods for classifying land cover to quantify loss of Jerdon's Courser habitat. The scrub habitats on which this species depends decreased in area by 11-15% during this short period (9.6 years), predominantly as a result of scrub clearance and conversion to agriculture. The remaining scrub patches were smaller and further from human settlements in 2000 than in 1991, implying that much of the scrub loss had occurred close to human population centres. We discuss the implications of our results for the conservation of Jerdon's Courser and the use of remote sensing methods in conservation.

Breeding success of Spotted Flycatchers Muscicapa striata in southern England - is woodland a good habitat for this species?

The UK population of the Spotted Flycatcher Muscicapa striata has declined markedly in the last 30 years but there have been few recent studies of the species. This study examined the relationship between nest success and the predominant habitat type around Spotted Flycatcher nests in two contrasting areas of England. A breeding population in eastern England, a region where numbers of Spotted Flycatchers are known to have decreased dramatically in recent decades, was compared with another in southwest England, where numbers have remained stable or even increased. Whilst there was no difference in breeding success between the two study areas, there were significant differences between habitats, with garden nests more successful than those in farmland or woodland, at both egg and chick stages. Estimates of productivity per nesting attempt were also lower in farmland and woodland, with nests in gardens fledging twice as many chicks as those in either woodland or farmland. The proximate cause of lower success in farmland and woodland was higher nest predation rates during both egg and chick stages. In terms of nesting success, farmland and woodland appear to be similar in quality for this species, but both appear to be suboptimal habitats when compared with gardens, providing evidence of a problem on the breeding grounds for this species, in at least these two habitats.

Investigating the effects of predator removal and habitat management on nest success and breeding population size of a farmland passerine: a case study

Passerines are especially vulnerable to predation at the pre-independence stage. Although the role of nest success in British farmland passerine declines is contentious, improvement in nest success through sympathetic management could play a role in their reversal. Because habitat is known to interact with predation, management options for mitigation will need to consider effects of nest predation. We present results from an observational study of a population of Common Blackbird Turdus merula on a farm which has experienced a range of agri-environment and game-management options, including a period with nest predator control, as a case study to address some of these issues. We used an information theoretic model comparison procedure to look for evidence of interactions between habitat and nest predation, and then asked whether habitat management and nest predator abundances could explain population trends at the site through their effects on nest success. Interactions were detected between measures of predator abundance and habitat variables, and these varied with nest stage - habitat within the vicinity of the nest appeared to be important at the egg stage, and nest-placement characteristics were important at the nestling stage. Although predator control appeared to have a positive influence on Blackbird breeding population size, the non-experimental set-up meant we could not eliminate other potential explanations. Variation in breeding population size did not appear to be influenced by variation in nest success alone. Our study demonstrates that observational data can only go so far in detection of such effects, and we discuss how it might be taken further. Agri-environment and game-management techniques are likely to influence nest predation pressure on farmland passerines, but the patterns, mechanisms and importance to population processes remain not wholly understood.

Investigating the effects of predator removal and habitat management on nest success and breeding population size of a farmland passerine: a case study

Passerines are especially vulnerable to predation at the pre-independence stage. Although the role of nest success in British farmland passerine declines is contentious, improvement in nest success through sympathetic management could play a role in their reversal. Because habitat is known to interact with predation, management options for mitigation will need to consider effects of nest predation. We present results from an observational study of a population of Common Blackbird Turdus merula on a farm which has experienced a range of agri-environment and game-management options, including a period with nest predator control, as a case study to address some of these issues. We used an information theoretic model comparison procedure to look for evidence of interactions between habitat and nest predation, and then asked whether habitat management and nest predator abundances could explain population trends at the site through their effects on nest success. Interactions were detected between measures of predator abundance and habitat variables, and these varied with nest stage - habitat within the vicinity of the nest appeared to be important at the egg stage, and nest-placement characteristics were important at the nestling stage. Although predator control appeared to have a positive influence on Blackbird breeding population size, the non-experimental set-up meant we could not eliminate other potential explanations. Variation in breeding population size did not appear to be influenced by variation in nest success alone. Our study demonstrates that observational data can only go so far in detection of such effects, and we discuss how it might be taken further. Agri-environment and game-management techniques are likely to influence nest predation pressure on farmland passerines, but the patterns, mechanisms and importance to population processes remain not wholly understood.

Variance estimation for systematic sampling from deliberately ordered populations

The systematic sampling (SYS) design (Madow and Madow, 1944) is widely used by statistical offices due to its simplicity and efficiency (e.g., Iachan, 1982). But it suffers from a serious defect, namely, that it is impossible to unbiasedly estimate the sampling variance (Iachan, 1982) and usual variance estimators (Yates and Grundy, 1953) are inadequate and can overestimate the variance significantly (Särndal et al., 1992). We propose a novel variance estimator which is less biased and that can be implemented with any given population order. We will justify this estimator theoretically and with a Monte Carlo simulation study.

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Background: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.

Mesoporous concentric magnetic FePt core-shells nanoparticle with functionalized surfaces for capturing metal ions and DNA molecules

It is demonstrated that monodisperse magnetic FePt nanoparticle can be engineered into a protective dense silica layer, followed by concentric outer mesoporous silica layers with tailored -SH, -SO3H and -NH2 surface groups, these new materials can be used to capture heavy metal ions and DNA molecules from solution specifically by their internal or/and external functionalised surfaces by magnetic means.

Cats about town: is predation by free-ranging pet cats Felis catus likely to affect urban bird populations?

Even though they are fed daily by their owners, free-ranging pet cats Felis catus may kill wild birds and, given their high densities (typically > 200 cats/km(2)), it has been postulated that cat predation could be a significant negative factor affecting the dynamics of urban bird populations. In this study, we: (1) used questionnaire surveys in 10 sites within the city of Bristol, UK, to estimate cat density; (2) estimated the number of birds killed annually in five sites by asking cat owners to record prey animals returned home; and then (3) compared the number of birds killed with breeding density and productivity to estimate the potential impact of cat predation. In addition, we (4) compared the condition of those birds killed by cats versus those killed in collisions, e.g. window strikes. Mean (+/- sd) cat density was 348 +/- 86 cats/km(2) (n = 10 sites); considering the eight species most commonly taken by cats, the mean ratios of adult birds/cats and juvenile birds/cats across the five sites were 1.17 +/- 0.23 and 3.07 +/- 0.74, respectively. Approximately 60% of the cats studied for up to 1 year at each site never returned any prey home; despite this, the estimated number of birds killed was large relative to their breeding density and productivity in many sites. Across species, cat-killed birds were in significantly poorer condition than those killed following collisions; this is consistent with the notion that cat predation represents a compensatory rather than additive form of mortality. Interpretation of these results is, however, complicated by patterns of body mass regulation in passerines. The predation rates estimated in this study would suggest that cats were likely to have been a major cause of mortality for some species of birds. The effect of cat predation in urban landscapes therefore warrants further investigation. The potential limitations of the current study are discussed, along with suggestions for resolving them.

Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna

Background: Ibuprofen and other nonsteroidal anti-inflammatory drugs have been designed to interrupt eicosanoid metabolism in mammals, but little is known of how they affect nontarget organisms. Here we report a systems biology study that simultaneously describes the transcriptomic and phenotypic stress responses of the model crustacean Daphnia magna after exposure to ibuprofen. Results: Our findings reveal intriguing similarities in the mode of action of ibuprofen between vertebrates and invertebrates, and they suggest that ibuprofen has a targeted impact on reproduction at the molecular, organismal, and population level in daphnids. Microarray expression and temporal real-time quantitative PCR profiles of key genes suggest early ibuprofen interruption of crustacean eicosanoid metabolism, which appears to disrupt signal transduction affecting juvenile hormone metabolism and oogenesis. Conclusion: Combining molecular and organismal stress responses provides a guide to possible chronic consequences of environmental stress for population health. This could improve current environmental risk assessment by providing an early indication of the need for higher tier testing. Our study demonstrates the advantages of a systems approach to stress ecology, in which Daphnia will probably play a major role.

The genome of Rhizobium leguminosarum has recognizable core and accessory components

Background: Rhizobium leguminosarum is an alpha-proteobacterial N-2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. Results: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes ( Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were overrepresented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens. Conclusion: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.

Climate change and coastal waterbird populations - past declines and future impacts

Considerable attention has been given to the impact of climate change on avian populations over the last decade. In this paper we examine two issues with respect to coastal bird populations in the UK: (1) is there any evidence that current populations are declining due to climate change, and (2) how might we predict the response of populations in the future? We review the cause of population decline in two species associated with saltmarsh habitats. The abundance of Common Redshank Tringa totanus breeding on saltmarsh declined by about 23% between the mid-1980s and mid-1990s, but the decline appears to have been caused by an increase in grazing pressure. The number of Twite Carduelis flavirostris wintering on the coast of East Anglia has declined dramatically over recent decades; there is evidence linking this decline with habitat loss but a causal role for climate change is unclear. These examples illustrate that climate change could be having population-level impacts now, but also show that it is dangerous to become too narrowly focused on single issues affecting coastal birds. Making predictions about how populations might respond to future climate change depends on an adequate understanding of important ecological processes at an appropriate spatial scale. We illustrate this with recent work conducted on the Icelandic population of Black-tailed Godwits Limosa limosa islandica that shows large-scale regulatory processes. Most predictive models to date have focused on local populations (single estuary or a group of neighbouring estuaries). We discuss the role such models might play in risk assessment, and the need for them to be linked to larger-scale ecological processes. We argue that future work needs to focus on spatial scale issues and on linking physical models of coastal environments with important ecological processes.