Combining global climate and regional landscape models to improve prediction of invasion risk

Aim
It is widely acknowledged that species distributions result from a variety of biotic and abiotic factors operating at different spatial scales. Here, we aimed to (1) determine the extent to which global climate niche models (CNMs) can be improved by the addition of fine-scale regional data; (2) examine climatic and environmental factors influencing the range of 15 invasive aquatic plant species; and (3) provide a case study for the use of such models in invasion management on an island.

Location
Global, with a case study of species invasions in Ireland.

Methods
Climate niche models of global extent (including climate only) and regional environmental niche models (with additional factors such as human influence, land use and soil characteristics) were generated using maxent for 15 invasive aquatic plants. The performance of these models within the invaded range of the study species in Ireland was assessed, and potential hotspots of invasion suitability were determined. Models were projected forward up to 2080 based on two climate scenarios.

Results
While climate variables are important in defining the global range of species, factors related to land use and nutrient level were of greater importance in regional projections. Global climatic models were significantly improved at the island scale by the addition of fine-scale environmental variables (area under the curve values increased by 0.18 and true skill statistic values by 0.36), and projected ranges decreased from an average of 86% to 36% of the island.

Main conclusions
Refining CNMs with regional data on land use, human influence and landscape may have a substantial impact on predictive capacity, providing greater value for prioritization of conservation management at subregional or local scales.

The Kepler-10 Planetary System Revisited by HARPS-N: A Hot Rocky World and a Solid Neptune-Mass Planet

Kepler-10b was the first rocky planet detected by the Kepler satellite and confirmed with radial velocity follow-up observations from Keck-HIRES. The mass of the planet was measured with a precision of around 30%, which was
insufficient to constrain models of its internal structure and composition in detail. In addition to Kepler-10b, a second planet transiting the same star with a period of 45 days was statistically validated, but the radial velocities were only
good enough to set an upper limit of 20 M⊕ for the mass of Kepler-10c. To improve the precision on the mass for planet b, the HARPS-N Collaboration decided to observe Kepler-10 intensively with the HARPS-N spectrograph
on the Telescopio Nazionale Galileo on La Palma. In total, 148 high-quality radial-velocity measurements were obtained over two observing seasons. These new data allow us to improve the precision of the mass determination for Kepler-10b to 15%. With a mass of 3.33 ± 0.49 M⊕ and an updated radius of 1.47+0.03 −0.02 R⊕, Kepler-10b has a density of 5.8 ± 0.8 g cm−3, very close to the value predicted by models with the same internal structure and composition as the Earth. We were also able to determine a mass for the 45-day period planet Kepler-10c, with an even better precision of 11%. With a mass of 17.2 ± 1.9 M⊕ and radius of 2.35+0.09 −0.04 R⊕, Kepler-10c has a density of 7.1 ± 1.0 g cm−3. Kepler-10c appears to be the first strong evidence of a class of more massive solid planets with longer orbital periods

Characterization of the Kepler-101 planetary system with HARPS-N. A hot super-Neptune with an Earth-sized low-mass companion

We characterize the planetary system Kepler-101 by performing a combined differential evolution Markov chain Monte Carlo analysisof Kepler data and forty radial velocities obtained with the HARPS-N spectrograph. This system was previously validated and iscomposed of a hot super-Neptune, Kepler-101b, and an Earth-sized planet, Kepler-101c. These two planets orbit the slightly evolvedand metal-rich G-type star in 3.49 and 6.03 days, respectively. With mass Mp = 51.1+5.1−4.7 M⊕, radius Rp = 5.77+0.85−0.79 R⊕, and density ρp = 1.45+0.83 −0.48 g cm−3, Kepler-101b is the first fully characterized super-Neptune, and its density suggests that heavy elements makeup a significant fraction of its interior; more than 60% of its total mass. Kepler-101c has a radius of 1.25+0.19−0.17 R⊕, which implies theabsence of any H/He envelope, but its mass could not be determined because of the relative faintness of the parent star for highly precise radial-velocity measurements (Kp = 13.8) and the limited number of radial velocities. The 1σ upper limit, Mp < 3.8 M⊕, excludes a pure iron composition with a probability of 68.3%. The architecture of the planetary system Kepler-101 − containing aclose-in giant planet and an outer Earth-sized planet with a period ratio slightly larger than the 3:2 resonance − is certainly of interest for scenarios of planet formation and evolution. This system does not follow the previously reported trend that the larger planet has the longer period in the majority of Kepler systems of planet pairs with at least one Neptune-sized or larger planet.

On Cherry-Picking ... or Trying to Have One’s Cake and Eating It: past principles and practice in the pursuit of an alternative to [full] EU membership

With the United Kingdom’s continued membership of the EU being increasingly questioned and the Prime Minister, David Cameron, committed to 're-negotiate’ the terms of membership, consideration is being given to what forms alternatives to [full] membership may take. While much current discussion focuses on the advantages and disadvantages of particular existing arrangements (e.g. European Economic Area, Swiss bilateralism), this paper examines the broader principles and practices that have to date underpinned – and undermined – EU’s attempts to develop alternatives to [full] EU membership. Drawing on an analysis of the evolution of association as an alternative to membership, the paper assesses the principled, practical and political limitations the EU faces – and imposes on itself – in offering an acceptable balance of rights and obligations to states not wishing to assume the mantle of full membership. In its assessment the paper considers various proposed models of affiliate and associate membership. It also situates consideration of the UK case in the broader context of the EU’s relations with other European non-member states for which membership may not be achievable and for which alternatives to membership (e.g. a form of privileged partnership) have been proposed. In doing so, the paper reflects on the precedent-setting consequences of any arrangement that the EU might reach with any state re-negotiating membership or withdrawing.

A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar

Pattern and process are inextricably linked in biogeographic analyses, though we can observe pattern, we must infer process. Inferences of process are often based on ad hoc comparisons using a single spatial predictor. Here, we present an alternative approach that uses mixed-spatial models to measure the predictive potential of combinations of hypotheses. Biodiversity patterns are estimated from 8,362 occurrence records from 745 species of Malagasy amphibians and reptiles. By incorporating 18 spatially explicit predictions of 12 major biogeographic hypotheses, we show that mixed models greatly improve our ability to explain the observed biodiversity patterns. We conclude that patterns are influenced by a combination of diversification processes rather than by a single predominant mechanism. A ‘one-size-fits-all’ model does not exist. By developing a novel method for examining and synthesizing spatial parameters such as species richness, endemism and community similarity, we demonstrate the potential of these analyses for understanding the diversification history of Madagascar’s biota.

Étude des impacts écologiques du dynamisme spatio-temporel des habitats naturels sur la faune menacée du Complexe Zones Humides Mahavavy-Kinkony, Madagascar.

This study of the Mahavavy-Kinkony Wetland Complex (MKWC) assesses the impacts of habitat change on the resident globally threatened fauna. Located in Boeny Region, northwest Madagascar, the Complex encompasses a range of habitats including freshwater lakes, rivers, marshes, mangrove forests, and deciduous forest. Spatial modelling and analysis tools were used to (i) identify the important habitats for selected, threatened fauna, (ii) assess their change from 1950 to 2005, (iii) detect the causes of change, (iv) simulate changes to 2050 and (v) evaluate the impacts of change. The approach for prioritising potential habitats for threatened species used ecological science techniques assisted by the decision support software Marxan. Nineteen species were analysed: nine birds, three primates, three fish, three bats and one reptile. Based on knowledge of local land use, supervised classification of Landsat images from 2005 was used to classify the land use of the Complex. Simulations of land use change to 2050 were carried out based on the Land Change Modeler module in Idrisi Andes with the neural network algorithm. Changes in land use at site level have occurred over time but they are not significant. However, reductions in the extent of reed marshes at Lake Kinkony and forests at Tsiombikibo and Marofandroboka directly threaten the species that depend on these habitats. Long term change monitoring is recommended for the Mahavavy Delta, in order to evaluate the predictions through time. The future change of Andohaomby forest is of great concern and conservation actions are recommended as a high priority. Abnormal physicochemical properties were detected in lake Kinkony due to erosion of the four watersheds to the south, therefore an anti-erosion management plan is required for these watersheds. Among the species of global conservation concern, Sakalava rail (Amaurornis olivieri), Crowned sifaka (Propithecus coronatus) and dambabe (Paretroplus dambabe) are estimated the most affected, but at the site level Decken’s sifaka (Propithecus deckeni), kotsovato (Paretroplus kieneri) and Madagascan big-headed turtle (Erymnochelys madagascariensis) are also threatened. Local enforcement of national legislation on hunting means that MKWC is among the sites where the flying fox (Pteropus rufus) and Madagascan rousette (Rousettus madagascariensis) are well protected. Ecological restoration, ecological research and actions to reduce anthropogenic pressures are recommended.

Defining the role of common variation in the genomic and biological architecture of adult human height

Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated 1/42,000, 1/43,700 and 1/49,500 SNPs explained 1/421%, 1/424% and 1/429% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/I 2-catenin and chondroitin sulfate-related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.

Molecular surveillance for carbapenemase genes in carbapenem-resistant Pseudomonas aeruginosa in Australian patients with cystic fibrosis.

Summary: The aim of this study was to assess the prevalence of acquired carbapenemase genes amongst carbapenem non-susceptible Pseudomonas aeruginosa isolates in Australian patients with cystic fibrosis (CF). Cross-sectional molecular surveillance for acquired carbapenemase genes was performed on CF P. aeruginosa isolates from two isolate banks comprising: (i) 662 carbapenem resistant P. aeruginosa isolates from 227 patients attending 10 geographically diverse Australian CF centres (2007-2009), and (ii) 519 P. aeruginosa isolates from a cohort of 173 adult patients attending one Queensland CF clinic in 2011. All 1189 P. aeruginosa isolates were tested by polymerase chain reaction (PCR) protocols targeting ten common carbapenemase genes, as well the Class 1 integron intI1 gene and the aadB aminoglycoside resistance gene. No carbapenemase genes were identified among all isolates tested. The intI1 and aadB genes were frequently detected and were significantly associated with the AUST-02 strain (OR 24.6, 95% CI 9.3-65.6; p < 0.0001) predominantly from Queensland patients. Despite the high prevalence of carbapenem resistance in P. aeruginosa in Australian patients with CF, no acquired carbapenemase genes were detected in the study, suggesting chromosomal mutations remain the key resistance mechanism in CF isolates. Systematic surveillance for carbapenemase-producing P. aeruginosa in CF by molecular surveillance is ongoing.

New genetic loci link adipose and insulin biology to body fat distribution

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

Genetic studies of body mass index yield new insights for obesity biology

Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10(-8)), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ∼2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.

Limitations of Dental Panoramic Tomography in the anterior mandible

Dental Panoramic Tomography (DPT) is a widely used and valuable examination in dentistry. One area prone to artefacts and therefore misinterpretation is the anterior region of the mandible. This case study discusses a periapical radiolucency related to lower anterior teeth that is discovered to be a radiographic artefact. Possible causes of the artefact include a pronounced depression in the mental region of the mandible or superimposition of intervertebral spaces. Additional limitations of the DPT image include superimposition of radio-opaque structures, reduced image detail compared to intra-oral views and uneven magnification. These problems often make the DPT inappropriate for imaging the anterior mandible.

CLINICAL RELEVANCE: Panoramic radiography is often unsuitable for radiographic examination of the anterior mandible.

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.

The Well-Aligned Orbit of Wasp-84b: Evidence for Disk Migration of a Hot Jupiter

We report the sky-projected orbital obliquity (spin–orbit angle) of WASP-84 b, a 0.69MJup planet in an 8.52 day orbit around a G9V/K0V star, to be λ = −0.3 ± 1.7°. We obtain a true obliquity of ψ = 17.3 ± 7.7° from a measurement of the inclination of the stellar spin axis with respect to the sky plane. Due to the young age and the weak tidal forcing of the system, we suggest that the orbit of WASP-84b is unlikely to have both realigned and circularized from the misaligned and/or eccentric orbit likely to have arisen from high-eccentricity migration. Therefore we conclude that the planet probably migrated via interaction with the protoplanetary disk. This would make it the first “hot Jupiter” (P d < 10 ) to have been shown to have migrated via this pathway. Further, we argue that the distribution of obliquities for planets orbiting cool stars (Teff < 6250 K) suggests that high-eccentricity migration is an important pathway for the formation of short-orbit, giant planets.

FKBPL: a marker of good prognosis in breast cancer

FK506-binding protein-like (FKBPL) has established roles as an anti-tumor protein, with a therapeutic peptide based on this protein, ALM201, shortly entering phase I/II clinical trials. Here, we evaluated FKBPL's prognostic ability in primary breast cancer tissue, represented on tissue microarrays (TMA) from 3277 women recruited into five independent retrospective studies, using immunohistochemistry (IHC). In a meta-analysis, FKBPL levels were a significant predictor of BCSS; low FKBPL levels indicated poorer breast cancer specific survival (BCSS) (hazard ratio (HR) = 1.30, 95% confidence interval (CI) 1.14-1.49, p < 0.001). The prognostic impact of FKBPL remained significant after adjusting for other known prognostic factors (HR = 1.25, 95% CI 1.07-1.45, p = 0.004). For the sub-groups of 2365 estrogen receptor (ER) positive patients and 1649 tamoxifen treated patients, FKBPL was significantly associated with BCSS (HR = 1.34, 95% CI 1.13-1.58, p < 0.001, and HR = 1.25, 95% CI 1.04-1.49, p = 0.02, respectively). A univariate analysis revealed that FKBPL was also a significant predictor of relapse free interval (RFI) within the ER positive patient group, but it was only borderline significant within the smaller tamoxifen treated patient group (HR = 1.32 95% CI 1.05-1.65, p = 0.02 and HR = 1.23 95% CI 0.99-1.54, p = 0.06, respectively). The data suggests a role for FKBPL as a prognostic factor for BCSS, with the potential to be routinely evaluated within the clinic.

Expertly validated models and phylogenetically-controlled analysis suggests responses to climate change are related to species traits in the Order Lagomorpha

Climate change during the last five decades has impacted significantly on natural ecosystems and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs) have been used widely to project changes in species’ bioclimatic envelopes under future climate scenarios. Here, we aimed to advance this technique by assessing future changes in the bioclimatic envelopes of an entire mammalian order, the Lagomorpha, using a novel framework for model validation based jointly on subjective expert evaluation and objective model evaluation statistics. SDMs were built using climatic, topographical and habitat variables for all 87 lagomorph species under past and current climate scenarios. Expert evaluation and Kappa values were used to validate past and current models and only those deemed ‘modellable’ within our framework were projected under future climate scenarios (58 species). Phylogenetically-controlled regressions were used to test whether species traits correlated with predicted responses to climate change. Climate change is likely to impact more than two-thirds of lagomorph species, with leporids (rabbits, hares and jackrabbits) likely to undertake poleward shifts with little overall change in range extent, whilst pikas are likely to show extreme shifts to higher altitudes associated with marked range declines, including the likely extinction of Kozlov’s Pika (Ochotona koslowi). Smaller-bodied species were more likely to exhibit range contractions and elevational increases, but showing little poleward movement, and fecund species were more likely to shift latitudinally and elevationally. Our results suggest that species traits may be important indicators of future climate change and we believe multi-species approaches, as demonstrated here, are likely to lead to more effective mitigation measures and conservation management. We strongly advocate studies minimising data gaps in our knowledge of the Order, specifically collecting more specimens for biodiversity archives and targeting data deficient geographic regions.