Compositional Divergence and Convergence in Local Communities and Spatially Structured Landscapes

Community structure depends on both deterministic and stochastic processes. However, patterns of community dissimilarity (e.g. difference in species composition) are difficult to interpret in terms of the relative roles of these processes. Local communities can be more dissimilar (divergence) than, less dissimilar (convergence) than, or as dissimilar as a hypothetical control based on either null or neutral models. However, several mechanisms may result in the same pattern, or act concurrently to generate a pattern, and much research has recently been focusing on unravelling these mechanisms and their relative contributions. Using a simulation approach, we addressed the effect of a complex but realistic spatial structure in the distribution of the niche axis and we analysed patterns of species co-occurrence and beta diversity as measured by dissimilarity indices (e.g. Jaccard index) using either expectations under a null model or neutral dynamics (i.e., based on switching off the niche effect). The strength of niche processes, dispersal, and environmental noise strongly interacted so that niche-driven dynamics may result in local communities that either diverge or converge depending on the combination of these factors. Thus, a fundamental result is that, in real systems, interacting processes of community assembly can be disentangled only by measuring traits such as niche breadth and dispersal. The ability to detect the signal of the niche was also dependent on the spatial resolution of the sampling strategy, which must account for the multiple scale spatial patterns in the niche axis. Notably, some of the patterns we observed correspond to patterns of community dissimilarities previously observed in the field and suggest mechanistic explanations for them or the data required to solve them. Our framework offers a synthesis of the patterns of community dissimilarity produced by the interaction of deterministic and stochastic determinants of community assembly in a spatially explicit and complex context.

Relative role of deterministic and stochastic determinants of soil animal community: a spatially explicit analysis of oribatid mites

1. Ecologists are debating the relative role of deterministic and stochastic determinants of community structure. Although the high diversity and strong spatial structure of soil animal assemblages could provide ecologists with an ideal ecological scenario, surprisingly little information is available on these assemblages.
2. We studied species-rich soil oribatid mite assemblages from a Mediterranean beech forest and a grassland. We applied multivariate regression approaches and analysed spatial autocorrelation at multiple spatial scales using Moran's eigenvectors. Results were used to partition community variance in terms of the amount of variation uniquely accounted for by environmental correlates (e.g. organic matter) and geographical position. Estimated neutral diversity and immigration parameters were also applied to a soil animal group for the first time to simulate patterns of community dissimilarity expected under neutrality, thereby testing neutral predictions.
3. After accounting for spatial autocorrelation, the correlation between community structure and key environmental parameters disappeared: about 40% of community variation consisted of spatial patterns independent of measured environmental variables such as organic matter. Environmentally independent spatial patterns encompassed the entire range of scales accounted for by the sampling design (from tens of cm to 100 m). This spatial variation could be due to either unmeasured but spatially structured variables or stochastic drift mediated by dispersal. Observed levels of community dissimilarity were significantly different from those predicted by neutral models.
4. Oribatid mite assemblages are dominated by processes involving both deterministic and stochastic components and operating at multiple scales. Spatial patterns independent of the measured environmental variables are a prominent feature of the targeted assemblages, but patterns of community dissimilarity do not match neutral predictions. This suggests that either niche-mediated competition or environmental filtering or both are contributing to the core structure of the community. This study indicates new lines of investigation for understanding the mechanisms that determine the signature of the deterministic component of animal community assembly.

Spatial patterns and autocorrelation in the response of microarthropods to soil pollutants: The example of oribatid mites in an abandoned mining and smelting area

Although exogenous factors such as pollutants can act on endogenous drivers (e.g. dispersion) of populations and create spatially autocorrelated distributions, most statistical techniques assume independence of error terms. As there are no studies on metal soil pollutants and microarthropods that explicitly analyse this key issue, we completed a field study of the correlation between Oribatida and metal concentrations in litter, organic matter and soil in an attempt to account for spatial patterns of both metals and mites. The 50-m wide study area had homogenous macroscopic features, steep Pb and Cu gradients and high levels of Zn and Cd. Spatial models failed to detect metal-oribatid relationships because the observed latitudinal and longitudinal gradients in oribatid assemblages were independent of the collinear gradients in the concentration of metals. It is therefore hypothesised that other spatially variable factors (e.g. fungi, reduced macrofauna) affect oribatid assemblages, which may be influenced by metals only indirectly. (C) 2009 Elsevier Ltd. All rights reserved.

An in situ spatially resolved analytical technique to simultaneously probe gas phase reactions and temperature within the packed bed of a plug flow reactor

This paper reports the detailed description and validation of a fully automated, computer controlled analytical method to spatially probe the gas composition and thermal characteristics in packed bed systems. As an exemplar, we have examined a heterogeneously catalysed gas phase reaction within the bed of a powdered oxide supported metal catalyst. The design of the gas sampling and the temperature recording systems are disclosed. A stationary capillary with holes drilled in its wall and a moveable reactor coupled with a mass spectrometer are used to enable sampling and analysis. This method has been designed to limit the invasiveness of the probe on the reactor by using the smallest combination of thermocouple and capillary which can be employed practically. An 80 mu m (O.D.) thermocouple has been inserted in a 250 mu m (O.D.) capillary. The thermocouple is aligned with the sampling holes to enable both the gas composition and temperature profiles to be simultaneously measured at equivalent spatially resolved positions. This analysis technique has been validated by studying CO oxidation over a 1% Pt/Al2O3 catalyst and the spatial resolution profiles of chemical species concentrations and temperature as a function of the axial position within the catalyst bed are reported.

Evidence and Spatial Planning for Sustainable Development: A Model for Spatially Allocating Material Flows

The aspiration the spatial planning should act as the main coordinating function for the transition to a sustainable society is grounded on the assumption that it is capable of incorporating both a strong evidence base of environmental accounting for policy, coupled with opportunities for open, deliberative decision-making. While there are a number of increasingly sophisticated methods (such as material flow analysis and ecological footprinting) that can be used to longitudinally determine the impact of policy, there are fewer that can provide a robust spatial assessment of sustainability policy. In this paper, we introduce the Spatial Allocation of Material Flow Analysis (SAMFA) model, which uses the concept of socio-economic metabolism to extrapolate the impact of local consumption patterns that may occur as a result of the local spatial planning process at multiple spatial levels. The initial application the SAMFA model is based on County Kildare in the Republic of Ireland, through spatial temporal simulation and visualisation of construction material flows and associated energy use in the housing sector. Thus, while we focus on an Ireland case study, the model is applicable to spatial planning and sustainability research more generally. Through the development and evaluation of alternative scenarios, the model appears to be successful in its prediction of the cumulative resource and energy impacts arising from consumption and development patterns. This leads to some important insights in relation to the differential spatial distribution of disaggregated allocation of material balance and energy use, for example that rural areas have greater resource accumulation (and are therefore in a sense “less sustainable”) than urban areas, confirming that rural housing in Ireland is both more material and energy intensive. This therefore has the potential to identify hotspots of higher material and energy use, which can be addressed through targeted planning initiatives or focussed community engagement. Furthermore, due to the ability of the model to allow manipulation of different policy criteria (increased density, urban conservation etc), it can also act as an effective basis for multi-stakeholder engagement.

Assessing Historical and Current Threats to Common Frog (Rana Temporaria) Populations in Ireland

Ponds are an ephemeral feature of the landscape but their large-scale loss can have profound implications for biodiversity and the persistence of amphibian populations. We quantified rates of pond loss throughout Ireland over a period of approximately 125 yr. Environmental parameters and perceived risk factors associated with the current occurrence and density of the Common Frog, Rana temporaria, were also analyzed. The numbers of farmland ponds declined by 54% between 1887–1913 and 2005–11, with most ponds and the greatest losses
in the East, coincident with agricultural intensification and human habitation. The decline of pond numbers was significant but, at approximately 0.5% per annum, was substantially less than losses recorded in other European countries. Losses were coincident with major changes to the agricultural landscape including extensive land drainage. However, losses of pond and natural wetland habitats throughout Ireland may have been partially or wholly mitigated by a synchronous expansion of artificial field margin ditches associated with drainage projects during the mid-20th Century. The ecology of the Common Frog in Ireland was similar to its ecology elsewhere and it appears largely unaffected by pollution and disturbance. Consequently, the conservation status of the frog in Ireland was judged ‘‘favorable’’ and should remain so for the foreseeable future.

SPATIALLY RESOLVED SPECTROSCOPY OF THE EXOPLANET HR 8799 c

HR 8799 is a multi-planet system detected in direct imaging, with three companions known so far. Here, we present spatially resolved Very Large Telescope/NACO 3.88-4.10 µm spectroscopy of the middle planet, HR 8799 c, which has an estimated mass of ~10 M Jup, temperature of ~1100 K, and projected separation of 38 AU. The spectrum shows some differences in the continuum from existing theoretical models, particularly longwards of 4 µm, implying that detailed cloud structure or non-equilibrium conditions may play an important role in the physics of young exoplanetary atmospheres.

Impact of different health systems on the burden of type 2 diabetes in two populations

Objectives: Health policy directs the management of patients with chronic disease in a country, but evaluating nationwide policies is difficult, not least because of the absence of suitable comparators. This paper examines the management of patients with type 2 diabetes in two demographically comparable populations with different health care systems to see if this represents a viable approach to evaluation.

Methods: A secondary analysis of centralized prescribing databases for 2010 was undertaken to compare the levels and costs of care of patients with type 2 diabetes in Northern Ireland’s National Health Service (NHS) (NI, n = 1.8 million) which has structured care, financial incentives related to diabetes care and an emphasis on generic prescribing, with that of the Republic of Ireland (ROI, n = 4.3 million) where management of diabetes care is guided solely by clinical and other guidelines.

Results: The prevalence of treated type 2 diabetes was 3.59% in NI and 3.09% in ROI, but there were similar and high levels of prescribing of secondary cardiovascular medications. Medication costs per person for anti-diabetic, anti-obesity and cardiovascular medication were 46% higher in ROI than NI, due to differences in levels of generic prescribing.

Conclusions: These different health care systems appear to be producing similar levels of care for patients with type 2 diabetes, although at different levels of cost. The findings question the need for financial incentives in NI and highlight the large cost savings potentially accruing from a greater shift to generic prescribing in ROI. Cross-country comparison, though not without difficulties, may prove a useful adjunct to within-country analysis of policy impact.

Environmental Challenges and Physiological Solutions: Comparative Energetic Daily Rhythms of Field Mice Populations from Different Ecosystems

Daily and seasonal variations in physiological characteristics of mammals can be considered adaptations to temporal habitat variables. Across different ecosystems, physiological adjustments are expected to be sensitive to different environmental signals such as changes in photoperiod, temperature or water and food availability; the relative importance of a particular signal being dependent on the ecosystem in question. Energy intake, oxygen consumption (VO) and body temperature (T) daily rhythms were compared between two populations of the broad-toothed field mouse Apodemus mystacinus, one from a Mediterranean and another from a sub-Alpine ecosystem. Mice were acclimated to short-day (SD) 'winter' and long-day (LD) 'summer' photoperiods under different levels of salinity simulating osmotic challenges. Mediterranean mice had higher VO values than sub-Alpine mice. In addition, mice exposed to short days had higher VO values when given water with a high salinity compared with mice exposed to long days. By comparison, across both populations, increasing salinity resulted in a decreased T in SD- but not in LD-mice. Thus, SD-mice may conserve energy by decreasing T during ('winter') conditions which are expected to be cool, whereas LD-mice might do the opposite and maintain a higher T during ('summer') conditions which are expected to be warm. LD-mice behaved to reduce energy expenditure, which might be considered a useful trait during 'summer' conditions. Overall, increasing salinity was a clear signal for Mediterranean-mice with resultant effects on VO and T daily rhythms but had less of an effect on sub-Alpine mice, which were more responsive to changes in photoperiod. Results provide an insight into how different populations respond physiologically to various environmental challenges.

Chlorophyll-a concentrations and macroinvertebrate declines coincide with the collapse of overwintering diving duck populations in a large eutrophic lake

1. Lough Neagh is one of the most important non-estuarine sites in the British Isles for overwinteringwildfowl. A change in the waterbird assemblage following the winter of 2000/2001 was drivenmainly by a rapid decline in the population of overwintering diving ducks. Sudden and discretechanges in resident as well as migratory waterbirds may suggest an intrinsic cause.
2. We compared the density and biomass of benthic macroinvertebrates, the food of overwinteringdiving ducks, in 2010 (following the diving duck population decline) with values from a baselinesurvey conducted in 1997/1998 (before the decline in diving ducks).
3. The mean total density of macroinvertebrates declined significantly by c. 65% from 15 300 m2in1997/1998 to 5136 m2in 2010. There was a concomitant c. 70% decline in mean macroinvertebratebiomass from 15 667 mg m2to 5112 mg m2. In terms of taxonomic composition, the relativecontribution of Tanypodinae, Glyptotendipes spp . and Tanytarsini declined, while the relativecontribution of Chironomus spp. increased.
4. We describe a shift in chlorophyll-a concentration, a proxy of phytoplankton biomass, in thelargest freshwater lake in the British Isles coincident with a significant reduction in macroinverte-brate density and biomass, with potential implications for ecosystem processes and ecologically andeconomically important consumer populations, including waterbirds and fishes

Extremely Complex Populations of Small RNAs in the Mouse Retina and RPE/Choroid

Purpose: MicroRNAs (miRNAs) are small non-coding RNAs of ~18-22 nucleotides in length that regulate gene expression. They are widely expressed in the retina, being both required for its normal development and perturbed in disease. The aim of this study was to apply new high-throughput sequencing techniques to more fully characterise the microRNAs and other small RNAs expressed in the retina and retinal pigment epithelium (RPE)/choroid of the mouse.

Methods: Retina and RPE/choroid were dissected from eyes of 3 month-old C57BL/6J mice. Small RNA libraries were prepared and deep sequencing performed on a Genome Analyzer (Illumina). Reads were annotated by alignment to miRBase, other non-coding RNA databases and the mouse genome.

Results: Annotation of 9 million reads to 320 microRNAs in retina and 340 in RPE/choroid provides the most comprehensive profiling of microRNAs to date. Two novel microRNAs were identified in retina. Members of the sensory organ specific miR-183,-182,-96 cluster were amongst the most highly expressed, retina-enriched microRNAs. Remarkably, microRNA 'isomiRs', which vary slightly in length and are differentially detected by Taqman RT-PCR assays, existed for all the microRNAs identified in both tissues. More variation occurred at the 3' ends, including non-templated additions of T and A. Drosha-independent mirtron microRNAs and other small RNAs derived from snoRNAs were also detected.

Conclusions: Deep sequencing has revealed the complexity of small RNA expression in the mouse retina and RPE/choroid. This knowledge will improve the design and interpretation of future functional studies of the role of microRNAs and other small RNAs in retinal disease.

Understanding macroalgal dispersal in a complex hydrodynamic environment: a combined population genetic and physical modelling approach

Gene flow in macroalgal populations can be strongly influenced by spore or gamete dispersal. This, in turn, is influenced by a convolution of the effects of current flow and specific plant reproductive strategies. Although several studies have demonstrated genetic variability in macroalgal populations over a wide range of spatial scales, the associated current data have generally been poorly resolved spatially and temporally. In this study, we used a combination of population genetic analyses and high-resolution hydrodynamic modelling to investigate potential connectivity between populations of the kelp Laminaria digitata in the Strangford Narrows, a narrow channel characterized by strong currents linking the large semi-enclosed sea lough, Strangford Lough, to the Irish Sea. Levels of genetic structuring based on six microsatellite markers were very low, indicating high levels of gene flow and a pattern of isolation-by-distance, where populations are more likely to exchange migrants with geographically proximal populations, but with occasional long-distance dispersal. This was confirmed by the particle tracking model, which showed that, while the majority of spores settle near the release site, there is potential for dispersal over several kilometres. This combined population genetic and modelling approach suggests that the complex hydrodynamic environment at the entrance to Strangford Lough can facilitate dispersal on a scale exceeding that proposed for L. digitata in particular, and the majority of macroalgae in general. The study demonstrates the potential of integrated physical–biological approaches for the prediction of ecological changes resulting from factors such as anthropogenically induced coastal zone changes.

Using ancestry-informative markers to identify fine structure across 15 populations of European origin

The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5%; we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia. 

FLT1 Genetic Variation Predisposes to Neovascular AMD in Ethnically Diverse Populations and Alters Systemic FLT1 Expression

Purpose: Current understanding of the genetic risk factors for age-related macular degeneration (AMD) is not sufficiently predictive of the clinical course. The VEGF pathway is a key therapeutic target for treatment of neovascular AMD; however, risk attributable to genetic variation within pathway genes is unclear. We sought to identify single nucleotide polymorphisms (SNPs) associated with AMD within the VEGF pathway.
Methods: Using a tagSNP, direct sequencing and meta-analysis approach within four ethnically diverse cohorts, we identified genetic risk present in FLT1, though not within other VEGF pathway genes KDR, VEGFA, or VASH1. We used ChIP and ELISA in functional analysis.
Results: The FLT1 SNPs rs9943922, rs9508034, rs2281827, rs7324510, and rs9513115 were significantly associated with increased risk of neovascular AMD. Each association was more significant after meta-analysis than in any one of the four cohorts. All associations were novel, within noncoding regions of FLT1 that do not tag for coding variants in linkage disequilibrium. Analysis of soluble FLT1 demonstrated higher expression in unaffected individuals homozygous for the FLT1 risk alleles rs9943922 (P = 0.0086) and rs7324510 (P = 0.0057). In silico analysis suggests that these variants change predicted splice sites and RNA secondary structure, and have been identified in other neovascular pathologies. These data were supported further by murine chromatin immunoprecipitation demonstrating that FLT1 is a target of Nr2e3, a nuclear receptor gene implicated in regulating an AMD pathway.
Conclusions: Although exact variant functions are not known, these data demonstrate relevancy across ethnically diverse genetic backgrounds within our study and, therefore, hold potential for global efficacy.