Immigration, species radiation and extinction in a highly diverse songbird lineage: white-eyes on Indian Ocean islands

Molecular phylogenetic hypotheses of species-rich lineages in regions where geological history can be reliably inferred may provide insights into the scale of processes driving diversification. Here we sample all extant or recently extinct white-eye (Zosterops) taxa of the southwest Indian Ocean, combined with samples from all principal continental lineages. Results support a high dispersal capability, with at least two independent continental sources for white-eyes of the region. An early (within 1.8 million years ago) expansion into the Indian Ocean may have originated either from Asia or Africa; the three resulting lineages show a disparate distribution consistent with considerable extinction following their arrival. Africa is supported as the origin of a later expansion into the region (within 1.2 million years ago). On two islands, a pair of Zosterops species derived from independent immigrations into the Indian Ocean co-occur or may have formerly co-occurred, providing strong support for their origin by double-island colonization rather than within-island (sympatric or microallopatric) speciation. On Mauritius and La Reunion, phylogenetic placement of sympatric white-eyes allow us to rule out a scenario in which independent within-island speciation occurred on both islands; one of the species pairs must have arisen by double colonization, while the other pair is likely to have arisen by the same mechanism. Long-distance immigration therefore appears to be responsible for much of the region's white-eye diversity. Independent immigrations into the region have resulted in lineages with mutually exclusive distributions and it seems likely that competition with congeneric species, rather than arrival frequency, may limit present-day diversity.

Island ecosystems - priorities for conservation?

In terms of their land area, many islands contain a disproportionate number of taxa for certain groups of organisms. Thus the IUCN/WWF Centres of Plant Diversity project, which identifies 234 first order sites that are globally most important from a botanical point of view, includes a considerable proportion of islands, and in Conservation International’s Hotspot programme, Madagascar and the Indian Ocean Islands, the Philippines, and the Caribbean are identified as three of the five “hottest of the hotspots”. Priority for conservation action is often assumed for islands because of the often dramatic losses already suffered and the serious level of threats to which plant or animal populations are subjected, largely as a result of direct or indirect human action. The practicalities of conservation are not, however, straightforward in many cases. In the conservation of island hotspots of biodiversity, in addition to the many scientific and technical issues involved, political, financial and socio-economic factors also have to be addressed. The priorities for conservation will be examined in the light of targets set by the recently approved CBD Global Strategy for Plant Conservation and in the wider context of sustainable development of island ecosystems and the needs and aspirations of the people who inhabit them. Particular attention will be given to the threats from invasive species and the resultant increasing homogenization of floras and faunas, leading to the ‘deinsularization’ of islands.

Atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit

Phenotypic and molecular genetic studies were performed on an unknown facultative anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from a pig manure storage pit. The unknown bacterium was nutritionally fastidious with growth enhanced by the addition of rumen fluid and was phenotypically initially identified as an Eubacterium species. Comparative 16S rRNA gene sequencing studies, however, revealed that the unknown bacterium was phylogenetically distant from Eubacterium limosum (the type species of the genus Eubacterium) and related organisms. Phylogenetically, the unknown species displayed a close association with an uncultured organism from human subgingival plaque and formed an unknown sub-line within a cluster of organisms which includes Alloioccoccus otitis, Alkalibacterium olivoapovliticus, Allofustis seminis, Dolosigranulum pigrum, and related organisms, within the low mol% G + C Gram-positive bacteria. Sequence divergence values of > 8% with all known taxonomically recognised taxa, however, clearly indicates the novel bacterium represents a hitherto unknown genus. Based on both phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig manure be classified in a new genus and species, as Atopostipes suicloacale gen. nov., sp. nov. The type strain of Atopostipes suicloacale is PPC79(T) = NRRL 23919(T) = DSM 15692(T). Crown Copyright (C) 2004 Published by Elsevier Ltd. All rights reserved.

Confocal imaging of pseudomonas syringae pv. phaseolicola colony development in bean reveals reduced multiplication of strains containing the genomic island PPHGI-1.

Pseudomonas syringae pv. phaseolicola is the seed borne causative agent of halo blight in the common bean Phaseolus vulgaris. Pseudomonas syringae pv. phaseolicola race 4 strain 1302A contains the avirulence gene hopAR1 (located on a 106-kb genomic island, PPHGI-1, and earlier named avrPphB), which matches resistance gene R3 in P. vulgaris cultivar Tendergreen (TG) and causes a rapid hypersensitive reaction (HR). Here, we have fluorescently labeled selected Pseudomonas syringae pv. phaseolicola 1302A and 1448A strains (with and without PPHGI-1) to enable confocal imaging of in-planta colony formation within the apoplast of resistant (TG) and susceptible (Canadian Wonder [CW]) P. vulgaris leaves. Temporal quantification of fluorescent Pseudomonas syringae pv. phaseolicola colony development correlated with in-planta bacterial multiplication (measured as CFU/ml) and is, therefore, an effective means of monitoring Pseudomonas syringae pv. phaseolicola endophytic colonization and survival in P. vulgaris. We present advances in the application of confocal microscopy for in-planta visualization of Pseudomonas syringae pv. phaseolicola colony development in the leaf mesophyll to show how the HR defense response greatly affects colony morphology and bacterial survival. Unexpectedly, the presence of PPHGI-1 was found to cause a reduction of colony development in susceptible P. vulgaris CW leaf tissue. We discuss the evolutionary consequences that the acquisition and retention of PPHGI-1 brings to Pseudomonas syringae pv. phaseolicola in planta.

Perturbation, extraction and refinement of invariant pairs for matrix polynomials

Generalizing the notion of an eigenvector, invariant subspaces are frequently used in the context of linear eigenvalue problems, leading to conceptually elegant and numerically stable formulations in applications that require the computation of several eigenvalues and/or eigenvectors. Similar benefits can be expected for polynomial eigenvalue problems, for which the concept of an invariant subspace needs to be replaced by the concept of an invariant pair. Little has been known so far about numerical aspects of such invariant pairs. The aim of this paper is to fill this gap. The behavior of invariant pairs under perturbations of the matrix polynomial is studied and a first-order perturbation expansion is given. From a computational point of view, we investigate how to best extract invariant pairs from a linearization of the matrix polynomial. Moreover, we describe efficient refinement procedures directly based on the polynomial formulation. Numerical experiments with matrix polynomials from a number of applications demonstrate the effectiveness of our extraction and refinement procedures.

The comfort, energy and health implications of London’s urban heat island

The urban heat island (UHI) is a well-known effect of urbanisation and is particularly important in world megacities. Overheating in such cities is expected to be exacerbated in the future as a result of further urban growth and climate change. Demonstrating and quantifying the impact of individual design interventions on the UHI is currently difficult using available software tools. The tools developed in the LUCID (‘The Development of a Local Urban Climate Model and its Application to the Intelligent Design of Cities’) research project will enable the related impacts to be better understood, quantified and addressed. This article summarises the relevant literature and reports on the ongoing work of the project.

An urban solar flux island: measurements from London

Solar irradiance measurements from a new high density urban network in London are presented. Annual averages demonstrate that central London receives 30 ± 10 Wm-2 less solar irradiance than outer London at midday, equivalent to 9 ± 3% less than the London average. Particulate matter and AERONET measurements combined with radiative transfer modeling suggest that the direct aerosol radiative effect could explain 33 to 40% of the inner London deficit and a further 27 to 50% could be explained by increased cloud optical depth due to the aerosol indirect effect. These results have implications for solar power generation and urban energy balance models. A new technique using ‘Langley flux gradients’ to infer aerosol column concentrations over clear periods of three hours has been developed and applied to three case studies. Comparisons with particulate matter measurements across London have been performed and demonstrate that the solar irradiance measurement network is able to detect aerosol distribution across London and transport of a pollution plume out of London.

Simulations of the London urban heat island

We present simulations of London's meteorology using the Met Office Unified Model with a new, sophisticated surface energy-balance scheme to represent the urban surfaces, called MORUSES. Simulations are performed with the urban surfaces represented and with the urban surfaces replaced with grass in order to calculate the urban increment on the local meteorology. The local urban effects were moderated to some extent by the passage of an onshore flow that propagated up the Thames estuary and across the city, cooling London slightly in the afternoon. Validations of screen-level temperature show encouraging agreement to within 1–2 K, when the urban increment is up to 5 K. The model results are then used to examine factors shaping the spatial and temporal structure of London's atmospheric boundary layer. The simulations reconcile the differences in the temporal evolution of the urban heat island (UHI) shown in various studies and demonstrate that the variation of UHI with time depends strongly on the urban fetch. The UHI at a location downwind of the city centre shows a decrease in UHI during the night, while the UHI at the city centre stays constant. Finally, the UHI at a location upwind of the city centre increases continuously. The magnitude of the UHI by the time of the evening transition increases with urban fetch. The urban increments are largest at night, when the boundary layer is shallow. The boundary layer experiences continued warming after sunset, as the heat from the urban fabric is released, and a weakly convective boundary layer develops across the city. The urban land-use fraction is the dominant control on the spatial structure in the sensible heat flux and the resulting urban increment, although even the weak advection present in this case study is sufficient to advect the peak temperature increments downwind of the most built-up areas. Copyright © 2011 Royal Meteorological Society and British Crown Copyright, the Met Office

Changes in race-specific virulence in pseudomonas syringae pv. phaseolicola are Associated with a chimeric transposable element and rare deletion events in a plasmid-borne pathogenicity island

Virulence for bean and soybean is determined by effector genes in a plasmid-borne pathogenicity island (PAI) in race 7 strain 1449B of Pseudomonas syringae pv. phaseolicola. One of the effector genes, avrPphF, confers either pathogenicity, virulence, or avirulence depending on the plant host and is absent from races 2, 3, 4, 6, and 8 of this pathogen. Analysis of cosmid clones and comparison of DNA sequences showed that the absence of avrPphF from strain 1448A is due to deletion of a continuous 9.5-kb fragment. The remainder of the PAI is well conserved in strains 1448A and 1449B. The left junction of the deleted region consists of a chimeric transposable element generated from the fusion of homologs of IS1492 from Pseudomonas putida and IS1090 from Ralstonia eutropha. The borders of the deletion were conserved in 66 P. syringae pv. phaseolicola strains isolated in different countries and representing the five races lacking avrPphF. However, six strains isolated in Spain had a 10.5-kb deletion that extended 1 kb further from the right junction. The perfect conservation of the 28-nucleotide right repeat of the IS1090 homolog in the two deletion types and in the other 47 insertions of the IS1090 homolog in the 1448A genome strongly suggests that the avrPphF deletions were mediated by the activity of the chimeric mobile element. Our data strongly support a clonal origin for the races of P. syringae pv. phaseolicola lacking avrPphF.

Transcriptional regulators of the GAD acid stress island are carried by effector protein-encoding prophages and indirectly control type III secretion in enterohemorrhagic Escherichia coli O157:H7

P>Type III secretion (T3S) plays a pivotal role in the colonization of ruminant hosts by Enterohemorrhagic Escherichia coli (EHEC). The T3S system translocates effector proteins into host cells to promote bacterial attachment and persistence. The repertoire and variation in prophage regions underpins differences in the pathogenesis and epidemiology of EHEC strains. In this study, we have used a collection of deletions in cryptic prophages and EHEC O157 O-islands to screen for novel regulators of T3S. Using this approach we have identified a family of homologous AraC-like regulators that indirectly repress T3S. These prophage-encoded secretion regulator genes (psr) are found exclusively on prophages and are associated with effector loci and the T3S activating Pch family of regulators. Transcriptional profiling, mutagenesis and DNA binding studies were used to show that these regulators usurp the conserved GAD acid stress resistance system to regulate T3S by increasing the expression of GadE (YhiE) and YhiF and that this regulation follows attachment to bovine epithelial cells. We further demonstrate that PsrA and effectors encoded within cryptic prophage CP933-N are required for persistence in a ruminant model of colonization.

The island and the world: kinship, friendship and living together in selected writings of Sam Selvon

This article argues that the ethical force of Trinidadian Sam Selvon’s creative writings comes from the particular configuration of living together that he is interested in, both in his Trinidadian novels and his London ones. It reads examples of this living together alongside and in difference that emerges through his focus on the relations between neighbours, friends and lovers, rather than the kinship relations of family. It argues that his works thereby map horizontal zones of attachment and possible solidarities across groupings that reconfigure vertically inscribed genealogical paradigms of belonging to place and each other based on models of historical continuity and inheritance.

Co-ordination of pathogenicity island expression by the BipA GTPase in enteropathogenic Escherichia coli (EPEC)

BipA is a novel member of the ribosome binding GTPase superfamily and is widely distributed in bacteria and plants. We report here that it regulates -multiple cell surface- and virulence-associated -components in the enteropathogenic Escherichia coli (EPEC) strain E2348/69. The regulated components include bacterial flagella, the espC pathogenicity island and a type III secretion system specified by the locus of enterocyte effacement (LEE). BipA positively regulated the espC and LEE gene clusters through transcriptional control of the LEE-encoded regulator, Ler. Additionally, it affected the pattern of proteolysis of intimin, a key LEE-encoded adhesin specified by the LEE. BipA control of the LEE operated independently of the previously characterized regulators Per, integration host factor and H-NS. In contrast, it negatively regulated the flagella-mediated motility of EPEC and in a Ler-independent manner. Our results indicate that the BipA GTPase functions high up in diverse regulatory cascades to co-ordinate the expression of key pathogenicity islands and other virulence-associated factors in E. coli.