You are not always what we think you eat: selective assimilation across multiple whole‐stream isotopic tracer studies - W. K. Dodds; S. M. Collins; S. K. Hamilton; J. L. Tank; S. Johnson; J. R. Webster; K. S. Simon; M. R. Whiles; H. M. Rantala; W. H. McDowell; S. D. Peterson; T. Riis; et al. (Ecology, 2014)
Analyses of 21 15 N stable isotope tracer experiments, designed to examine food web dynamics in streams around the world, indicated that the isotopic composition of food resources assimilated by primary consumers (mostly invertebrates) poorly reflected the presumed food sources. Modeling indicated that consumers assimilated only 33–50% of the N available in sampled food sources such as decomposing leaves, epilithon, and fine particulate detritus over feeding periods of weeks or more. Thus, common methods of sampling food sources consumed by animals in streams do not sufficiently reflect the pool of N they assimilate. Isotope tracer studies, combined with modeling and food separation techniques, can improve estimation of N pools in food sources that are assimilated by consumers. Food web studies that use putative food samples composed of actively cycling (more readily assimilable) and refractory (less assimilable) N fractions may draw erroneous conclusions about diets, N turnover, and trophic linkages of consumers. By extension, food web studies using stoichiometric or natural abundance approaches that rely on an accurate description of food‐source composition could result in errors when an actively cycling pool that is only a fraction of the N pool in sampled food resources is not accounted for.

Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.) - Raymond Campbell; Simon D. A. Pont; Jenny A. Morris; Gaynor McKenzie; Sanjeev Kumar Sharma; Pete E. Hedley; Gavin Ramsay; Glenn J. Bryan; Mark A. Taylor (Theoretical and Applied Genetics, 2014)

10Be, 18O and radiogenic isotopic constraints on the origin of adakitic signatures: a case study from Solander and Little Solander Islands, New Zealand - Fiona V. Foley; Simon Turner; Tracy Rushmer; John T. Caulfield; Nathan R. Daczko; Paul Bierman; Matthew Robertson; Craig D. Barrie; Adrian J. Boyce (Contributions to Mineralogy and Petrology, 2014)

Persistence and stability of Eastern Afromontane forests: evidence from brevicipitid frogs - Simon P. Loader; F. Sara Ceccarelli; Michele Menegon; Kim M. Howell; Roman Kassahun; Abebe A. Mengistu; Samy A. Saber; Fikirte Gebresenbet; Rafael de Sá; Tim R. B. Davenport; Joanna G. Larson; Hendrik Müller; et al. (Journal of Biogeography, 2014)
Aim The persistence and stability of habitats through time are considered predictors of high levels of biodiversity in some environments. Long‐term habitat persistence and stability may explain the species‐rich, endemic forest fauna and flora of the Eastern Afromontane Biodiversity Region ( EABR ). Using complementary phylogenetic and biogeographical approaches, we examine evolutionary patterns in EABR brevicipitid frogs. Using these data, we test whether brevicipitid history reflects patterns of long‐term forest persistence and/or stability across the EABR . Location East Africa. Methods A dated phylogeny for brevicipitids was constructed using two nuclear and three mitochondrial markers. Alternative diversification models were used to determine signal for constant or varying net diversification rates. Using our dated tree, we identified areas of high phylogenetic diversity ( PD ), and inferred ancestral areas using likelihood and Bayesian approaches. Results Brevicipitids have a long history, with generic diversification among extant lineages pre‐dating the Oligocene (> 33 Ma). Ancestral‐area reconstructions indicate the presence of brevicipitids in the EABR since the Oligocene, and support a scenario of palaeoendemics surviving in EABR refugia. Ancestral‐area reconstructions indicate that the central Eastern Arc Mountains ( EAM ) formed the initial centre of diversification of forest brevicipitids. Measures of PD show that diversity varies across the EABR but is highest in the EAM . Constant net diversification rate in brevicipitids is a significantly better fit than alternative, rate‐variable models. Main conclusions The degree of persistence of forest habitats appears to be a contributing factor to the varying levels of diversity across the EABR in brevicipitids (and other organisms). In contrast to the Southern Highlands and Ethiopian Bale Mountains, the EAM stands out as an area that enabled the constant accumulation of brevicipitid species over a long period of time.

Climate‐driven spatial mismatches between British orchards and their pollinators: increased risks of pollination deficits - Chiara Polce; Michael P Garratt; Mette Termansen; Julian Ramirez‐Villegas; Andrew J Challinor; Martin G Lappage; Nigel D Boatman; Andrew Crowe; Ayenew Melese Endalew; Simon G Potts; Kate E Somerwill; Jacobus C Biesmeijer (Global Change Biology, 2014)
Understanding how climate change can affect crop‐pollinator systems helps predict potential geographical mismatches between a crop and its pollinators, and therefore identify areas vulnerable to loss of pollination services. We examined the distribution of orchard species (apples, pears, plums and other top fruits) and their pollinators in Great Britain, for present and future climatic conditions projected for 2050 under the SRES A1B Emissions Scenario. We used a relative index of pollinator availability as a proxy for pollination service. At present, there is a large spatial overlap between orchards and their pollinators, but predictions for 2050 revealed that the most suitable areas for orchards corresponded to low pollinator availability. However, we found that pollinator availability may persist in areas currently used for fruit production, which are predicted to provide suboptimal environmental suitability for orchard species in the future. Our results may be used to identify mitigation options to safeguard orchard production against the risk of pollination failure in Great Britain over the next 50 years; for instance, choosing fruit tree varieties that are adapted to future climatic conditions, or boosting wild pollinators through improving landscape resources. Our approach can be readily applied to other regions and crop systems, and expanded to include different climatic scenarios.

An assessment of chemical contaminants in sediments from the St. Thomas East End Reserves, St. Thomas, USVI - Anthony S. Pait; S. Ian Hartwell; Andrew L. Mason; Robert A. Warner; Christopher F. G. Jeffrey; Anne M. Hoffman; Dennis A. Apeti; Simon J. Pittman (Environmental Monitoring and Assessment, 2014)

Validated age and growth estimates for Carcharhinus obscurus in the northwestern Atlantic Ocean, with pre- and post management growth comparisons - Lisa J. Natanson; Brian J. Gervelis; Megan V. Winton; Li Ling Hamady; Simon J. B. Gulak; John K. Carlson (Environmental Biology of Fishes, 2014)

The Role of Nitrogen Deposition in Widespread Plant Community Change Across Semi-natural Habitats - Chris D. Field; Nancy B. Dise; Richard J. Payne; Andrea J. Britton; Bridget A. Emmett; Rachel C. Helliwell; Steve Hughes; Laurence Jones; Steven Lees; Jonathan R. Leake; Ian D. Leith; Gareth K. Phoenix; et al. (Ecosystems, 2014)

A new index for variations in the position of the South Pacific convergence zone 1910/11–2011/2012 - M. J. Salinger; Simon McGree; Florent Beucher; Scott B. Power; François Delage (Climate Dynamics, 2014)

Bubble development in explosive silicic eruptions: insights from pyroclast vesicularity textures from Raoul volcano (Kermadec arc) - Melissa D. Rotella; Colin J. N. Wilson; Simon J. Barker; Katharine V. Cashman; Bruce F. Houghton; Ian C. Wright (Bulletin of Volcanology, 2014)

Aborigine‐managed forest, savanna and grassland: biome switching in montane eastern Australia - Don W. Butler; Roderick J. Fensham; Brett P. Murphy; Simon G. Haberle; Sarah J. Bury; David M. J. S. Bowman (Journal of Biogeography, 2014)
Aim To assess hypotheses about the role of anthropogenic fire in the maintenance and origin of a fine‐scale vegetation mosaic of rain forest, eucalypt savanna and grassland. Location Bunya Mountains, subtropical eastern Australia. Methods A time series of vegetation maps was compiled from historical and recent aerial photography and field surveys. Geospatial models were constructed of environmental domains for rain forest, savanna and grassland, and for areas of biome change. Grassland soils were analysed for carbon isotope ratios (δ 13 C), and radiocarbon ( 14 C) dates were acquired for bulk samples from a range of depths. Results Analysis revealed weak associations between topography and the distribution of rain forest, savanna and grassland, and their patterns of recent change. Grassland occupied an environmental domain intermediate between rain forest and savanna and was more than four times as likely to occur within a matrix of rain forest rather than savanna. There was a large proportional reduction in the area of both grassland (−35%) and savanna (−19%) between 1961 and 2006 because of the expansion of rain forest. However, the greater initial extent of savanna meant that the areal loss of savanna was an order of magnitude greater than for grassland (1433 vs. 146 ha). There was no evidence of abrupt changes in δ 13 C in grassland soil profiles, indicating stability of the vegetation over the last 2000 years. Main conclusions There is no simple gradient in ‘tree suitability’ from rain forest, through savanna, to treeless grassland on the Bunya Mountains. A general absence of fire since the 19th century has greatly reduced the extent of grassy savanna and grassland formations, to the advantage of rain forest. These results support the hypothesis that the vegetation mosaic on the Bunya Mountains is a cultural artefact and testament to millennia of skilful and persistent burning. We could not conclusively reject the hypothesis that the grasslands are Pleistocene relicts that have declined throughout the Holocene; nonetheless, an explanation more consistent with the evidence overall is that the grasslands must have had periods of expansion during the Holocene, probably as a consequence of severe fires that have destroyed patches of rain forest.

Markedly divergent estimates of A mazon forest carbon density from ground plots and satellites - Edward T. A. Mitchard; Ted R. Feldpausch; Roel J. W. Brienen; Gabriela Lopez‐Gonzalez; Abel Monteagudo; Timothy R. Baker; Simon L. Lewis; Jon Lloyd; Carlos A. Quesada; Manuel Gloor; Hans ter Steege; Patrick Meir; et al. (Global Ecology and Biogeography, 2014)
Aim The accurate mapping of forest carbon stocks is essential for understanding the global carbon cycle, for assessing emissions from deforestation, and for rational land‐use planning. Remote sensing ( RS ) is currently the key tool for this purpose, but RS does not estimate vegetation biomass directly, and thus may miss significant spatial variations in forest structure. We test the stated accuracy of pantropical carbon maps using a large independent field dataset. Location Tropical forests of the A mazon basin. The permanent archive of the field plot data can be accessed at: http://dx.doi.org/10.5521/FORESTPLOTS.NET/2014_1 Methods Two recent pantropical RS maps of vegetation carbon are compared to a unique ground‐plot dataset, involving tree measurements in 413 large inventory plots located in nine countries. The RS maps were compared directly to field plots, and kriging of the field data was used to allow area‐based comparisons. Results The two RS carbon maps fail to capture the main gradient in Amazon forest carbon detected using 413 ground plots, from the densely wooded tall forests of the north‐east, to the light‐wooded, shorter forests of the south‐west. The differences between plots and RS maps far exceed the uncertainties given in these studies, with whole regions over‐ or under‐estimated by > 25%, whereas regional uncertainties for the maps were reported to be Main conclusions Pantropical biomass maps are widely used by governments and by projects aiming to reduce deforestation using carbon offsets, but may have significant regional biases. Carbon‐mapping techniques must be revised to account for the known ecological variation in tree wood density and allometry to create maps suitable for carbon accounting. The use of single relationships between tree canopy height and above‐ground biomass inevitably yields large, spatially correlated errors. This presents a significant challenge to both the forest conservation and remote sensing communities, because neither wood density nor species assemblages can be reliably mapped from space.

Heather Moorland Vegetation and Air Pollution: A Comparison and Synthesis of Three National Gradient Studies - Richard J. Payne; Simon J. M. Caporn; Christopher D. Field; Jacky A. Carroll; Jill L. Edmondson; Andrea Britton; Nancy B. Dise (Water, Air, & Soil Pollution, 2014)

Science into policy; improving uptake and adoption of research: outcomes and conclusions - Paul De Barro; Stephen Goldson; Detlef Bartsch; Mikael Hirsch; Martyn Jeggo; John W. Lowenthal; Philip Macdonald; Ryan R. J. McAllister; Rod McCrea; Fiona McFarlane; Cathy Robinson; Kim Ritman; et al. (Journal of Consumer Protection and Food Safety, 2014)

The eruptive history and chemical stratigraphy of a post-caldera, steady-state volcano: Yasur, Vanuatu - Chris W. Firth; Heather K. Handley; Shane J. Cronin; Simon P. Turner (Bulletin of Volcanology, 2014)

Characterizing the socially transmitted foraging tactic “sponging” by bottlenose dolphins ( Tursiops sp.) in the western gulf of Shark Bay, Western Australia - Anna M. Kopps; Michael Krützen; Simon J. Allen; Kathrin Bacher; William B. Sherwin (Marine Mammal Science, 2014)
Individual foraging tactics are widespread in animals and have ecological and evolutionary implications. Indo‐Pacific bottlenose dolphins ( Tursiops sp.) in Shark Bay, Western Australia, exhibit a foraging tactic involving tool use, called “sponging.” Sponging is vertically, socially transmitted through the matriline and, to date, has been described in detail in the eastern gulf of Shark Bay ( ESB ). Here, we characterize sponging in the western gulf of Shark Bay ( WSB ), in which a different matriline engages in the behavior. We identified 40 individual “spongers” in 9 mo of boat‐based surveys over three field seasons. As is the case in ESB , the majority of WSB spongers was female and engaged in sponging in deep channel habitats. In contrast to ESB , however, there was no difference in the number of associates between spongers and nonspongers in WSB , and activity budgets differed between spongers and deep‐water nonspongers; spongers foraged more frequently and rested less than nonspongers. Group sizes in deep channel habitat, where sponging was prevalent, were typically larger than those in shallow habitat, except for foraging, perhaps indicative of higher predator abundance and/or scattered prey distribution in deep‐water habitat. This research improves our understanding of within‐population foraging variations in bottlenose dolphins.

Testate amoebae as a proxy for reconstructing Holocene water table dynamics in southern Patagonian peat bogs - SIMON VAN BELLEN; DMITRI MAUQUOY; RICHARD J. PAYNE; THOMAS P. ROLAND; TIM J. DALEY; PAUL D. M. HUGHES; NEIL J. LOADER; F. ALAYNE STREET‐PERROTT; EMMA M. RICE; VERÓNICA A. PANCOTTO (Journal of Quaternary Science, 2014)
Testate amoebae are abundant and diverse in Sphagnum peat bogs and have been used extensively as indicators of past water table depths. Although these unicellular protists are widely dispersed with globally similar hydrological preferences, regional variations in communities demand region‐specific transfer functions. Here we present the first transfer function for southern Patagonian bogs, based on 154 surface samples obtained from transects in five bogs sampled in 2012 and 2013. Significant variance was explained by pH, electrical conductivity and, in particular, water table depth. Transfer functions for water table were constructed using weighted averaging and evaluated by cross‐validation and independent test sets. The optimal transfer function has predictive ability, but relatively high prediction errors given the wide range in sampled water tables. The use of independent test sets, as well as cross‐validation, allows a more rigorous assessment of model performance than most previous studies. For a subset of locations we compare surface and subsurface samples to demonstrate significant differences in community composition, possibly due to vertical zonation. Our results provide the first quantification of hydrological optima and tolerances for several rare species, which may include Southern Hemisphere endemics and pave the way for palaeohydrological reconstructions in southern Patagonian bogs.

Transcriptional profiling of G ram‐positive A rthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds - Tanja R. Scheublin; Simon Deusch; Silvia K. Moreno‐Forero; Jochen A. Müller; Jan Roelof van der Meer; Johan H. J. Leveau (Environmental Microbiology, 2014)
Summary A rthrobacter chlorophenolicus A 6 is a G ram‐positive, 4‐chlorophenol‐degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome‐wide expression profile of A . chlorophenolicus on leaves of common bean ( P haseolus vulgaris ) compared with growth on agar surfaces. In phyllosphere‐grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf‐induced expression of a subset of the so‐called cph genes for the degradation of 4‐chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3‐oxoadipate, and was shown to be induced not only by 4‐chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P . vulgaris by gas chromatography‐mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere‐based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation.

The Wadi Zaghra metasediments of Sinai, Egypt: new constraints on the late Cryogenian–Ediacaran tectonic evolution of the northernmost Arabian–Nubian Shield - Arild Andresen; Mahrous M. Abu El-Enen; Robert J. Stern; Simon A. Wilde; Kamal A. Ali (International Geology Review, 2014)

Cerebellar Contributions to Verbal Working Memory - Simon P. Tomlinson; Nick J. Davis; Helen M. Morgan; R. Martyn Bracewell (The Cerebellum, 2014)

Testing Biodegradable Seedling Containers as an Alternative for Polythene Tubes in Tropical Small-Scale Tree Nurseries - Jonathan K. Muriuki; Anne W. Kuria; Catherine W. Muthuri; Athanase Mukuralinda; Anthony J. Simons; Ramni H. Jamnadass (Small-scale Forestry, 2014)

The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data - Paul M. Thompson; Jason L. Stein; Sarah E. Medland; Derrek P. Hibar; Alejandro Arias Vasquez; Miguel E. Renteria; Roberto Toro; Neda Jahanshad; Gunter Schumann; Barbara Franke; Margaret J. Wright; Nicholas G. Martin; et al. (Brain Imaging and Behavior, 2014)

Development of anonymous nuclear markers from Illumina paired-end data for Seychelles caecilian amphibians (Gymnophiona: Indotyphlidae) - Claire J. Lewis; Simon T. Maddock; Julia J. Day; Ronald A. Nussbaum; Charles Morel; Mark Wilkinson; Peter G. Foster; David J. Gower (Conservation Genetics Resources, 2014)
Anonymous nuclear markers were developed for Seychelles caecilian amphibians. Using a previously published bioinformatics pipeline (developed for Roche 454 data), 36 candidate anonymous nuclear loci (ANL) of at least 180 bp length were identified from Illumina MiSeq next generation sequencing data for five Seychelles species. We designed primer pairs for the 36 candidate ANL and tested these by PCR and Sanger sequencing. Seven ANL amplified and sequenced well for at least five of the six nominal Seychelles caecilian species (in three genera), and represent potentially useful markers for systematics and conservation.

Genome-wide association study of subtype-specific epithelial ovarian cancer risk alleles using pooled DNA - Madalene A. Earp; Linda E. Kelemen; Anthony M. Magliocco; Kenneth D. Swenerton; Georgia Chenevix-Trench; Yi Lu; Alexander Hein; Arif B. Ekici; Matthias W. Beckmann; Peter A. Fasching; Diether Lambrechts; Evelyn Despierre; et al. (Human Genetics, 2014)

Combined Computational and Experimental Approach to Improve the Assessment of Mitral Regurgitation by Echocardiography - Simon J. Sonntag; Wei Li; Michael Becker; Wiebke Kaestner; Martin R. Büsen; Nikolaus Marx; Dorit Merhof; Ulrich Steinseifer (Annals of Biomedical Engineering, 2014)

Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline - Thomas M. Vignaud; Jeffrey A. Maynard; Raphael Leblois; Mark G. Meekan; Ricardo Vázquez‐Juárez; Dení Ramírez‐Macías; Simon J. Pierce; David Rowat; Michael L. Berumen; Champak Beeravolu; Sandra Baksay; Serge Planes (Molecular Ecology, 2014)
This study presents genetic evidence that whale sharks, Rhincodon typus , are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks from the Gulf of Mexico with sharks from the Indo‐Pacific. If mixing occurs between the Indian and Atlantic Oceans, it is not sufficient to counter genetic drift. This suggests whale sharks are not all part of a single global metapopulation. The significant population expansion we found was indicated by both microsatellite and mitochondrial DNA . The expansion may have happened during the Holocene, when tropical species could expand their range due to sea‐level rise, eliminating dispersal barriers and increasing plankton productivity. However, the historic trend of population increase may have reversed recently. Declines in genetic diversity are found for 6 consecutive years at Ningaloo Reef in Australia. The declines in genetic diversity being seen now in Australia may be due to commercial‐scale harvesting of whale sharks and collision with boats in past decades in other countries in the Indo‐Pacific. The study findings have implications for models of population connectivity for whale sharks and advocate for continued focus on effective protection of the world's largest fish at multiple spatial scales.

Reproductive effort accelerates actuarial senescence in wild birds: an experimental study - Jelle J. Boonekamp; Martijn Salomons; Sandra Bouwhuis; Cor Dijkstra; Simon Verhulst (Ecology Letters, 2014)
Optimality theories of ageing predict that the balance between reproductive effort and somatic maintenance determines the rate of ageing. Laboratory studies find that increased reproductive effort shortens lifespan, but through increased short‐term mortality rather than ageing. In contrast, high fecundity in early life is associated with accelerated senescence in free‐living vertebrates, but these studies are non‐experimental. We performed lifelong brood size manipulation in free‐living jackdaws. Actuarial senescence – the increase in mortality rate with age – was threefold higher in birds rearing enlarged‐ compared to reduced broods, confirming a key prediction of the optimality theory of ageing. Our findings contrast with the results of single‐year brood size manipulation studies carried out in many species, in which there was no overall discernible manipulation effect on mortality. We suggest that our and previous findings are in agreement with predictions based on the reliability theory of ageing and propose further tests of this proposition.

Fast demographic traits promote high diversification rates of Amazonian trees - Timothy R. Baker; R. Toby Pennington; Susana Magallon; Emanuel Gloor; William F. Laurance; Miguel Alexiades; Esteban Alvarez; Alejandro Araujo; Eric J. M. M. Arets; Gerardo Aymard; Atila Alves de Oliveira; Iêda Amaral; et al. (Ecology Letters, 2014)
The Amazon rain forest sustains the world's highest tree diversity, but it remains unclear why some clades of trees are hyperdiverse, whereas others are not. Using dated phylogenies, estimates of current species richness and trait and demographic data from a large network of forest plots, we show that fast demographic traits – short turnover times – are associated with high diversification rates across 51 clades of canopy trees. This relationship is robust to assuming that diversification rates are either constant or decline over time, and occurs in a wide range of Neotropical tree lineages. This finding reveals the crucial role of intrinsic, ecological variation among clades for understanding the origin of the remarkable diversity of Amazonian trees and forests.

Population trajectories for the Antarctic bivalve Laternula elliptica: identifying demographic bottlenecks in differing environmental futures - Claire I. Guy; Vonda J. Cummings; Andrew M. Lohrer; Sofia Gamito; Simon F. Thrush (Polar Biology, 2014)

The order effect of combined endurance and strength loadings on force and hormone responses: effects of prolonged training - Moritz Schumann; Simon Walker; Mikel Izquierdo; Robert U. Newton; William J. Kraemer; Keijo Häkkinen (European Journal of Applied Physiology, 2014)

A Fast, Accurate, and Reliable Reconstruction Method of the Lumbar Spine Vertebrae Using Positional MRI - Craig J. Simons; Loren Cobb; Bradley S. Davidson (Annals of Biomedical Engineering, 2014)

Oligoamides of 2-amino-5-alkylthiazole 4-carboxylic acids: anti-trypanosomal compounds - Stuart Lang; Abedawn I. Khalaf; David Breen; Judith K. Huggan; Carol J. Clements; Simon P. MacKay; Colin J. Suckling (Medicinal Chemistry Research, 2014)

Modeling regional impacts of climate teleconnections using functional data analysis - Simon J. Bonner; Nathaniel K. Newlands; Nancy E. Heckman (Environmental and Ecological Statistics, 2014)

Aberrant connectivity of areas for decoding degraded speech in patients with auditory verbal hallucinations - Mareike Clos; Kelly M. J. Diederen; Anne Lotte Meijering; Iris E. Sommer; Simon B. Eickhoff (Brain Structure and Function, 2014)

Isolation and characterization of fifteen microsatellite loci in Leopard grouper (Mycteroperca rosacea) via 454 pyrosequencing - Alexis M. Jackson; Adrian Munguía-Vega; Avian S. Lain; Simon A. Stokes; Aneese J. Williams; Giacomo Bernardi (Conservation Genetics Resources, 2014)

Intent Recognition in a Powered Lower Limb Prosthesis Using Time History Information - Aaron J. Young; Ann M. Simon; Nicholas P. Fey; Levi J. Hargrove (Annals of Biomedical Engineering, 2014)

The legacy of mid‐Holocene fire on a Tasmanian montane landscape - Michael‐Shawn Fletcher; Brent B. Wolfe; Cathy Whitlock; David P. Pompeani; Hendrik Heijnis; Simon G. Haberle; Patricia S. Gadd; David M. J. S. Bowman (Journal of Biogeography, 2014)
Aim To assess the long‐term impacts of landscape fire on a mosaic of pyrophobic and pyrogenic woody montane vegetation. Location South‐west T asmania, A ustralia. Methods We undertook a high‐resolution multiproxy palaeoecological analysis of sediments deposited in L ake O sborne ( H artz M ountains N ational P ark, southern T asmania), employing analyses of pollen, macroscopic and microscopic charcoal, organic and inorganic geochemistry and magnetic susceptibility. Results Sequential fires within the study catchment over the past 6500 years have resulted in the reduction of pyrophobic rain forest taxa and the establishment of pyrogenic E ucalyptus ‐dominated vegetation. The vegetation change was accompanied by soil erosion and nutrient losses. The rate of post‐fire recovery of widespread rain forest taxa ( N othofagus cunninghamii and E ucryphia spp.) conforms to ecological models, as does the local extinction of fire‐sensitive rain forest taxa ( N othofagus gunnii and C upressaceae) following successive fires. Main conclusions The sedimentary analyses indicate that recurrent fires over several centuries caused a catchment‐wide transition from pyrophobic rain forest to pyrophytic eucalypt‐dominated vegetation. The fires within the lake catchment during the 6500‐year long record appear to coincide with high‐frequency E l N iño events in the equatorial Pacific Ocean, signalling a potential threat to these highly endemic rain forests if E l N iño intensity amplifies as predicted under future climate scenarios.

Immunocytochemical localization of carbonic anhydrase in the pseudobranch tissue of the rainbow trout Oncorhynchus my-kiss - S. M. Rahim; A. G. Mazlan; K. D. Simon; J. P. Delaunoy; P. Laurent (Journal of Zhejiang University-SCIENCE B, 2014)

A statistical approach to distinguish telomere elongation from error in longitudinal datasets - Mirre J. P. Simons; Gert Stulp; Shinichi Nakagawa (Biogerontology, 2014)

Limited habitat and conservation value of a young artificial reef - Simon J. Walker; Thomas A. Schlacher (Biodiversity and Conservation, 2014)

The current decline of tropical marsupials in A ustralia: is history repeating? - Diana O. Fisher; Chris N. Johnson; Michael J. Lawes; Susanne A. Fritz; Hamish McCallum; Simon P. Blomberg; Jeremy VanDerWal; Brett Abbott; Anke Frank; Sarah Legge; Mike Letnic; Colette R. Thomas; et al. (Global Ecology and Biogeography, 2014)
Aim A third of all modern (after 1500) mammal extinctions (24/77) are Australian species. These extinctions have been restricted to southern A ustralia, predominantly in species of ‘critical weight range’ (35–5500 g) in drier climate zones. Introduced red foxes ( V ulpes vulpes ) that prey on species in this range are often blamed. A new wave of declines is now affecting a globally significant proportion of marsupial species (19 species) in the fox‐free northern tropics. We aim to test plausible causes of recent declines in range and determine if mechanisms differ between current tropical declines and past declines, which were in southern (non‐tropical) regions. Location A ustralian continent Methods We used multiple regression and random forest models to analyse traits that were associated with declines in species range, and compare variables associated with past extinctions in the southern zones with current tropical (northern) declines. Results The same two key variables, body mass and habitat structure, were associated with proportion‐of‐decline in range throughout the continent, but the form of relationships differs with latitude. In the south, medium‐sized species in open habitats of lower rainfall were most likely to decline. In the tropics, small species that occupy open vegetation with moderate rainfall (savanna) are now experiencing the most severe declines. Throughout the continent, large‐bodied species and those in structurally complex habitats (rainforest) are secure. Main conclusions Our results indicate that there is no mid‐sized ‘critical weight range’ in the north. Because foxes are absent from the tropics, we suggest that northern Australian marsupial declines are associated with predation by feral cats ( F elis catus ) exacerbated by reduced ground level vegetation in non‐rainforest habitats. To test this, we recommend experiments to remove cats from some locations where tropical mammals are threatened. Our results show that comparative analysis can help to diagnose potential causes of multi‐species decline.

Inertia in an ombrotrophic bog ecosystem in response to 9 years' realistic perturbation by wet deposition of nitrogen, separated by form - Lucy J. Sheppard; Ian D. Leith; Toshie Mizunuma; Sarah Leeson; Sanna Kivimaki; J. Neil Cape; Netty van Dijk; David Leaver; Mark A. Sutton; David Fowler; Leon J.L. Van den Berg; Alan Crossley; et al. (Global Change Biology, 2014)
Wet deposition of nitrogen (N) occurs in oxidized (nitrate) and reduced (ammonium) forms. Whether one form drives vegetation change more than the other is widely debated, as field evidence has been lacking. We are manipulating N form in wet deposition to an ombrotrophic bog, Whim (Scottish Borders), and here report nine years of results. Ammonium and nitrate were provided in rainwater spray as NH 4 Cl or NaNO 3 at 8, 24 or 56 kg N ha −1 yr −1 , plus a rainwater only control, via an automated system coupled to site meteorology. Detrimental N effects were observed in sensitive nonvascular plant species, with higher cumulative N loads leading to more damage at lower annual doses. Cover responses to N addition, both in relation to form and dose, were species specific and mostly dependent on N dose. Some species were generally indifferent to N form and dose, while others were dose sensitive. Calluna vulgaris showed a preference for higher N doses as ammonium N and Hypnum jutlandicum for nitrate N. However, after 9 years, the magnitude of change from wet deposited N on overall species cover is small, indicating only a slow decline in key species. Nitrogen treatment effects on soil N availability were likewise small and rarely correlated with species cover. Ammonium caused most N accumulation and damage to sensitive species at lower N loads, but toxic effects also occurred with nitrate. However, because different species respond differently to N form, setting of ecosystem level critical loads by N form is challenging. We recommend implementing the lowest value of the critical load range where communities include sensitive nonvascular plants and where ammonium dominates wet deposition chemistry. In the context of parallel assessment at the same site, N treatments for wet deposition showed overall much smaller effects than corresponding inputs of dry deposition as ammonia.

Bergmann's rule is maintained during a rapid range expansion in a damselfly - Christopher Hassall; Simon Keat; David J. Thompson; Phillip C. Watts (Global Change Biology, 2014)
Climate‐induced range shifts result in the movement of a sample of genotypes from source populations to new regions. The phenotypic consequences of those shifts depend upon the sample characteristics of the dispersive genotypes, which may act to either constrain or promote phenotypic divergence, and the degree to which plasticity influences the genotype–environment interaction. We sampled populations of the damselfly Erythromma viridulum from northern Europe to quantify the phenotypic (latitude–body size relationship based on seven morphological traits) and genetic (variation at microsatellite loci) patterns that occur during a range expansion itself. We find a weak spatial genetic structure that is indicative of high gene flow during a rapid range expansion. Despite the potentially homogenizing effect of high gene flow, however, there is extensive phenotypic variation among samples along the invasion route that manifests as a strong, positive correlation between latitude and body size consistent with Bergmann's rule. This positive correlation cannot be explained by variation in the length of larval development (voltinism). While the adaptive significance of latitudinal variation in body size remains obscure, geographical patterns in body size in odonates are apparently underpinned by phenotypic plasticity and this permits a response to one or more environmental correlates of latitude during a range expansion.

Bacterial social networks: structure and composition of M yxococcus xanthus outer membrane vesicle chains - Jonathan P. Remis; Dongguang Wei; Amita Gorur; Marcin Zemla; Jessica Haraga; Simon Allen; H. Ewa Witkowska; J. William Costerton; James E. Berleman; Manfred Auer (Environmental Microbiology, 2014)
Summary The social soil bacterium, M yxococcus xanthus , displays a variety of complex and highly coordinated behaviours, including social motility, predatory rippling and fruiting body formation. Here we show that M . xanthus cells produce a network of outer membrane extensions in the form of outer membrane vesicle chains and membrane tubes that interconnect cells. We observed peritrichous display of vesicles and vesicle chains, and increased abundance in biofilms compared with planktonic cultures. By applying a range of imaging techniques, including three‐dimensional ( 3D ) focused ion beam scanning electron microscopy, we determined these structures to range between 30 and 60 nm in width and up to 5 μm in length. Purified vesicle chains consist of typical M . xanthus lipids, fucose, mannose, N ‐acetylglucosamine and N ‐acetylgalactoseamine carbohydrates and a small set of cargo protein. The protein content includes CglB and Tgl outer membrane proteins known to be transferable between cells in a contact‐dependent manner. Most significantly, the 3D organization of cells within biofilms indicates that cells are connected via an extensive network of membrane extensions that may connect cells at the level of the periplasmic space. Such a network would allow the transfer of membrane proteins and other molecules between cells, and therefore could provide a mechanism for the coordination of social activities.

Hunting Down the Chimera of Multiple Disciplinarity in Conservation Science - SIMON P. POOLEY; J. ANDREW MENDELSOHN; E. J. MILNER‐GULLAND (Conservation Biology, 2014)
The consensus is that both ecological and social factors are essential dimensions of conservation research and practice. However, much of the literature on multiple disciplinary collaboration focuses on the difficulties of undertaking it. This review of the challenges of conducting multiple disciplinary collaboration offers a framework for thinking about the diversity and complexity of this endeavor. We focused on conceptual challenges, of which 5 main categories emerged: methodological challenges, value judgments, theories of knowledge, disciplinary prejudices, and interdisciplinary communication. The major problems identified in these areas have proved remarkably persistent in the literature surveyed (c.1960–2012). Reasons for these failures to learn from past experience include the pressure to produce positive outcomes and gloss over disagreements, the ephemeral nature of many such projects and resulting lack of institutional memory, and the apparent complexity and incoherence of the endeavor. We suggest that multiple disciplinary collaboration requires conceptual integration among carefully selected multiple disciplinary team members united in investigating a shared problem or question. We outline a 9‐point sequence of steps for setting up a successful multiple disciplinary project. This encompasses points on recruitment, involving stakeholders, developing research questions, negotiating power dynamics and hidden values and conceptual differences, explaining and choosing appropriate methods, developing a shared language, facilitating on‐going communications, and discussing data integration and project outcomes. Although numerous solutions to the challenges of multiple disciplinary research have been proposed, lessons learned are often lost when projects end or experienced individuals move on. We urge multiple disciplinary teams to capture the challenges recognized, and solutions proposed, by their researchers while projects are in process. A database of well‐documented case studies would showcase theories and methods from a variety of disciplines and their interactions, enable better comparative study and evaluation, and provide a useful resource for developing future projects and training multiple disciplinary researchers. Cazando la Quimera de la Multidisciplina en la Ciencia de la Conservación

Limited genetic structure among broad-scale regions for two commercially harvested, tropical deep-water snappers in New Caledonia - Kim L. Loeun; Sharyn Goldstien; Dianne Gleeson; Simon J. Nicol; Corey J. A. Bradshaw (Fisheries Science, 2014)

Muscle strength and its relationship with skeletal muscle mass indices as determined by segmental bio-impedance analysis - Omid Alizadehkhaiyat; David H. Hawkes; Graham J. Kemp; Anthony Howard; Simon P. Frostick (European Journal of Applied Physiology, 2014)

Assimilation of preexisting Pleistocene intrusions at Long Valley by periodic magma recharge accelerates rhyolite generation: rethinking the remelting model - Justin I. Simon; Dominique Weis; Donald J. DePaolo; Paul R. Renne; Roland Mundil; Axel K. Schmitt (Contributions to Mineralogy and Petrology, 2014)

A systematic review of brain frontal lobe parcellation techniques in magnetic resonance imaging - Simon R. Cox; Karen J. Ferguson; Natalie A. Royle; Susan D. Shenkin; Sarah E. MacPherson; Alasdair M. J. MacLullich; Ian J. Deary; Joanna M. Wardlaw (Brain Structure and Function, 2014)

Detailed multidisciplinary monitoring reveals pre- and co-eruptive signals at Nyamulagira volcano (North Kivu, Democratic Republic of Congo) - Benoît Smets; Nicolas d’Oreye; François Kervyn; Matthieu Kervyn; Fabien Albino; Santiago R. Arellano; Montfort Bagalwa; Charles Balagizi; Simon A. Carn; Thomas H. Darrah; José Fernández; Bo Galle; et al. (Bulletin of Volcanology, 2014)

Can gray seals maintain heading within areas of high tidal current? Preliminary results from numerical modeling and GPS observations - Damien Chevaillier; Mikhail Karpytchev; Bernie J. Mcconnell; Simon Moss; Cecile Vincent (Marine Mammal Science, 2014)

Reestablishment of former wintering grounds by New Zealand southern right whales - Emma L. Carroll; William J. Rayment; Alana M. Alexander; C. Scott Baker; Nathalie J. Patenaude; Debbie Steel; Rochelle Constantine; Rosalind Cole; Laura J. Boren; Simon Childerhouse (Marine Mammal Science, 2014)
Historically, the range of the southern right whale ( SRW ) included winter calving grounds around the North and South Islands (mainland) of New Zealand ( NZ ) and in the NZ subantarctic Auckland and Campbell Islands. Due to extensive whaling in the 19th and 20th centuries, no SRW was seen around mainland NZ for nearly four decades (1928–1963). Here we present evidence for the regular use of the mainland NZ wintering ground, presumably from a remnant population that persisted in the NZ subantarctic Auckland and Campbell Islands. SRW s have been sighted every year around mainland NZ since 1988, with 125 sightings during the focus of this work: from 2003 to 2010. There were 28 cow‐calf pairs sighted around mainland NZ from 2003 to 2010, compared with 11 sightings from 1991 to 2002. Furthermore, two females, identified by DNA profiles, were sighted with calves around mainland at 4 yr intervals: the first evidence of female site fidelity to the mainland NZ calving ground. Individual identification from photographs of natural markings and DNA profiles provided information on within‐year movements and residency around the mainland, and further evidence for exchange between the mainland and subantarctic wintering grounds. Despite these promising signs, the distribution of NZ SRW s remains primarily concentrated in the NZ subantarctic.

Basin‐scale phenology and effects of climate variability on global timing of initial seaward migration of Atlantic salmon ( Salmo salar ) - Jaime Otero; Jan Henning L'Abée‐Lund; Ted Castro‐Santos; Kjell Leonardsson; Geir O. Storvik; Bror Jonsson; Brian Dempson; Ian C. Russell; Arne J. Jensen; Jean‐Luc Baglinière; Mélanie Dionne; John D. Armstrong; et al. (Global Change Biology, 2014)
Migrations between different habitats are key events in the lives of many organisms. Such movements involve annually recurring travel over long distances usually triggered by seasonal changes in the environment. Often, the migration is associated with travel to or from reproduction areas to regions of growth. Young anadromous Atlantic salmon ( Salmo salar ) emigrate from freshwater nursery areas during spring and early summer to feed and grow in the North Atlantic Ocean. The transition from the freshwater (‘parr’) stage to the migratory stage where they descend streams and enter salt water (‘smolt’) is characterized by morphological, physiological and behavioural changes where the timing of this parr‐smolt transition is cued by photoperiod and water temperature. Environmental conditions in the freshwater habitat control the downstream migration and contribute to within‐ and among‐river variation in migratory timing. Moreover, the timing of the freshwater emigration has likely evolved to meet environmental conditions in the ocean as these affect growth and survival of the post‐smolts. Using generalized additive mixed‐effects modelling, we analysed spatio‐temporal variations in the dates of downstream smolt migration in 67 rivers throughout the North Atlantic during the last five decades and found that migrations were earlier in populations in the east than the west. After accounting for this spatial effect, the initiation of the downstream migration among rivers was positively associated with freshwater temperatures, up to about 10 °C and levelling off at higher values, and with sea‐surface temperatures. Earlier migration occurred when river discharge levels were low but increasing. On average, the initiation of the smolt seaward migration has occurred 2.5 days earlier per decade throughout the basin of the North Atlantic. This shift in phenology matches changes in air, river, and ocean temperatures, suggesting that Atlantic salmon emigration is responding to the current global climate changes.

Land‐sharing versus land‐sparing logging: reconciling timber extraction with biodiversity conservation - David P. Edwards; James J. Gilroy; Paul Woodcock; Felicity A. Edwards; Trond H. Larsen; David J. R. Andrews; Mia A. Derhé; Teegan D. S. Docherty; Wayne W. Hsu; Simon L. Mitchell; Takahiro Ota; Leah J. Williams; et al. (Global Change Biology, 2014)
Selective logging is a major driver of rainforest degradation across the tropics. Two competing logging strategies are proposed to meet timber demands with the least impact on biodiversity: land sharing, which combines timber extraction with biodiversity protection across the concession; and land sparing, in which higher intensity logging is combined with the protection of intact primary forest reserves. We evaluate these strategies by comparing the abundances and species richness of birds, dung beetles and ants in Borneo, using a protocol that allows us to control for both timber yield and net profit across strategies. Within each taxonomic group, more species had higher abundances with land‐sparing than land‐sharing logging, and this translated into significantly higher species richness within land‐sparing concessions. Our results are similar when focusing only on species found in primary forest and restricted in range to Sundaland, and they are independent of the scale of sampling. For each taxonomic group, land‐sparing logging was the most promising strategy for maximizing the biological value of logging operations.

Signatures of adaptation and genetic structure among the mainland populations of Pinus radiata (D. Don) inferred from SNP loci - Shannon K. Dillon; Maureen F. Nolan; Philippe Matter; Washington J. Gapare; Jason G. Bragg; Simon G. Southerton (Tree Genetics & Genomes, 2013)

Surface Charges of the Membrane Crucially Affect Regulation of Na,K-ATPase by Phospholemman (FXYD1) - Erica Cirri; Corinna Kirchner; Simon Becker; Adriana Katz; Steven J. Karlish; Hans-Jürgen Apell (The Journal of Membrane Biology, 2013)

Circulating galectin-3 in infections and non-infectious inflammatory diseases - J. Oever; E. J. Giamarellos-Bourboulis; F. L. Veerdonk; F. F. Stelma; A. Simon; M. Janssen; M. Johnson; A. Pachot; B.-J. Kullberg; L. A. B. Joosten; M. G. Netea (European Journal of Clinical Microbiology & Infectious Diseases, 2013)

Predicting species distributions for conservation decisions - Antoine Guisan; Reid Tingley; John B. Baumgartner; Ilona Naujokaitis‐Lewis; Patricia R. Sutcliffe; Ayesha I. T. Tulloch; Tracey J. Regan; Lluis Brotons; Eve McDonald‐Madden; Chrystal Mantyka‐Pringle; Tara G. Martin; Jonathan R. Rhodes; et al. (Ecology Letters, 2013)
Species distribution models (SDMs) are increasingly proposed to support conservation decision making. However, evidence of SDMs supporting solutions for on‐ground conservation problems is still scarce in the scientific literature. Here, we show that successful examples exist but are still largely hidden in the grey literature, and thus less accessible for analysis and learning. Furthermore, the decision framework within which SDMs are used is rarely made explicit. Using case studies from biological invasions, identification of critical habitats, reserve selection and translocation of endangered species, we propose that SDMs may be tailored to suit a range of decision‐making contexts when used within a structured and transparent decision‐making process. To construct appropriate SDMs to more effectively guide conservation actions, modellers need to better understand the decision process, and decision makers need to provide feedback to modellers regarding the actual use of SDMs to support conservation decisions. This could be facilitated by individuals or institutions playing the role of ‘translators’ between modellers and decision makers. We encourage species distribution modellers to get involved in real decision‐making processes that will benefit from their technical input; this strategy has the potential to better bridge theory and practice, and contribute to improve both scientific knowledge and conservation outcomes.

Environmental stress, facilitation, competition, and coexistence - Simon P. Hart; Dustin J. Marshall (Ecology, 2013)
The major theories regarding the combined influence of the environment and species interactions on population and community dynamics appear to conflict. Stress/disturbance gradient models of community organization, such as the stress gradient hypothesis, emphasize a diminished role for competition in harsh environments whereas modern coexistence theory does not. Confusion about the role of species interactions in harsh environments is perpetuated by a disconnect between population dynamics theory and data. We linked theory and data using response surface experiments done in the field to parameterize mathematical, population‐dynamic competition models. We replicated our experiment across two environments that spanned a common and important environmental stress gradient for determining community structure in benthic marine systems. We generated quantitative estimates of the effects of environmental stress on population growth rates and the direction and strength of intra‐ and interspecific interactions within each environment. Our approach directly addressed a perpetual blind spot in this field by showing how the effects of competition can be intensified in stressful environments even though the apparent strength of competition remains unchanged. Furthermore, we showed how simultaneous, reciprocal competitive and facilitative effects can stabilize population dynamics in multispecies communities in stressful environments.

Erratum to: The European Modern Pollen Database (EMPD) project - Basil A. S. Davis; Marco Zanon; Pamella Collins; Achille Mauri; Johan Bakker; Doris Barboni; Alexandra Barthelmes; Celia Beaudouin; H. John B. Birks; Anne E. Bjune; Elissaveta Bozilova; Richard H. W. Bradshaw; et al. (Vegetation History and Archaeobotany, 2013)

The European Modern Pollen Database (EMPD) project - Basil A. S. Davis; Marco Zanon; Pamella Collins; Achille Mauri; Johan Bakker; Doris Barboni; Alexandra Barthelmes; Celia Beaudouin; Anne E. Bjune; Elissaveta Bozilova; Richard H. W. Bradshaw; Barbara A. Brayshay; et al. (Vegetation History and Archaeobotany, 2013)

Co-occurrence patterns of Bornean vertebrates suggest competitive exclusion is strongest among distantly related species - Lydia Beaudrot; Matthew J. Struebig; Erik Meijaard; S. van Balen; Simon Husson; Andrew J. Marshall (Oecologia, 2013)

Individual quality persists between years: individuals retain body condition from one winter to the next in Teal - Matthieu Guillemain; Andy J. Green; Géraldine Simon; Michel Gauthier-Clerc (Journal of Ornithology, 2013)

Pup to adult photo‐ ID : Evidence of pelage stability in gray seals - William D. Paterson; Paula Redman; Lex A. Hiby; Simon E. W. Moss; Ailsa J. Hall; Paddy Pomeroy (Marine Mammal Science, 2013)

Warming effects on greenhouse gas fluxes in peatlands are modulated by vegetation composition - Susan E. Ward; Nicholas J. Ostle; Simon Oakley; Helen Quirk; Peter A. Henrys; Richard D. Bardgett (Ecology Letters, 2013)
Understanding the effects of warming on greenhouse gas feedbacks to climate change represents a major global challenge. Most research has focused on direct effects of warming, without considering how concurrent changes in plant communities may alter such effects. Here, we combined vegetation manipulations with warming to investigate their interactive effects on greenhouse gas emissions from peatland. We found that although warming consistently increased respiration, the effect on net ecosystem CO 2 exchange depended on vegetation composition. The greatest increase in CO 2 sink strength after warming was when shrubs were present, and the greatest decrease when graminoids were present. CH 4 was more strongly controlled by vegetation composition than by warming, with largest emissions from graminoid communities. Our results show that plant community composition is a significant modulator of greenhouse gas emissions and their response to warming, and suggest that vegetation change could alter peatland carbon sink strength under future climate change.

Trophic Flexibility and the Persistence of Understory Birds in Intensively Logged Rainforest - DAVID P. EDWARDS; PAUL WOODCOCK; ROB J. NEWTON; FELICITY A. EDWARDS; DAVID J. R. ANDREWS; TEEGAN D. S. DOCHERTY; SIMON L. MITCHELL; TAKAHIRO OTA; SUZAN BENEDICK; SIMON H. BOTTRELL; KEITH C. HAMER (Conservation Biology, 2013)
Effects of logging on species composition in tropical rainforests are well known but may fail to reveal key changes in species interactions. We used nitrogen stable‐isotope analysis of 73 species of understory birds to quantify trophic responses to repeated intensive logging of rainforest in northern Borneo and to test 4 hypotheses: logging has significant effects on trophic positions and trophic‐niche widths of species, and the persistence of species in degraded forest is related to their trophic positions and trophic‐niche widths in primary forest. Species fed from higher up the food chain and had narrower trophic‐niche widths in degraded forest. Species with narrow trophic‐niche widths in primary forest were less likely to persist after logging, a result that indicates a higher vulnerability of dietary specialists to local extinction following habitat disturbance. Persistence of species in degraded forest was not related to a species’ trophic position. These results indicate changes in trophic organization that were not apparent from changes in species composition and highlight the importance of focusing on trophic flexibility over the prevailing emphasis on membership of static feeding guilds. Our results thus support the notion that alterations to trophic organization and interactions within tropical forests may be a pervasive and functionally important hidden effect of forest degradation. Flexibilidad Trófica y la Persistencia de Aves de Sotobosque en un Bosque Lluvioso Talado Intensivamente

Variable resistance training promotes greater fatigue resistance but not hypertrophy versus constant resistance training - Simon Walker; Juha J. Hulmi; Mathias Wernbom; Kai Nyman; William J. Kraemer; Juha P. Ahtiainen; Keijo Häkkinen (European Journal of Applied Physiology, 2013)

Evidence for covalently bonded chlorine–fullerene formed by ozonation and chlorination at room temperature - Alla L. Alpatova; Melissa J. Baumann; Simon H. Davies; Susan J. Masten (Environmental Chemistry Letters, 2013)

Could some coral reefs become sponge reefs as our climate changes? - James J. Bell; Simon K. Davy; Timothy Jones; Michael W. Taylor; Nicole S. Webster (Global Change Biology, 2013)
Coral reefs across the world have been seriously degraded and have a bleak future in response to predicted global warming and ocean acidification ( OA ). However, this is not the first time that biocalcifying organisms, including corals, have faced the threat of extinction. The end‐Triassic mass extinction (200 million years ago) was the most severe biotic crisis experienced by modern marine invertebrates, which selected against biocalcifiers; this was followed by the proliferation of another invertebrate group, sponges. The duration of this sponge‐dominated period far surpasses that of alternative stable‐ecosystem or phase‐shift states reported on modern day coral reefs and, as such, a shift to sponge‐dominated reefs warrants serious consideration as one future trajectory of coral reefs. We hypothesise that some coral reefs of today may become sponge reefs in the future, as sponges and corals respond differently to changing ocean chemistry and environmental conditions. To support this hypothesis, we discuss: (i) the presence of sponge reefs in the geological record; (ii) reported shifts from coral‐ to sponge‐dominated systems; and (iii) direct and indirect responses of the sponge holobiont and its constituent parts (host and symbionts) to changes in temperature and pH . Based on this evidence, we propose that sponges may be one group to benefit from projected climate change and ocean acidification scenarios, and that increased sponge abundance represents a possible future trajectory for some coral reefs, which would have important implications for overall reef functioning.

Regime shifts in a social-ecological system - Steven J. Lade; Alessandro Tavoni; Simon A. Levin; Maja Schlüter (Theoretical Ecology, 2013)

Quantification of the Relative Abundance of Plastome to Nuclear Genome in Leaf and Root Tissues of Carrot (Daucus carota L.) Using Quantitative PCR - Megan J. Bowman; Philipp W. Simon (Plant Molecular Biology Reporter, 2013)

UHP metamorphic rocks from the Chinese continental scientific drilling project: I. Petrology and geochemistry of the main hole (0–2,050 m) - Zeming Zhang; Yilin Xiao; Zhiqin Xu; Jochen Hoefs; Jinsui Yang; Fulai Liu; J. G. Liou; Klaus Simon (Contributions to Mineralogy and Petrology, 2013)

Analysis of longitudinal profiles along the eastern margin of the Qinghai-Tibetan Plateau - Simon J. Aiken; Gary J. Brierley (Journal of Mountain Science, 2013)
Resulting from the collision of the Eurasian and Indian plates, the Qinghai-Tibetan Plateau is commonly known as the ‘roof of the world’. Collectively the Yarlung Tsangpo, Nu, Lancang, Yangtze, Yalong, and Yellow River basins drain the eastern margin of the plateau. In this paper, we utilize Shuttle Radar Topography Mission elevation data to examine morphometric and relief attributes of these basins to reveal insights into tectonic activity and rates of incision. A robust technique using Matlab is proposed to alleviate errors associated with SRTM data in the derivation of river longitudinal profiles. Convex longitudinal profiles are interpreted to be a product of uplift rates that exceed rates of channel incision along the entire margin of the Qinghai-Tibetan Plateau. Highest relief towards the south reflects extensive fluvial incision. High relief is also prominent along major active faults. Erosion patterns are related to distance from knickpoints. Highest rates of erosion and incision are evident towards the south, with decreasing values towards the north, suggesting a link between tectonic activity and erosion.

Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME - Patricio Godoy; Nicola J. Hewitt; Ute Albrecht; Melvin E. Andersen; Nariman Ansari; Sudin Bhattacharya; Johannes Georg Bode; Jennifer Bolleyn; Christoph Borner; Jan Böttger; Albert Braeuning; Robert A. Budinsky; et al. (Archives of Toxicology, 2013)

When condition trumps location: seed consumption by fruit‐eating birds removes pathogens and predator attractants - Evan C. Fricke; Melissa J. Simon; Karen M. Reagan; Douglas J. Levey; Jeffrey A. Riffell; Tomás A. Carlo; Joshua J. Tewksbury (Ecology Letters, 2013)
Seed ingestion by frugivorous vertebrates commonly benefits plants by moving seeds to locations with fewer predators and pathogens than under the parent. For plants with high local population densities, however, movement from the parent plant is unlikely to result in ‘escape’ from predators and pathogens. Changes to seed condition caused by gut passage may also provide benefits, yet are rarely evaluated as an alternative. Here, we use a common bird‐dispersed chilli pepper ( Capsicum chacoense ) to conduct the first experimental comparison of escape‐related benefits to condition‐related benefits of animal‐mediated seed dispersal. Within chilli populations, seeds dispersed far from parent plants gained no advantage from escape alone, but seed consumption by birds increased seed survival by 370% – regardless of dispersal distance – due to removal during gut passage of fungal pathogens and chemical attractants to granivores. These results call into question the pre‐eminence of escape as the primary advantage of dispersal within populations and document two overlooked mechanisms by which frugivores can benefit fruiting plants.

Effect of amount and timing of subsurface drip irrigation on corn yield - Simon J. van Donk; James L. Petersen; Don R. Davison (Irrigation Science, 2013)

The influence of motor cortical stimulus intensity on the relaxation rate of human lower limb muscles - Chris J. McNeil; Marlous S. Bredius; Joery P. Molenaar; Simon C. Gandevia (Experimental Brain Research, 2013)

Environmental Influences on Faecal Indicator Organisms in Coastal Waters and Their Accumulation in Bivalve Shellfish - Carlos J. A. Campos; Simon R. Kershaw; Ron J. Lee (Estuaries and Coasts, 2013)

An ocean observation system for monitoring the affects of climate change on the ecology and sustainability of pelagic fisheries in the Pacific Ocean - Simon J. Nicol; Valerie Allain; Graham M. Pilling; Jeff Polovina; Marta Coll; Johann Bell; Paul Dalzell; Peter Sharples; Robert Olson; Shane Griffiths; Jeffrey M. Dambacher; Jock Young; et al. (Climatic Change, 2013)

Subsurface behavior of bottlenose dolphins ( Tursiops truncatus ) interacting with fish trawl nets in northwestern Australia: Implications for bycatch mitigation - Vanessa F. Jaiteh; Simon J. Allen; Jessica J. Meeuwig; Neil R. Loneragan (Marine Mammal Science, 2013)
Most studies of delphinid‐trawler interactions have documented the surface behavior of dolphins feeding on discarded bycatch, but not their subsurface behavior around demersal trawl gear. Using video cameras mounted inside trawl nets, we recorded the subsurface behavior of common bottlenose dolphins ( Tursiops truncatus ) in a demersal fish trawl fishery in northwestern Australia. Footage from 36 trawls across the fishery was analyzed to determine the extent of dolphin‐gear interactions and the behavior of dolphins inside the nets. Interaction rates were high, with dolphins present inside and outside the nets during 29 and 34 trawls, respectively, and for up to 99% of the trawl duration. The proportion of foraging behaviors exhibited inside the nets was higher than the proportions of traveling and socializing behaviors. Twenty‐nine individuals were identified inside the net, seven of which returned repeatedly within and between trawls and fishing trips, but were observed primarily in the same localized areas in which they were first recorded. Our results suggest that entering trawl nets may be a frequently occurring, yet specialized behavior exhibited by a small subset of trawler‐associated dolphins. We propose that gear modifications, not spatial or temporal adjustments to fishing effort, have the greatest potential to reduce dolphin bycatch.

Occurrence and seasonal prevalence of the coconut mite, Aceria guerreronis (Eriophyidae), and associated arthropods in Oman - Abdulaziz Al-Shanfari; Fabien C. C. Hountondji; Hamid Al-Zawamri; Hassan Rawas; Yussef Al-Mashiki; Gilberto J. de Moraes; Dave Moore; Simon R. Gowen (Experimental and Applied Acarology, 2013)

Whisker growth in wild Eurasian badgers Meles meles: implications for stable isotope and bait marking studies - Andrew Robertson; Robbie A. McDonald; Richard J. Delahay; Simon D. Kelly; Stuart Bearhop (European Journal of Wildlife Research, 2013)

A Novel Acquisition Technique to Utilize Swan-Ganz Catheter data as a Surrogate for High-fidelity Micromanometry within the Right Ventricle and Pulmonary Circuit - T. N. Bachman; J. J. Bursic; M. A. Simon; H. C. Champion (Cardiovascular Engineering and Technology, 2013)

Identification of Resting and Active State EEG Features of Alzheimer’s Disease using Discrete Wavelet Transform - Parham Ghorbanian; David M. Devilbiss; Ajay Verma; Allan Bernstein; Terry Hess; Adam J. Simon; Hashem Ashrafiuon (Annals of Biomedical Engineering, 2013)

The shore fishes of the Trindade–Martin Vaz insular complex: an update - T. Simon; R. M. Macieira; J.‐C. Joyeux (Journal of Fish Biology, 2013)
A compilation of historical and recent collections and observations of shore fishes yielded 154 recorded species for Trindade and 67 for Martin Vaz. Twelve taxa, mostly small cryptobenthic species with limited dispersal capabilities and low ecological amplitude, are endemic to this insular complex. In several cases, the seamounts of the Vitória‐Trindade Chain appear to have acted as stepping stones between the mainland and islands in periods of low sea level.

Genetic characterization and mapping of the Rht-1 homoeologs and flanking sequences in wheat - Edward P. Wilhelm; Rhian M. Howells; Nadia Al-Kaff; Jizeng Jia; Catherine Baker; Michelle A. Leverington-Waite; Simon Griffiths; Andy J. Greenland; Margaret I. Boulton; Wayne Powell (Theoretical and Applied Genetics, 2013)

Purine nucleoside phosphorylase deficiency presenting as severe combined immune deficiency - Raz Somech; Atar Lev; Galia Grisaru-Soen; Shelly I. Shiran; Amos J. Simon; Eyal Grunebaum (Immunologic Research, 2013)

Cigarette smoking and risk of ovarian cancer: a pooled analysis of 21 case–control studies - Mette T. Faber; Susanne K. Kjær; Christian Dehlendorff; Jenny Chang-Claude; Klaus K. Andersen; Estrid Høgdall; Penelope M. Webb; Susan J. Jordan; Mary Anne Rossing; Jennifer A. Doherty; Galina Lurie; Pamela J. Thompson; et al. (Cancer Causes & Control, 2013)

Consistent proportional macronutrient intake selected by adult domestic cats (Felis catus) despite variations in macronutrient and moisture content of foods offered - Adrian K. Hewson-Hughes; Victoria L. Hewson-Hughes; Alison Colyer; Andrew T. Miller; Simon R. Hall; David Raubenheimer; Stephen J. Simpson (Journal of Comparative Physiology B, 2013)

Reconciling biodiversity and carbon conservation - Chris D Thomas; Barbara J Anderson; Atte Moilanen; Felix Eigenbrod; Andreas Heinemeyer; Tristan Quaife; David B Roy; Simon Gillings; Paul R Armsworth; Kevin J Gaston (Ecology Letters, 2013)
Climate change is leading to the development of land‐based mitigation and adaptation strategies that are likely to have substantial impacts on global biodiversity. Of these, approaches to maintain carbon within existing natural ecosystems could have particularly large benefits for biodiversity. However, the geographical distributions of terrestrial carbon stocks and biodiversity differ. Using conservation planning analyses for the New World and Britain, we conclude that a carbon‐only strategy would not be effective at conserving biodiversity, as have previous studies. Nonetheless, we find that a combined carbon‐biodiversity strategy could simultaneously protect 90% of carbon stocks (relative to a carbon‐only conservation strategy) and > 90% of the biodiversity (relative to a biodiversity‐only strategy) in both regions. This combined approach encapsulates the principle of complementarity, whereby locations that contain different sets of species are prioritised, and hence disproportionately safeguard localised species that are not protected effectively by carbon‐only strategies. It is efficient because localised species are concentrated into small parts of the terrestrial land surface, whereas carbon is somewhat more evenly distributed; and carbon stocks protected in one location are equivalent to those protected elsewhere. Efficient compromises can only be achieved when biodiversity and carbon are incorporated together within a spatial planning process.

Asynchronous food‐web pathways could buffer the response of Serengeti predators to El Niño Southern Oscillation - A. R. E. Sinclair; Kristine L. Metzger; John M. Fryxell; Craig Packer; Andrea E. Byrom; Meggan E. Craft; Katie Hampson; Tiziana Lembo; Sarah M. Durant; Guy J. Forrester; John Bukombe; John Mchetto; et al. (Ecology, 2013)
Understanding how entire ecosystems maintain stability in the face of climatic and human disturbance is one of the most fundamental challenges in ecology. Theory suggests that a crucial factor determining the degree of ecosystem stability is simply the degree of synchrony with which different species in ecological food webs respond to environmental stochasticity. Ecosystems in which all food‐web pathways are affected similarly by external disturbance should amplify variability in top carnivore abundance over time due to population interactions, whereas ecosystems in which a large fraction of pathways are nonresponsive or even inversely responsive to external disturbance will have more constant levels of abundance at upper trophic levels. To test the mechanism underlying this hypothesis, we used over half a century of demographic data for multiple species in the Serengeti (Tanzania) ecosystem to measure the degree of synchrony to variation imposed by an external environmental driver, the El Niño Southern Oscillation (ENSO). ENSO effects were mediated largely via changes in dry‐season vs. wet‐season rainfall and consequent changes in vegetation availability, propagating via bottom‐up effects to higher levels of the Serengeti food web to influence herbivores, predators and parasites. Some species in the Serengeti food web responded to the influence of ENSO in opposite ways, whereas other species were insensitive to variation in ENSO. Although far from conclusive, our results suggest that a diffuse mixture of herbivore responses could help buffer top carnivores, such as Serengeti lions, from variability in climate. Future global climate changes that favor some pathways over others, however, could alter the effectiveness of such processes in the future.

Retention of a transgenerational marker (137Barium) in tissues of adult female anemonefish and assessment of physiological stress - Alexandra-Sophie Roy; Ashley J. Frisch; Craig Syms; Simon R. Thorrold; Geoffrey P. Jones (Environmental Biology of Fishes, 2013)

Close-range hyperspectral imaging for geological field studies: workflow and methods - Tobias H. Kurz; Simon J. Buckley; John A. Howell (International Journal of Remote Sensing, 2013)

Synthesis of BVD15 Peptide Analogues as Models for Radioligands in Tumour Imaging - Mengjie Liu; Simon J. Mountford; Lei Zhang; I-Chieh Lee; Herbert Herzog; Philip E. Thompson (International Journal of Peptide Research and Therapeutics, 2013)

Potentially inappropriate drug use among older persons in Finland: application of a new national categorization - J. Simon Bell; Jouni Ahonen; Piia Lavikainen; Sirpa Hartikainen (European Journal of Clinical Pharmacology, 2013)

Administrative Co-management: The Case of Special-Use Forest Conservation in Vietnam - Nguyen KimDung; Simon Bush; Arthur P. J. Mol (Environmental Management, 2013)

Altered Sea Ice Thickness and Permanence Affects Benthic Ecosystem Functioning in Coastal Antarctica - Andrew M. Lohrer; Vonda J. Cummings; Simon F. Thrush (Ecosystems, 2013)

Characterization of 12 novel microsatellite loci and cross-amplification of four loci in the endangered Australian sea lion (Neophoca cinerea) - Heidi Ahonen; Andrew D. Lowther; Simon D. Goldsworthy; Robert G. Harcourt; Adam J. Stow (Conservation Genetics Resources, 2013)

Broad‐scale movements and pelagic habitat of the dusky shark C archarhinus obscurus off S outhern A ustralia determined using pop‐up satellite archival tags - Paul J. Rogers; Charlie Huveneers; Simon D. Goldsworthy; James G. Mitchell; Laurent Seuront (Fisheries Oceanography, 2013)
We investigated the broad‐scale movements and pelagic habitats of large juvenile dusky sharks ( Carcharhinus obscurus ) off Southern Australia. Pop‐up satellite archival tags ( PSAT s) were deployed on three large juvenile dusky sharks (∼2.2–2.6 m total length) for 6 months in Spencer Gulf during 2010. Tagged dusky sharks all migrated westward and across the Great Australian Bight ( GAB ) during autumn to offshore shelf waters off Western Australia. Estimated minimum distances travelled ranged from 1760 to 2736 km. Depths occupied by tagged dusky sharks ranged from the surface to 355 m. The most common thermal ranges occupied were 19–22°C. Broad‐scale movements of large juvenile dusky sharks across the continental shelves combined with periods of residency in semi‐protected gulf waters indicated that a multi‐jurisdictional management approach may be appropriate for this species.

A spatial mark–resight model augmented with telemetry data - Rahel Sollmann; Beth Gardner; Arielle W. Parsons; Jessica J. Stocking; Brett T. McClintock; Theodore R. Simons; Kenneth H. Pollock; Allan F. O'Connell (Ecology, 2013)
Abundance and population density are fundamental pieces of information for population ecology and species conservation, but they are difficult to estimate for rare and elusive species. Mark–resight models are popular for estimating population abundance because they are less invasive and expensive than traditional mark–recapture. However, density estimation using mark–resight is difficult because the area sampled must be explicitly defined, historically using ad hoc approaches. We developed a spatial mark–resight model for estimating population density that combines spatial resighting data and telemetry data. Incorporating telemetry data allows us to inform model parameters related to movement and individual location. Our model also allows Procyon lotor ) on South Core Banks, a barrier island in Cape Lookout National Seashore, North Carolina, USA. We estimated a population of 186.71 ± 14.81 individuals, which translated to a density of 8.29 ± 0.66 individuals/km 2 (mean ± SD). The model presented here will have widespread utility in future applications, especially for species that are not naturally marked.

Soil biotransformation of thiodiglycol, the hydrolysis product of mustard gas: understanding the factors governing remediation of mustard gas contaminated soil - Hong Li; Robert Muir; Neil R. McFarlane; Richard J. Soilleux; Xiaohong Yu; Ian P. Thompson; Simon A. Jackman (Biodegradation, 2013)

Ecological and evolutionary genomics of marine photosynthetic organisms - Susana M. Coelho; Nathalie Simon; Sophia Ahmed; J. Mark Cock; Frédéric Partensky (Molecular Ecology, 2013)
Environmental (ecological) genomics aims to understand the genetic basis of relationships between organisms and their abiotic and biotic environments. It is a rapidly progressing field of research largely due to recent advances in the speed and volume of genomic data being produced by next generation sequencing ( NGS ) technologies. Building on information generated by NGS ‐based approaches, functional genomic methodologies are being applied to identify and characterize genes and gene systems of both environmental and evolutionary relevance. Marine photosynthetic organisms ( MPO s) were poorly represented amongst the early genomic models, but this situation is changing rapidly. Here we provide an overview of the recent advances in the application of ecological genomic approaches to both prokaryotic and eukaryotic MPO s. We describe how these approaches are being used to explore the biology and ecology of marine cyanobacteria and algae, particularly with regard to their functions in a broad range of marine ecosystems. Specifically, we review the ecological and evolutionary insights gained from whole genome and transcriptome sequencing projects applied to MPO s and illustrate how their genomes are yielding information on the specific features of these organisms.

Genome‐wide patterns of divergence and gene flow across a butterfly radiation - Nicola J. Nadeau; Simon H. Martin; Krzysztof M. Kozak; Camilo Salazar; Kanchon K. Dasmahapatra; John W. Davey; Simon W. Baxter; Mark L. Blaxter; James Mallet; Chris D. Jiggins (Molecular Ecology, 2013)
The H eliconius butterflies are a diverse recent radiation comprising multiple levels of divergence with ongoing gene flow between species. The recently sequenced genome of H eliconius melpomene allowed us to investigate the genomic evolution of this group using dense RAD marker sequencing. Phylogenetic analysis of 54 individuals robustly supported reciprocal monophyly of H . melpomene and H eliconius cydno and refuted previous phylogenetic hypotheses that H . melpomene may be paraphylectic with respect to H . cydno . H eliconius timareta also formed a monophyletic clade closely related but distinct from H . cydno with H eliconius heurippa falling within this clade. We find evidence for genetic admixture between sympatric populations of the sister clades H . melpomene and H . cydno/timareta , particularly between H . cydno and H . melpomene from Central America and between H . timareta and H . melpomene from the eastern slopes of the A ndes. Between races, divergence is primarily explained by isolation by distance and there is no detectable genetic population structure between parapatric races, suggesting that hybrid zones between races are not zones of secondary contact. Our results also support previous findings that colour pattern loci are shared between populations and species with similar colour pattern elements. Furthermore, this pattern is almost unique to these genomic regions, with only a very small number of other loci showing significant similarity between populations and species with similar colour patterns.

Population Trends in Pacific Oceanic Sharks and the Utility of Regulations on Shark Finning - Shelley C. Clarke; Shelton J. Harley; Simon D. Hoyle; Joel S. Rice (Conservation Biology, 2013)
Accurate assessment of shark population status is essential for conservation but is often constrained by limited and unreliable data. To provide a basis for improved management of shark resources, we analyzed a long‐term record of species‐specific catches, sizes, and sexes of sharks collected by onboard observers in the western and central Pacific Ocean from 1995 to 2010. Using generalized linear models, we estimated population‐status indicators on the basis of catch rate and biological indicators of fishing pressure on the basis of median size to identify trends for blue ( Prionace glauca ), mako ( Isurus spp.), oceanic whitetip ( Carcharhinus longimanus ), and silky ( Carcharhinus falciformis ) sharks. Standardized catch rates of longline fleets declined significantly for blue sharks in the North Pacific (by 5% per year [CI 2% to 8%]), for mako sharks in the North Pacific (by 7% per year [CI 3% to 11%]), and for oceanic whitetip sharks in tropical waters (by 17% per year [CI 14% to 20%]). Median lengths of silky and oceanic whitetip sharks decreased significantly in their core habitat, and almost all sampled silky sharks were immature. Our results are consistent with results of analyses of similar data sets. Combined, these results and evidence of targeted fishing for sharks in some regional fisheries heighten concerns for sustainable utilization, particularly for oceanic whitetip and North Pacific blue sharks. Regional regulations that prohibit shark finning (removal of fins and discarding of the carcass) were enacted in 2007 and are in many cases the only form of control on shark catches. However, there is little evidence of a reduction of finning in longline fisheries. In addition, silky and oceanic whitetip sharks are more frequently retained than finned, which suggests that even full implementation of and adherence to a finning prohibition may not substantially reduce mortality rates for these species. We argue that finning prohibitions divert attention from assessing whether catch levels are sustainable and that the need for management of sharks should not be addressed by measures that are simple to implement but complex to enforce and evaluate. Tendencias Poblacionales de Tiburones del Océano Pacífico y la Utilidad de Regulaciones sobre Cercenamiento de Aletas

Decreased serum glucose and glycosylated hemoglobin levels in patients with Chuvash polycythemia: a role for HIF in glucose metabolism - Donald A. McClain; Khadega A. Abuelgasim; Mehdi Nouraie; Juan Salomon-Andonie; Xiaomei Niu; Galina Miasnikova; Lydia A. Polyakova; Adelina Sergueeva; Daniel J. Okhotin; Rabia Cherqaoui; David Okhotin; James E. Cox; et al. (Journal of Molecular Medicine, 2013)

A genome-wide association study of breast cancer in women of African ancestry - Fang Chen; Gary K. Chen; Daniel O. Stram; Robert C. Millikan; Christine B. Ambrosone; Esther M. John; Leslie Bernstein; Wei Zheng; Julie R. Palmer; Jennifer J. Hu; Tim R. Rebbeck; Regina G. Ziegler; et al. (Human Genetics, 2013)

Diabetes and risk of pancreatic cancer: a pooled analysis from the pancreatic cancer cohort consortium - Joanne W. Elena; Emily Steplowski; Kai Yu; Patricia Hartge; Geoffrey S. Tobias; Michelle J. Brotzman; Stephen J. Chanock; Rachael Z. Stolzenberg-Solomon; Alan A. Arslan; H. Bas Bueno-de-Mesquita; Kathy Helzlsouer; Eric J. Jacobs; et al. (Cancer Causes & Control, 2013)

Trait-dependent declines of species following conversion of rain forest to oil palm plantations - Michael J. M. Senior; Keith C. Hamer; Simon Bottrell; David P. Edwards; Tom M. Fayle; Jennifer M. Lucey; Peter J. Mayhew; Robert Newton; Kelvin S.-H. Peh; Frederick H. Sheldon; Christopher Stewart; Alison R. Styring; et al. (Biodiversity and Conservation, 2013)

Microfluidic System for Facilitated Quantification of Nanoparticle Accumulation to Cells Under Laminar Flow - Jiro Kusunose; Hua Zhang; M. Karen J. Gagnon; Tingrui Pan; Scott I. Simon; Katherine W. Ferrara (Annals of Biomedical Engineering, 2013)

The use of genetic correlations to evaluate associations between SNP markers and quantitative traits - J. T. Brawner; S. K. Dillon; D. J. Lee; A. R. Meder; M. J. Dieters; Simon G. Southerton (Tree Genetics & Genomes, 2012)

Genome-wide association study of glioma and meta-analysis - Preetha Rajaraman; Beatrice S. Melin; Zhaoming Wang; Roberta McKean-Cowdin; Dominique S. Michaud; Sophia S. Wang; Melissa Bondy; Richard Houlston; Robert B. Jenkins; Margaret Wrensch; Meredith Yeager; Anders Ahlbom; et al. (Human Genetics, 2012)

Dynamic response characteristics of hyperaemia in the human calf muscle: effect of exercise intensity and relation to electromyographic activity - Elizabeth J. Reeder; Simon Green (European Journal of Applied Physiology, 2012)

Fire Accelerates Assimilation and Transfer of Photosynthetic Carbon from Plants to Soil Microbes in a Northern Peatland - Susan E. Ward; Nick J. Ostle; Simon Oakley; Helen Quirk; Andrew Stott; Peter A. Henrys; W. Andrew Scott; Richard D. Bardgett (Ecosystems, 2012)

Infectious mononucleosis and risk of breast cancer in a prospective study of women - J. Massa; A. Hamdan; K. C. Simon; K. Bertrand; G. Wulf; R. M. Tamimi; A. Ascherio (Cancer Causes & Control, 2012)

The Effect of Dietary Organic Chromium on Specific Growth Rate, Tissue Chromium Concentrations, Enzyme Activities and Histology in Common Carp, Cyprinus carpio L. - Arafat R. Ahmed; Awadhesh N. Jha; Simon J. Davies (Biological Trace Element Research, 2012)

Structural dynamics of muscle protein phosphorylation - Brett A. Colson; Simon J. Gruber; David D. Thomas (Journal of Muscle Research and Cell Motility, 2012)

Transcriptomics of coping strategies in free‐swimming Lepeophtheirus salmonis (Copepoda) larvae responding to abiotic stress - Ben J. G. Sutherland; Stuart G. Jantzen; Motoshige Yasuike; Dan S. Sanderson; Ben F. Koop; Simon R. M. Jones (Molecular Ecology, 2012)
The salmon louse Lepeophtheirus salmonis is a marine ectoparasite of wild and farmed salmon in the Northern Hemisphere. Infections of farmed salmon are of economic and ecological concern. Nauplius and copepodid salmon lice larvae are free‐swimming and disperse in the water column until they encounter a host. In this study, we characterized the sublethal stress responses of L. salmonis copepodid larvae by applying a 38K oligonucleotide microarray to profile transcriptomes following 24 h exposures to suboptimal salinity (30–10 parts per thousand ( ‰ )) or temperature (16–4 °C) environments. Hyposalinity exposure resulted in large‐scale gene expression changes relative to those elicited by a thermal gradient. Subsequently, transcriptome responses to a more finely resolved salinity gradient between 30 ‰ and 25 ‰ were profiled. Minimal changes occurred at 29 ‰ or 28 ‰ , a threshold of response was identified at 27 ‰ , and the largest response was at 25 ‰. Differentially expressed genes were clustered by pattern of expression, and clusters were characterized by functional enrichment analysis. Results indicate larval copepods adopt two distinct coping strategies in response to short‐term hyposaline stress: a primary response using molecular chaperones and catabolic processes at 27 ‰ ; and a secondary response up‐regulating ion pumps, transporters, a different suite of chaperones and apoptosis‐related transcripts at 26 ‰ and 25 ‰ . The results further our understanding of the tolerances of L. salmonis copepodids to salinity and temperature gradients and may assist in the development of salmon louse management strategies.

Viral latency drives ‘memory inflation’: a unifying hypothesis linking two hallmarks of cytomegalovirus infection - Christof K. Seckert; Marion Grießl; Julia K. Büttner; Sabine Scheller; Christian O. Simon; Kai A. Kropp; Angélique Renzaho; Birgit Kühnapfel; Natascha K. A. Grzimek; Matthias J. Reddehase (Medical Microbiology and Immunology, 2012)

Change and variability in sea ice during the 2007–2008 Canadian International Polar Year program - David G. Barber; Matthew G. Asplin; Richard L. Raddatz; Lauren M. Candlish; Scot Nickels; Stephanie Meakin; Klaus P. Hochheim; Jennifer V. Lukovich; Ryan J. Galley; Simon J. Prinsenberg (Climatic Change, 2012)

ABO blood group and risk of epithelial ovarian cancer within the Ovarian Cancer Association Consortium - Elizabeth M. Poole; Margaret A. Gates; Brigit A. High; Stephen J. Chanock; Daniel W. Cramer; Julie M. Cunningham; Brooke L. Fridley; Simon A. Gayther; Ellen L. Goode; Edwin S. Iversen; Jolanta Lissowska; Rachel T. Palmieri Weber; et al. (Cancer Causes & Control, 2012)

Maternal effects on begging behaviour: an experimental demonstration of the effects of laying sequence, hatch order, nestling sex and brood size - Amanda J. Gilby; Enrico Sorato; Simon C. Griffith (Behavioral Ecology and Sociobiology, 2012)

Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex - J. Jaquiéry; S. Stoeckel; P. Nouhaud; L. Mieuzet; F. Mahéo; F. Legeai; N. Bernard; A. Bonvoisin; R. Vitalis; J‐C. Simon (Molecular Ecology, 2012)
A major goal in evolutionary biology is to uncover the genetic basis of adaptation. Divergent selection exerted on ecological traits may result in adaptive population differentiation and reproductive isolation and affect differentially the level of genetic divergence along the genome. Genome‐wide scan of large sets of individuals from multiple populations is a powerful approach to identify loci or genomic regions under ecologically divergent selection. Here, we focused on the pea aphid, a species complex of divergent host races, to explore the organization of the genomic divergence associated with host plant adaptation and ecological speciation. We analysed 390 microsatellite markers located at variable distances from predicted genes in replicate samples of sympatric populations of the pea aphid collected on alfalfa, red clover and pea, which correspond to three common host‐adapted races reported in this species complex. Using a method that accounts for the hierarchical structure of our data set, we found a set of 11 outlier loci that show higher genetic differentiation between host races than expected under the null hypothesis of neutral evolution. Two of the outliers are close to olfactory receptor genes and three other nearby genes encoding salivary proteins. The remaining outliers are located in regions with genes of unknown functions, or which functions are unlikely to be involved in interactions with the host plant. This study reveals genetic signatures of divergent selection across the genome and provides an inventory of candidate genes responsible for plant specialization in the pea aphid, thereby setting the stage for future functional studies.

Predicting the century‐long post‐fire responses of reptiles - Dale. G. Nimmo; Luke T. Kelly; Lisa M. Spence‐Bailey; Simon J. Watson; Angie Haslem; John G. White; Mike F. Clarke; Andrew F. Bennett (Global Ecology and Biogeography, 2012)
Aim We examined the century‐long post‐fire responses of reptiles to (1) determine the time‐scales over which fauna – fire relationships occur, (2) assess the capacity of a conceptual model to predict faunal response to fire, and (3) investigate the degree to which models of fauna – fire relationships can predict species occurrence and are transferable across space. Location A 104,000 km 2 area in the semi‐arid Murray Mallee region of south‐eastern Australia. Methods We surveyed reptiles at 280 sites across a century‐long post‐fire chronosequence. We developed generalized additive mixed models (GAMMs) of the relationship between time since fire and the occurrence of 17 species in two subregions, and compared modelled responses with predictions derived from the conceptual model. The predictive capacity of GAMMs was then assessed (1) within the subregion the model was developed and (2) when transferred into a novel subregion. Results Eleven species displayed a significant relationship with time‐since‐fire, with changes in species probability of occurrence continuing up to 100 years post‐fire. Predictions of the timing of species post‐fire peak in occurrence were accurate for 9 of 13 species models for which a significant fire response was detected, but little success was achieved in predicting the shape of a species' response. GAMMs predicted species occurrence more accurately when applied within the subregion in which they were developed than when transferred into a novel subregion, primarily due to some species responding to fire more strongly in one part of their geographic range. Main conclusions Fire influences the occurrence of reptiles in semi‐arid ecosystems over century‐long time frames. Habitat‐use conceptual models have value in predicting the peak occurrence of species following fire, particularly for species with distributions strongly shaped by fire. Species relationships with fire can differ across their geographic range, probably associated with variation in climatic influences on post‐fire succession and the consequent provision of habitat resources.

Where do adaptive shifts occur during invasion? A multidisciplinary approach to unravelling cold adaptation in a tropical ant species invading the Mediterranean area - Olivier Rey; Arnaud Estoup; Merav Vonshak; Anne Loiseau; Simon Blanchet; Luis Calcaterra; Lucila Chifflet; Jean‐Pierre Rossi; Gaël J. Kergoat; Julien Foucaud; Jérôme Orivel; Maurice Leponce; et al. (Ecology Letters, 2012)
Evolution may improve the invasiveness of populations, but it often remains unclear whether key adaptation events occur after introduction into the recipient habitat (i.e. post‐introduction adaptation scenario), or before introduction within the native range (i.e. prior‐adaptation scenario) or at a primary site of invasion (i.e. bridgehead scenario). We used a multidisciplinary approach to determine which of these three scenarios underlies the invasion of the tropical ant Wasmannia auropunctata in a Mediterranean region (i.e. Israel). Species distribution models ( SDM ), phylogeographical analyses at a broad geographical scale and laboratory experiments on appropriate native and invasive populations indicated that Israeli populations followed an invasion scenario in which adaptation to cold occurred at the southern limit of the native range before dispersal to Israel. We discuss the usefulness of combining SDM , genetic and experimental approaches for unambiguous determination of eco‐evolutionary invasion scenarios.

Abiotic drivers and plant traits explain landscape‐scale patterns in soil microbial communities - Franciska T. de Vries; Pete Manning; Jerry R. B. Tallowin; Simon R. Mortimer; Emma S. Pilgrim; Kathryn A. Harrison; Phil J. Hobbs; Helen Quirk; Bill Shipley; Johannes H. C. Cornelissen; Jens Kattge; Richard D. Bardgett (Ecology Letters, 2012)
The controls on aboveground community composition and diversity have been extensively studied, but our understanding of the drivers of belowground microbial communities is relatively lacking, despite their importance for ecosystem functioning. In this study, we fitted statistical models to explain landscape‐scale variation in soil microbial community composition using data from 180 sites covering a broad range of grassland types, soil and climatic conditions in England. We found that variation in soil microbial communities was explained by abiotic factors like climate, pH and soil properties. Biotic factors, namely community‐weighted means (CWM) of plant functional traits, also explained variation in soil microbial communities. In particular, more bacterial‐dominated microbial communities were associated with exploitative plant traits versus fungal‐dominated communities with resource‐conservative traits, showing that plant functional traits and soil microbial communities are closely related at the landscape scale.

Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project - Abdel Ayadi; Marie-Christine Birling; Joanna Bottomley; James Bussell; Helmut Fuchs; Martin Fray; Valérie Gailus-Durner; Simon Greenaway; Richard Houghton; Natasha Karp; Sophie Leblanc; Christoph Lengger; et al. (Mammalian Genome, 2012)

Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits - Anatole Ghazalpour; Christoph D. Rau; Charles R. Farber; Brian J. Bennett; Luz D. Orozco; Atila van Nas; Calvin Pan; Hooman Allayee; Simon W. Beaven; Mete Civelek; Richard C. Davis; Thomas A. Drake; et al. (Mammalian Genome, 2012)

Composition, age, and origin of the ~620 Ma Humr Akarim and Humrat Mukbid A-type granites: no evidence for pre-Neoproterozoic basement in the Eastern Desert, Egypt - Kamal A. Ali; Abdel-Kader M. Moghazi; Ayman E. Maurice; Sayed A. Omar; Qiang Wang; Simon A. Wilde; Ewais M. Moussa; William I. Manton; Robert J. Stern (International Journal of Earth Sciences, 2012)

Odontocete bycatch and depredation in longline fisheries: A review of available literature and of potential solutions - Derek J. Hamer; Simon J. Childerhouse; Nick J. Gales (Marine Mammal Science, 2012)
Operational interactions between odontocetes ( i.e. , toothed whales) and longline gear are a global phenomenon that may threaten the conservation of odontocete populations and the economic viability of longline fisheries. This review attempts to define the issue, summarize the trends and geographical extent of its occurrence over the last half century, explore the potential impact on odontocetes and on fisheries, and describe potential acoustic and physical mitigation solutions. Reports of odontocete bycatch rates are highly variable (between 0.002 and 0.231 individuals killed per set) and at least 20 species may be involved. Information about marine mammal population size, migration patterns and life history characteristics are scarce, although at least one population may be in decline due to losses attributable to longline bycatch. Information about the financial impact of depredation on pelagic longline fisheries is also scarce, although estimates of daily fleet‐wide losses range between US$1,034 and US$8,495 (overall fleet income was not reported). Such biological and financial losses may be unsustainable. Recent developments in acoustic and physical mitigation technologies have yielded mixed results. Acoustic mitigation technologies have no moving parts, although require complex electronics. To date, they are insufficiently developed and their efficacy has been difficult to assess. Physical mitigation technologies generally require complex moving parts, although they are relatively simple to develop and assess. Further development and testing remains necessary before widespread implementation would be possible. Development of these approaches should be prioritized and a “toolbox” of various strategies and solutions should be compiled, because a single panacea to the problem is unlikely to emerge.

Dynamic macroecology and the future for biodiversity - Karel Mokany; Thomas D. Harwood; Kristen J. Williams; Simon Ferrier (Global Change Biology, 2012)
Reliable projections of climate‐change impacts on biodiversity are vital in formulating conservation and management strategies that best retain biodiversity into the future. While recent modelling has focussed largely on individual species, macroecology has the potential to add significant value to these efforts, by incorporating important community‐level constraints and processes. Here we show how a new dynamic macroecological approach can project climate‐change impacts collectively across all species in a diverse taxonomic group, overcoming shortfalls in our knowledge of biodiversity, while incorporating the key processes of dispersal and community assembly. Our approach applies a recently published technique ( Dynamic FOAM ) to predict the present composition of every community, which form the initial conditions for a new metacommunity model (M‐ SET ) that projects changes in composition over time, under specified climate and habitat scenarios. Applying this approach at fine resolution to plant biodiversity in Tasmania (2,051 species; 1,157,587 communities), we project high average turnover in community composition from 2010 to 2100 (mean Sorensen's dissimilarity = 0.71 (±7.0 × 10 −5 )), with major reductions in species richness (32.9 (±0.02) species lost per community) and no plant species benefitting from climate change in the long term. We also demonstrate how our modelling approach can identify habitat likely to be of high value for retaining rare and poorly reserved species under climate change. Our analyses highlight the potential value of this dynamic macroecological approach, that incorporates key ecological processes in projecting climate change impacts for all species simultaneously and uses simple macroecological inputs that can be derived even for highly diverse and poorly studied taxa.

Mineralisation of Weathered Crude Oil by a Hydrocarbonoclastic Consortia in Marine Mesocosms - Krishna K. Kadali; Keryn L. Simons; Petra J. Sheppard; Andrew S. Ball (Water, Air, & Soil Pollution, 2012)

Urban biodiversity: comparison of insect assemblages on native and non-native trees - Alvin J. Helden; Gemma C. Stamp; Simon R. Leather (Urban Ecosystems, 2012)

Effect of stock type characteristics and time of planting on field performance of aspen (Populus tremuloides Michx.) seedlings on boreal reclamation sites - Simon M. Landhäusser; Javier Rodriguez-Alvarez; Eckehart H. Marenholtz; Victor J. Lieffers (New Forests, 2012)

Evaluation of PRDM9 variation as a risk factor for recurrent genomic disorders and chromosomal non-disjunction - Christelle Borel; Fanny Cheung; Helen Stewart; David A. Koolen; Christopher Phillips; N. Simon Thomas; Patricia A. Jacobs; Stephan Eliez; Andrew J. Sharp (Human Genetics, 2012)

Dissociable contributions of motor-execution and action-observation to intramanual transfer - Spencer J. Hayes; Digby Elliott; Matthew Andrew; James W. Roberts; Simon J. Bennett (Experimental Brain Research, 2012)

Breaking with tradition: redefining measures for diet description with a case study of the Aleutian skate Bathyraja aleutica (Gilbert 1896) - Simon C. Brown; Joseph J. Bizzarro; Gregor M. Cailliet; David A. Ebert (Environmental Biology of Fishes, 2012)

Changes in the choice of colorectal cancer screening tests in primary care settings from 7,845 prospectively collected surveys - Martin C. S. Wong; George K. John; Hoyee W. Hirai; Thomas Y. T. Lam; Arthur K. C. Luk; Jessica Y. L. Ching; Simon S. M. Ng; Francis K. L. Chan; Sian M. Griffiths; Joseph J. Y. Sung (Cancer Causes & Control, 2012)

Revisiting competition in a classic model system using formal links between theory and data - Simon P. Hart; Jacqueline R. Burgin; Dustin J. Marshall (Ecology, 2012)
Formal links between theory and data are a critical goal for ecology. However, while our current understanding of competition provides the foundation for solving many derived ecological problems, this understanding is fractured because competition theory and data are rarely unified. Conclusions from seminal studies in space‐limited benthic marine systems, in particular, have been very influential for our general understanding of competition, but rely on traditional empirical methods with limited inferential power and compatibility with theory. Here we explicitly link mathematical theory with experimental field data to provide a more sophisticated understanding of competition in this classic model system. In contrast to predictions from conceptual models, our estimates of competition coefficients show that a dominant space competitor can be equally affected by interspecific competition with a poor competitor (traditionally defined) as it is by intraspecific competition. More generally, the often‐invoked competitive hierarchies and intransitivities in this system might be usefully revisited using more sophisticated empirical and analytical approaches.

Effects of stimulant drugs on actual and simulated driving: perspectives from four experimental studies conducted as part of the DRUID research consortium - J. G. Ramaekers; K. P. C. Kuypers; W. M. Bosker; K. A. Brookhuis; J. A. Veldstra; R. Simons; M. Martens; M. Hjälmdahl; Å. Forsman; A. Knoche (Psychopharmacology, 2012)

The spherical Slepian basis as a means to obtain spectral consistency between mean sea level and the geoid - D. C. Slobbe; F. J. Simons; R. Klees (Journal of Geodesy, 2012)

Hospital-acquired Clostridium difficile infection: determinants for severe disease - J. M. Wenisch; D. Schmid; H.-W. Kuo; E. Simons; F. Allerberger; V. Michl; P. Tesik; G. Tucek; C. Wenisch (European Journal of Clinical Microbiology & Infectious Diseases, 2012)

The Efficacy of Chromium as a Growth Enhancer for Mirror Carp (Cyprinus carpio L): An Integrated Study Using Biochemical, Genetic, and Histological Responses - Arafat R. Ahmed; Awadhesh N. Jha; Simon J. Davies (Biological Trace Element Research, 2012)

Contrasting pyroclast density spectra from subaerial and submarine silicic eruptions in the Kermadec arc: implications for eruption processes and dredge sampling - Simon J. Barker; Melissa D. Rotella; Colin J. N. Wilson; Ian C. Wright; Richard J. Wysoczanski (Bulletin of Volcanology, 2012)

Paternity assignment and demographic closure in the New Zealand southern right whale - EMMA L. CARROLL; SIMON J. CHILDERHOUSE; MARK CHRISTIE; SHANE LAVERY; NATHALIE PATENAUDE; ALANA ALEXANDER; ROCHELLE CONSTANTINE; DEBBIE STEEL; LAURA BOREN; C. SCOTT BAKER (Molecular Ecology, 2012)
The identification and characterization of reproductively isolated subpopulations or ‘stocks’ are essential for effective conservation and management decisions. This can be difficult in vagile marine species like marine mammals. We used paternity assignment and ‘gametic recapture’ to examine the reproductive autonomy of southern right whales ( Eubalaena australis ) on their New Zealand (NZ) calving grounds. We derived DNA profiles for 34 mother–calf pairs from skin biopsy samples, using sex‐specific markers, 13 microsatellite loci and mtDNA haplotypes. We constructed DNA profiles for 314 adult males, representing 30% of the census male abundance of the NZ stock, previously estimated from genotypic mark‐recapture modelling to be 1085 (95% CL 855, 1416). Under the hypothesis of demographic closure and the assumption of equal reproductive success among males, we predict: (i) the proportion of paternities assigned will reflect the proportion of the male population sampled and (ii) the gametic mark–recapture (GMR) estimate of male abundance will be equivalent to the census male estimate for the NZ stock. Consistent with these predictions, we found that the proportion of assigned paternities equalled the proportion of the census male population size sampled. Using the sample of males as the initial capture, and paternity assignment as the recapture, the GMR estimate of male abundance was 1001 (95% CL 542, 1469), similar to the male census estimate. These findings suggest that right whales returning to the NZ calving ground are reproductively autonomous on a generational timescale, as well as isolated by maternal fidelity on an evolutionary timescale, from others in the Indo‐Pacific region.

Deglaciation and catchment ontogeny in coastal south‐west Greenland: implications for terrestrial and aquatic carbon cycling - Melanie J. Leng; Bernd Wagner; N. John Anderson; Ole Bennike; Ewan Woodley; Simon J. Kemp (Journal of Quaternary Science, 2012)
Here we present Holocene organic carbon, nitrogen, sulphur, carbon isotope ratio and macrofossil data from a small freshwater lake near Sisimiut in south‐west Greenland. The lake was formed c. 11 cal ka BP following retreat of the ice sheet margin and is located above the marine limit in this area. The elemental and isotope data suggest a complex deglaciation history of interactions between the lake and its catchment, reflecting glacial retreat and post‐glacial hydrological flushing probably due to periodic melting of local remnant glacial ice and firn areas between 11 and 8.5 cal ka BP. After 8.5 cal ka BP, soil development and associated vegetation processes began to exert a greater control on terrestrial–aquatic carbon cycling. By 5.5 cal ka BP, in the early Neoglacial cooling, the sediment record indicates a change in catchment–lake interactions with consistent δ 13 C while C/N exhibits greater variability. The period after 5.5 cal ka BP is also characterized by higher organic C accumulation in the lake. These changes (total organic carbon, C/N, δ 13 C) are most likely the result of increasing contribution (and burial) of terrestrial organic matter as a result of enhanced soil instability, as indicated by an increase in Cenococcum remains, but also Sphagnum and Empetrum . The impact of glacial retreat and relatively subdued mid‐ to late Holocene climate variation at the coast is in marked contrast to the greater environmental variability seen in inland lakes closer to the present‐day ice sheet margin. Copyright © 2012 John Wiley & Sons, Ltd.

Isolating early cortical generators of visual-evoked activity: a systems identification approach - Jeremy W. Murphy; Simon P. Kelly; John J. Foxe; Edmund C. Lalor (Experimental Brain Research, 2012)

Use of linezolid in neonatal and pediatric inpatient facilities—results of a retrospective multicenter survey - A. Simon; E. Müllenborn; M. Prelog; W. Schenk; J. Holzapfel; F. Ebinger; A. Klabunde-Cherwon; J. Faber; A. H. Groll; K. Masjosthusmann; C. Dohna-Schwake; K. Beutel; et al. (European Journal of Clinical Microbiology & Infectious Diseases, 2012)

Treatment duration with selective serotonin reuptake inhibitors among children and adolescents in Finland: a nationwide register study - Leena K. Saastamoinen; Mika Wallin; Piia Lavikainen; Marja S. Airaksinen; Andre Sourander; J. Simon Bell (European Journal of Clinical Pharmacology, 2012)

International workshop on developing strategies for monitoring data-limited deepwater demersal line fisheries in the Pacific Ocean - Ashley J. Williams; Simon J. Nicol; Nokome Bentley; Paul J. Starr; Stephen J. Newman; Mike A. McCoy; Jeff Kinch; Peter G. Williams; Franck Magron; Graham M. Pilling; Ian Bertram; Mike Batty (Reviews in Fish Biology and Fisheries, 2012)

The socioeconomics of food crop production and climate change vulnerability: a global scale quantitative analysis of how grain crops are sensitive to drought - Elisabeth Simelton; Evan D. G. Fraser; Mette Termansen; Tim G. Benton; Simon N. Gosling; Andrew South; Nigel W. Arnell; Andrew J. Challinor; Andrew J. Dougill; Piers M. Forster (Food Security, 2012)

Characterisation of nine microsatellite loci in the caecilian amphibian Boulengerula uluguruensis (Gymnophiona), and their cross-species utility in three congeneric species - Christopher D. Barratt; Gavin J. Horsburgh; Deborah A. Dawson; David J. Gower; Mark Wilkinson; Simon P. Loader; Robert Jehle (Conservation Genetics Resources, 2012)

Water Dynamics in Fresh and Frozen Yeasted Dough - Simon M. Loveday; Victor T. Huang; David S. Reid; Ray J. Winger (Critical Reviews in Food Science and Nutrition, 2012)

Nutrient utilisation by shallow water temperate sponges in New Zealand - Alejandra Perea-Blázquez; Simon K. Davy; James J. Bell (Hydrobiologia, 2012)

Control of foliar diseases in barley: towards an integrated approach - Dale R. Walters; Anna Avrova; Ian J. Bingham; Fiona J. Burnett; James Fountaine; Neil D. Havis; Stephen P. Hoad; Gareth Hughes; Mark Looseley; Simon J. P. Oxley; Alan Renwick; Cairistiona F. E. Topp; et al. (European Journal of Plant Pathology, 2012)

Erratum to: The ecotoxicological recovery of Ely Creek and tributaries (Lee County, VA) after remediation of acid mine drainage - Matthew L. Simon; Donald S. Cherry; Rebecca J. Currie; Carl E. Zipper (Environmental Monitoring and Assessment, 2012)

Defoliation increases risk of carbon starvation in root systems of mature aspen - Simon M. Landhäusser; Victor J. Lieffers (Trees, 2012)

Assessing trophic position from nitrogen isotope ratios: effective calibration against spatially varying baselines - Paul Woodcock; David P. Edwards; Rob J. Newton; Felicity A. Edwards; Chey Vun Khen; Simon H. Bottrell; Keith C. Hamer (The Science of Nature, 2012)

Effects of ozone on species composition in an upland grassland - Kerstin V. Wedlich; Naomi Rintoul; Simon Peacock; J. Neil Cape; Mhairi Coyle; Sylvia Toet; Jeremy Barnes; Mike Ashmore (Oecologia, 2012)

Optimizing Hippocampal Segmentation in Infants Utilizing MRI Post-Acquisition Processing - Deanne K. Thompson; Zohra M. Ahmadzai; Stephen J. Wood; Terrie E. Inder; Simon K. Warfield; Lex W. Doyle; Gary F. Egan (Neuroinformatics, 2012)

Stable isotope ratios of a tropical marine predator: confounding effects of nutritional status during growth - Larisa Lee Cruz; Rona A. R. McGill; Simon J. Goodman; Keith C. Hamer (Marine Biology, 2012)

A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder - Jillian P. Casey; Tiago Magalhaes; Judith M. Conroy; Regina Regan; Naisha Shah; Richard Anney; Denis C. Shields; Brett S. Abrahams; Joana Almeida; Elena Bacchelli; Anthony J. Bailey; Gillian Baird; et al. (Human Genetics, 2012)

Using a Down-Scaled Bioclimate Envelope Model to Determine Long-Term Temporal Connectivity of Garry oak (Quercus garryana) Habitat in Western North America: Implications for Protected Area Planning - Marlow G. Pellatt; Simon J. Goring; Karin M. Bodtker; Alex J. Cannon (Environmental Management, 2012)

Aspects of the reproductive biology of two archer fishes Toxotes chatareus, (Hamilton 1822) and Toxotes jaculatrix (Pallas 1767) - K. D. Simon; Y. Bakar; A. G. Mazlan; C. C. Zaidi; A. Samat; A. Arshad; S. E. Temple; N. J. Brown-Peterson (Environmental Biology of Fishes, 2012)

E-Selectin Ligands as Mechanosensitive Receptors on Neutrophils in Health and Disease - S. D. Chase; J. L. Magnani; S. I. Simon (Annals of Biomedical Engineering, 2012)

Global threats to pinnipeds - Kit M. Kovacs; Alex Aguilar; David Aurioles; Vladimir Burkanov; Claudio Campagna; Nick Gales; Tom Gelatt; Simon D. Goldsworthy; Simon J. Goodman; Greg J. G. Hofmeyr; Tero Härkönen; Lloyd Lowry; et al. (Marine Mammal Science, 2012)

Fire and vegetation change during the Early Pleistocene in southeastern Australia - J. M. Kale Sniderman; Simon G. Haberle (Journal of Quaternary Science, 2012)
Early Pleistocene vegetation in upland southeastern Australia included diverse rainforests and sclerophyll forests, which alternated on precessional timescales. The nature and timing of transitions between these biomes, and the role of fire in maintaining or driving transitions between them, are uncertain. Here we present a high‐resolution pollen record from Stony Creek Basin, a small Early Pleistocene palaeolake in southeastern Australia. The pollen record documents a pattern of vegetation change, over ca. 10 ka at ca. 1590–1600 ka, between sclerophyll forests, dominated by Eucalyptus , Callitris (Cupressaceae) or Casuarinaceae, and rainforests dominated by either angiosperms or conifers of the family Podocarpaceae. Transitions between these biomes typically occurred within ca. 1–2 ka. The associated charcoal record suggests that greatest biomass combustion occurred when local vegetation was dominated by Eucalyptus , and the least biomass combustion occurred when local vegetation was dominated by Podocarpaceae. However, local fires burnt in both sclerophyll and angiosperm‐dominated rainforest vegetation, at least once every several centuries. Fire was very rare (less than about one fire per millennium) only when the local vegetation was rainforest dominated by Podocarpaceae. This suggests that fire was an irregular presence in both sclerophyll‐ and angiosperm‐dominated rainforest biomes during the late Neogene, though was largely absent in Podocarpaceae‐dominated rainforests. Copyright © 2011 John Wiley & Sons, Ltd.

Impacts of atmospheric nitrogen deposition: responses of multiple plant and soil parameters across contrasting ecosystems in long‐term field experiments - Gareth K. Phoenix; Bridget A. Emmett; Andrea J. Britton; Simon J. M. Caporn; Nancy B. Dise; Rachel Helliwell; Laurence Jones; Jonathan R. Leake; Ian D. Leith; Lucy J. Sheppard; Alwyn Sowerby; Michael G. Pilkington; et al. (Global Change Biology, 2012)
Atmospheric nitrogen ( N ) deposition is a global and increasing threat to biodiversity and ecosystem function. Much of our current understanding of N deposition impacts comes from field manipulation studies, although interpretation may need caution where simulations of N deposition (in terms of dose, application rate and N form) have limited realism. Here, we review responses to simulated N deposition from the UKREATE network, a group of nine experimental sites across the UK in a diversity of heathland, grassland, bog and dune ecosystems which include studies with a high level of realism and where many are also the longest running globally on their ecosystem type. Clear responses were seen across the sites with the greatest sensitivity shown in cover and species richness of bryophytes and lichens. Productivity was also increased at sites where N was the limiting nutrient, while flowering also showed high sensitivity, with increases and declines seen in dominant shrub and forb species, respectively. Critically, these parameters were responsive to some of the lowest additional loadings of N (7.7–10 kg ha −1 yr −1 ) showing potential for impacts by deposition rates seen in even remote and ‘unpolluted’ regions of E urope. Other parameters were less sensitive, but nevertheless showed response to higher doses. These included increases in soil % N and ‘plant available’ KCl extractable N , N cycling rates and acid–base status. Furthermore, an analysis of accumulated dose that quantified response against the total N input over time suggested that N impacts can ‘build up’ within an ecosystem such that even relatively low N deposition rates can result in ecological responses if continued for long enough. Given the responses have important implications for ecosystem structure, function, and recovery from N loading, the clear evidence for impacts at relatively low N deposition rates across a wide range of habitats is of considerable concern.

Verification of Design Spaces Developed at Subscale - Thomas Garcia; Vincent McCurdy; Timothy N. J. Watson; Mary am Ende; Penny Butterell; Kimberly Vukovinsky; Alex Chueh; Jonathan Coffman; Simon Cooper; Bernd Schuemmelfeder (Journal of Pharmaceutical Innovation, 2012)

The distinct effects of habitat fragmentation on population size - Kathy W. Herbener; Simon J. Tavener; N. Thompson Hobbs (Theoretical Ecology, 2012)

Movement strategies in vertical aiming of older adults - Simon J. Bennett; Digby Elliott; Andre Rodacki (Experimental Brain Research, 2012)

Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.) - H. Zhu; D. Senalik; B. H. McCown; E. L. Zeldin; J. Speers; J. Hyman; N. Bassil; K. Hummer; P. W. Simon; J. E. Zalapa (Theoretical and Applied Genetics, 2012)

Quantitative in vivo MRI measurement of cortical development in the fetus - Cédric Clouchoux; Dimitri Kudelski; Ali Gholipour; Simon K. Warfield; Sophie Viseur; Marine Bouyssi-Kobar; Jean-Luc Mari; Alan C. Evans; Adre J. du Plessis; Catherine Limperopoulos (Brain Structure and Function, 2012)

Transforming growth factor beta signaling in adult cardiovascular diseases and repair - Thomas Doetschman; Joey V. Barnett; Raymond B. Runyan; Todd D. Camenisch; Ronald L. Heimark; Henk L. Granzier; Simon J. Conway; Mohamad Azhar (Cell and Tissue Research, 2012)

Yield losses in grain sorghum due to rust infection - Jodie A. White; Malcolm J. Ryley; Doug L. George; Gary A. Kong; Simon C. White (Australasian Plant Pathology, 2012)

Temporal and vertical variations of lipid biomarkers during a bottom ice diatom bloom in the Canadian Beaufort Sea: further evidence for the use of the IP25 biomarker as a proxy for spring Arctic sea ice - Thomas A. Brown; Simon T. Belt; Benoît Philippe; Christopher J. Mundy; Guillaume Massé; Michel Poulin; Michel Gosselin (Polar Biology, 2011)

Hypomethylation of functional retrotransposon-derived genes in the human placenta - Erin C. Macaulay; Robert J. Weeks; Simon Andrews; Ian M. Morison (Mammalian Genome, 2011)

Tracking and mapping sun-synchronous migrations and diel space use patterns of Haemulon sciurus and Lutjanus apodus in the U.S. Virgin Islands - Steven Hitt; Simon J. Pittman; Kerry A. Brown (Environmental Biology of Fishes, 2011)

Experimental study of the dehydration of 10-Å phase, with implications for its H2O content and stability in subducted lithosphere - Alison R. Pawley; Nicholas J. Chinnery; Simon M. Clark; Michael J. Walter (Contributions to Mineralogy and Petrology, 2011)

Influence of insects and fungal pathogens on individual and population parameters of Cirsium arvense in its native and introduced ranges - Michael G. Cripps; Graeme W. Bourdôt; David J. Saville; Hariet L. Hinz; Simon V. Fowler; Grant R. Edwards (Biological Invasions, 2011)

Ovaprim treatment promotes oocyte development and milt fertilization rate in diploid and triploid African catfish (Clarias gariepinus) - Ali Karami; Annie Christianus; Hadi Zokaeifar; Khairul Zamri Saad; Fahmi T. J. Imraan; Shahram Shakibazadeh; Hossien Negarestan; Simon C. Courtenay (Aquaculture International, 2011)

The origin of high δ18O zircons: marbles, megacrysts, and metamorphism - Aaron J. Cavosie; John W. Valley; Noriko T. Kita; Michael J. Spicuzza; Takayuki Ushikubo; Simon A. Wilde (Contributions to Mineralogy and Petrology, 2011)

What factors do cancer patients believe contribute to the development of their cancer? (New South Wales, Australia) - Simon J. Willcox; Bernard W. Stewart; Freddy Sitas (Cancer Causes & Control, 2011)

Immunologically restricted patients exhibit a pronounced inflammation and inadequate response to hypoxia in fracture hematomas - Paula Hoff; T. Gaber; K. Schmidt-Bleek; U. Sentürk; C. L. Tran; K. Blankenstein; S. Lütkecosmann; J. Bredahl; H. J. Schüler; P. Simon; G. Wassilew; F. Unterhauser; et al. (Immunologic Research, 2011)

To know or not to know: influence of explicit advance knowledge of occlusion on interceptive actions - Pieter Tijtgat; Simon J. Bennett; Geert J. P. Savelsbergh; Dirk De Clercq; Matthieu Lenoir (Experimental Brain Research, 2011)

Rapid diagnosis of Clostridium difficile infection by multiplex real-time PCR - F. Barbut; M. Monot; A. Rousseau; S. Cavelot; T. Simon; B. Burghoffer; V. Lalande; J. Tankovic; J.-C. Petit; B. Dupuy; C. Eckert (European Journal of Clinical Microbiology & Infectious Diseases, 2011)

Exotic tree species displace indigenous ones on farms at intermediate altitudes around Mount Kenya - Katja Kehlenbeck; Roeland Kindt; Fergus L. Sinclair; Anthony J. Simons; Ramni Jamnadass (Agroforestry Systems, 2011)

The RNA chaperone, Hfq, controls two luxR ‐type regulators and plays a key role in pathogenesis and production of antibiotics in Serratia sp. ATCC 39006 - Nabil M. Wilf; Neil R. Williamson; Joshua P. Ramsay; Simon Poulter; Kasia J. Bandyra; George P. C. Salmond (Environmental Microbiology, 2011)
Summary Serratia sp. ATCC 39006 (S39006) is a Gram‐negative bacterium that is virulent in plant (potato) and animal ( Caenorhabditis elegans ) models. It produces two secondary metabolite antibiotics, a prodigiosin and a carbapenem, and the exoenzymes, pectate lyase and cellulase. A complex regulatory network that includes quorum sensing (QS) controls production of prodigiosin. While many aspects of the regulation of the metabolites and exoenzymes are well understood, the potential role in this network of the RNA chaperone Hfq and dependent small regulatory RNAs has not been characterized. Hfq is an RNA chaperone involved in post‐transcriptional regulation that plays a key role in stress response and virulence in diverse bacterial species. To explore whether Hfq‐dependent processes might contribute to the regulation of antibiotic production we constructed an S39006 Δ hfq mutant. Production of prodigiosin and carbapenem was abolished in this mutant strain, while production of the QS signalling molecule, butanoyl homoserine lactone (BHL), was unaffected. Using transcriptional fusions, we found that Hfq regulates the QS response regulators, SmaR and CarR. Additionally, exoenzyme production and swimming motility were decreased in a Δ hfq mutant, and virulence was attenuated in potato and C. elegans models. These results suggest that an Hfq‐dependent pathway is involved in the regulation of virulence and secondary metabolite production in S39006.

Pressure Buildup During CO2 Injection into a Closed Brine Aquifer - Simon A. Mathias; Gerardo J. González Martínez de Miguel; Kate E. Thatcher; Robert W. Zimmerman (Transport in Porous Media, 2011)

Fitness consequences of individual specialisation in resource use and trophic morphology in European eels - Julien Cucherousset; Anthony Acou; Simon Blanchet; J. Robert Britton; William R. C. Beaumont; Rodolphe E. Gozlan (Oecologia, 2011)

The Tyndall coastal simulator - Mustafa Mokrech; Susan Hanson; Robert J. Nicholls; Judith Wolf; Mike Walkden; Corentin M. Fontaine; Sophie Nicholson-Cole; Simon R. Jude; James Leake; Peter Stansby; Andrew R. Watkinson; Mark D. A. Rounsevell; et al. (Journal of Coastal Conservation, 2011)

Observed dissolved and particulate nitrogen concentrations in a mini flume - Simon J. Ussher; Andrew J. Manning; Alan D. Tappin; Mark F. Fitzsimons (Hydrobiologia, 2011)

Sleep and environmental context: interactive effects for memory - Scott A. Cairney; Simon J. Durrant; Hazel Musgrove; Penelope A. Lewis (Experimental Brain Research, 2011)

Use of standard vocabulary services in validation of water resources data described in XML - Jonathan Yu; Simon Cox; Gavin Walker; Paul J. Box; Paul Sheahan (Earth Science Informatics, 2011)

A decade of change in the saproxylic beetle fauna of eucalypt logs in the Warra long-term log-decay experiment, Tasmania. 2. Log-size effects, succession, and the functional significance of rare species - Simon J. Grove; Lynette Forster (Biodiversity and Conservation, 2011)

A decade of change in the saproxylic beetle fauna of eucalypt logs in the Warra long-term log-decay experiment, Tasmania. 1. Description of the fauna and seasonality patterns - Simon J. Grove; Lynette Forster (Biodiversity and Conservation, 2011)

Massive icebergs, alteration in primary food resources and change in benthic communities at Cape Evans, Antarctica - Simon F. Thrush; Vonda J. Cummings (Marine Ecology, 2011)
The presence of massive icebergs in the Southwestern Ross Sea (Antarctica) in the early‐to‐mid‐2000s changed the regional sea ice regime and phytoplankton productivity. We exploit data on benthic macro‐ and megafaunal communities collected on six occasions between 2001 and 2009 in the shallow waters adjacent to Cape Evans to link these oceanographic shifts to changes in benthic ecology. Changes in the abundance of individual species and community composition were generally strongest, and mostly negative, in 2002 and 2003, which exhibited the largest decrease in water column productivity and thick and persistent sea ice. This pattern of decreasing numbers from the start of sampling in 2001 to the lowest values in 2003 is consistent with the impact of the icebergs and a lagged response on the part of the benthic populations in response to food shortage. The patterns of stronger effects on macrofauna than on megafauna, and on abundance rather than species richness, are consistent with a change in food supply and/or recruitment for short‐lived species, rather than a physical disturbance effect. Nevertheless, recovery patterns are likely to reflect changes in benthic communities associated with larval supply and changes in top‐down control after the years of predicted lowest food supply. There are many potential manifestations of climate change in Antarctica, and many of the ecological responses to environmental change are likely to be mediated through the foodweb. Long‐term studies in different locations are essential if we are to understand and forecast changes in sea‐floor ecosystems.

Landsat mapping of annual inundation (1979–2006) of the Macquarie Marshes in semi-arid Australia - Rachael F. Thomas; Richard T. Kingsford; Yi Lu; Simon J. Hunter (International Journal of Remote Sensing, 2011)

Venous occlusion plethysmography versus Doppler ultrasound in the assessment of leg blood flow during calf exercise - Simon Green; R. Thorp; E. J. Reeder; J. Donnelly; G. Fordy (European Journal of Applied Physiology, 2011)

Hypoxia-induced oxidative DNA damage links with higher level biological effects including specific growth rate in common carp, Cyprinus carpio L. - Sanaa A. Mustafa; Sherain N. Al-Subiai; Simon J. Davies; Awadhesh N. Jha (Ecotoxicology, 2011)

The Role of Abandoned Channels as Refugia for Sustaining Pioneer Riparian Forest Ecosystems - John C. Stella; Maya K. Hayden; John J. Battles; Hervé Piégay; Simon Dufour; Alexander K. Fremier (Ecosystems, 2011)