How Effective is Reduced Tillage–Cover Crop Management in Reducing N2O Fluxes from Arable Crop Soils? - M. Abdalla; K. Rueangritsarakul; M. Jones; B. Osborne; M. Helmy; B. Roth; J. Burke; P. Nolan; P. Smith; M. Williams (Water, Air, & Soil Pollution, 2012)

Propagation of the loud “tchó” call of golden-backed uakaris, Cacajao melanocephalus, in the black-swamp forests of the upper Amazon - Bruna M. Bezerra; Antonio S. Souto; Gareth Jones (Primates, 2012)

cry1 and GPA1 signaling genetically interact in hook opening and anthocyanin synthesis in Arabidopsis - Ana R. Fox; Gabriela C. Soto; Alan M. Jones; Jorge J. Casal; Jorge P. Muschietti; María A. Mazzella (Plant Molecular Biology, 2012)

Influence of passive lower-body heating on muscle metabolic perturbation and high-intensity exercise tolerance in humans - Stephen J. Bailey; Daryl P. Wilkerson; Jonathan Fulford; Andrew M. Jones (European Journal of Applied Physiology, 2012)

Lifetime risk for cancer death by sex and smoking status: the lifetime risk pooling project - Andrew Gawron; Lifang Hou; Hongyan Ning; Jarett D. Berry; Donald M. Lloyd-Jones (Cancer Causes & Control, 2012)

Phylogenetic analysis of Ostreococcus virus sequences from the Patagonian Coast - Julieta M. Manrique; Andrea Y. Calvo; Leandro R. Jones (Virus Genes, 2012)

Simulating climate change in UK cities using a regional climate model, HadRM3 - M. P. McCarthy; C. Harpham; C. M. Goodess; P. D. Jones (International Journal of Climatology, 2012)
A regional climate model (RCM) at 25 km resolution, coupled to a simple urban land‐surface scheme has been used to assess the sensitivity of UK urban climates to large‐scale greenhouse gas (GHG) induced climate change, local forcing from urban land use, and anthropogenic heat flux (AHF) resulting from energy use in urban areas. GHG‐induced climate change is similar over both urban and rural land surfaces in the model, suggesting that under a changing climate the relative magnitude of urban heat islands in the UK would remain the same. However, indirect effects from urbanisation or changes in energy consumption within UK cities would contribute to further localized anthropogenic climate change that can be quantified by this model. The presence of the urban heat island also has a significant impact on the frequency of extreme high temperatures both in present and future climates, and will exacerbate the impact of climate change on the urban population. The simple urban land‐surface exchange scheme is a cost effective additional component of the RCM. It is shown to provide a realistic city‐scale urban heat island responding to the dynamical weather of the model at every model time‐step, with a magnitude and variability comparable to observed values. The climate model provides long integrations to derive large samples of heat islands under a full range of simulated dynamical conditions, and in this study sampling more than 100 years of climate change. Copyright © 2011 Royal Meteorological Society and British Crown copyright, the Met Office

A selective reversible monoamine oxidase B inhibitor in smoking cessation: effects on its own and in association with transdermal nicotine patch - Ivan Berlin; Ian M. Hunneyball; Doris Greiling; Stephen P. Jones; Hermann Fuder; Hans-Detlev Stahl (Psychopharmacology, 2012)

Individuals with non-specific low back pain in an active episode demonstrate temporally altered torque responses and direction-specific enhanced muscle activity following unexpected balance perturbations - Stephanie L. Jones; Juvena R. Hitt; Michael J. DeSarno; Sharon M. Henry (Experimental Brain Research, 2012)

Prolonged carriage of resistant E. coli by returned travellers: clonality, risk factors and bacterial characteristics - B. A. Rogers; K. J. Kennedy; H. E. Sidjabat; M. Jones; P. Collignon; D. L. Paterson (European Journal of Clinical Microbiology & Infectious Diseases, 2012)

High rate of prey consumption in a small predatory fish on coral reefs - W. E. Feeney; O. M. Lönnstedt; Y. Bosiger; J. Martin; G. P. Jones; R. J. Rowe; M. I. McCormick (Coral Reefs, 2012)

Dalliances and doubtful dads: what determines extra-pair paternity in socially monogamous wandering albatrosses? - M. Genevieve W. Jones; N. M. S. Mareile Techow; Peter G. Ryan (Behavioral Ecology and Sociobiology, 2012)

A female preference for experienced males in the almond moth, Cadra cautella - Kathryn B. McNamara; Julia L. McKenzie; Mark A. Elgar; Therésa M. Jones (Behavioral Ecology and Sociobiology, 2012)

Potential feeding deterrents found in hemlock woolly adelgid, Adelges tsugae - Anne C. Jones; Donald E. Mullins; Tappey H. Jones; Scott M. Salom (The Science of Nature, 2012)

Influence of sea surface wind wave turbulence upon wind-induced circulation, tide–surge interaction and bed stress - Jiuxing Xing; Alan M. Davies; John Eric Jones (Ocean Dynamics, 2012)

Jelly-falls historic and recent observations: a review to drive future research directions - Mario Lebrato; Kylie A. Pitt; Andrew K. Sweetman; Daniel O. B. Jones; Joan E. Cartes; Andreas Oschlies; Robert H. Condon; Juan Carlos Molinero; Laetitia Adler; Christian Gaillard; Domingo Lloris; David S. M. Billett (Hydrobiologia, 2012)

Fish body condition and recruitment success reflect antecedent flows in an Australian dryland river - Stephen R. Balcombe; Jaye S. Lobegeiger; Sharon M. Marshall; Jonathan C. Marshall; Diana Ly; Darryl N. Jones (Fisheries Science, 2012)

Influence of initial metabolic rate on the power–duration relationship for all-out exercise - Len Parker Simpson; Andrew M. Jones; Anni Vanhatalo; Daryl P. Wilkerson (European Journal of Applied Physiology, 2012)

Haplotype analysis of Viviparous-1 gene in CIMMYT elite bread wheat germplasm - Y. W. Sun; H. D. Jones; Y. Yang; S. Dreisigacker; S. M. Li; X. M. Chen; P. R. Shewry; L. Q. Xia (Euphytica, 2012)

Erratum to: Mapping of earthworm distribution for the British Isles and Eire highlights the under-recording of an ecologically important group - Daniel Carpenter; Emma Sherlock; David T. Jones; Jim Chiminoides; Thomas Writer; Roy Neilson; Brian Boag; Aidan M. Keith; Paul Eggleton (Biodiversity and Conservation, 2012)

Size-assortative pairing across three developmental stages in the Zeus bug, Phoreticovelia disparata - Therésa M. Jones; Göran Arnqvist; Kathryn B. McNamara; Mark A. Elgar (Behavioral Ecology and Sociobiology, 2012)

Lake and catchment response to Holocene environmental change: spatial variability along a climate gradient in southwest Greenland - N. J. Anderson; A. C. Liversidge; S. McGowan; M. D. Jones (Journal of Paleolimnology, 2012)

Reconstruction of past methane availability in an Arctic Alaska wetland indicates climate influenced methane release during the past ~12,000 years - Matthew J. Wooller; John W. Pohlman; Benjamin V. Gaglioti; Peter Langdon; Miriam Jones; Katey M. Walter Anthony; Kevin W. Becker; Kai-Uwe Hinrichs; Marcus Elvert (Journal of Paleolimnology, 2012)

Quantification of total and particulate dimethylsulfoniopropionate (DMSP) in five Bermudian coral species across a depth gradient - D. M. Yost; R. Jones; C. L. Rowe; Carys Louise Mitchelmore (Coral Reefs, 2012)

Single-Injection HPLC Method for Rapid Analysis of a Combination Drug Delivery System - Robert M. Tucker; Benjamin W. Parcher; Ella F. Jones; Tejal A. Desai (AAPS PharmSciTech, 2012)

Putting biogeography’s cart back behind taxonomy’s horse: a response to Triantis et al. - Mark A. Carine; Katy Jones; Mónica Moura; M. Graciete Belo Maciel; Fred J. Rumsey; Hanno Schaefer (Journal of Biogeography, 2012)
In a recent paper, two of us discussed diversity patterns and diversification processes in the Azores flora. Triantis et al. (2012, Journal of Biogeography , 39, 1179–1184) challenged our hypothesis that palaeoclimatic differences had an effect on diversification rates and suggested that area, island age and isolation explain diversity patterns. They did not, however, fully address the results from our subsequent paper, in which we showed that diversity patterns evident from phylogeographic studies differ markedly from those suggested by checklists. Checklists are working hypotheses and we suggest that the discrepancies evident between molecular data and checklists may be indicative of deficiencies in our taxonomic understanding of the Azores flora. Patterns of molecular and morphological diversity need to be better understood, and the discrepancies between checklists and molecular data accounted for, before we can establish the relative importance of factors such as palaeoclimate, area, island age or isolation in generating endemic diversity patterns in the Azores flora.

Decreased soil microbial biomass and nitrogen mineralisation with Eucalyptus biochar addition to a coarse textured soil - D. N. Dempster; D. B. Gleeson; Z. M. Solaiman; D. L. Jones; D. V. Murphy (Plant and Soil, 2012)

Interference in foraging behaviour of European and American house dust mites Dermatophagoides pteronyssinus and Dermatophagoides farinae (Acari: Pyroglyphidae) by catmint, Nepeta cataria (Lamiaceae) - M. A. Khan; I. Jones; E. Loza-Reyes; M. M. Cameron; J. A. Pickett; M. A. Birkett (Experimental and Applied Acarology, 2012)

Recent climate change in the Arabian Peninsula: annual rainfall and temperature analysis of Saudi Arabia for 1978–2009 - Mansour Almazroui; M. Nazrul Islam; H. Athar; P. D. Jones; M. Ashfaqur Rahman (International Journal of Climatology, 2012)
The rainfall and temperature climatology over the Arabian Peninsula are analysed on an annual basis using various gridded datasets. For Saudi Arabia, the area of which represents almost 80% of the Peninsula, the climatic datasets from its 27 ground observations are analysed for the period 1978–2009, with additional gridded datasets used to describe the observed state and change of the present climate. The gridded datasets represent well the very dry (40–80 mm) area over the world's largest sand desert (Rub Al‐Khali), the dry (80–150 mm) area over middle‐to‐north of Saudi Arabia, and the wettest (>150 mm) region in the southwest of the Peninsula. The annual temperature is relatively high (24–27 °C) in the middle‐to‐south of the Peninsula and low ( 27 °C) is obtained over the Rub Al‐Khali. Over Saudi Arabia, the observed annual rainfall showed a significant decreasing trend (47.8 mm per decade) in the last half of the analysis period, with a relatively large interannual variability, while the maximum, mean and minimum temperatures have increased significantly at a rate of 0.71, 0.60, and 0.48 °C per decade, respectively. This information is invaluable to consider in any climate impact assessment studies in Saudi Arabia. Copyright © 2012 Royal Meteorological Society

The effects of PRX-07034, a novel 5-HT6 antagonist, on cognitive flexibility and working memory in rats - Eric G. Mohler; Phillip M. Baker; Kimberly S. Gannon; Simon S. Jones; Sharon Shacham; John A. Sweeney; Michael E. Ragozzino (Psychopharmacology, 2012)

Spatio-temporal patterns of tree establishment are indicative of biotic interactions during early invasion of a montane meadow - Janine M. Rice; Charles B. Halpern; Joseph A. Antos; Julia A. Jones (Plant Ecology, 2012)

Nitrogen fixation by pea and lentil green manures in a semi-arid agroecoregion: effect of planting and termination timing - Ann M. McCauley; Clain A. Jones; Perry R. Miller; Macdonald H. Burgess; Catherine A. Zabinski (Nutrient Cycling in Agroecosystems, 2012)

The atm-1 gene is required for genome stability in Caenorhabditis elegans - Martin R. Jones; Jim Chin Huang; Shu Yi Chua; David L. Baillie; Ann M. Rose (Molecular Genetics and Genomics, 2012)

Genomic Resources for Sea Lice: Analysis of ESTs and Mitochondrial Genomes - Motoshige Yasuike; Jong Leong; Stuart G. Jantzen; Kristian R. von Schalburg; Frank Nilsen; Simon R. M. Jones; Ben F. Koop (Marine Biotechnology, 2012)

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.

A High-throughput Platform for the Production and Analysis of Transgenic Cassava (Manihot esculenta) Plants - Nigel Taylor; Eliana Gaitán-Solís; Theodore Moll; Brent Trauterman; Tira Jones; Amita Pranjal; Cindy Trembley; Vince Abernathy; David Corbin; Claude M. Fauquet (Tropical Plant Biology, 2012)

Simulation of soil nitrogen, nitrous oxide emissions and mitigation scenarios at 3 European cropland sites using the ECOSSE model - M. J. Bell; E. Jones; J. Smith; P. Smith; J. Yeluripati; J. Augustin; R. Juszczak; J. Olejnik; M. Sommer (Nutrient Cycling in Agroecosystems, 2012)

Immune cell-mediated neuroprotection is independent of estrogen action through estrogen receptor-alpha - Junping Xin; Keith N. Fargo; Lisa Tanzer; Virginia M. Sanders; Kathryn J. Jones (Metabolic Brain Disease, 2012)

Accumulation and effects of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) exposure in the green anole (Anolis carolinensis) - S. T. McMurry; L. E. Jones; P. N. Smith; G. P. Cobb; T. A. Anderson; M. B. Lovern; S. Cox; X. Pan (Ecotoxicology, 2012)

Rising CO2 concentrations affect settlement behaviour of larval damselfishes - B. M. Devine; P. L. Munday; G. P. Jones (Coral Reefs, 2012)

Patterns of migration between feeding and spawning sites in a coral reef surgeonfish - J. A. B. Claydon; M. I. McCormick; G. P. Jones (Coral Reefs, 2012)

The Intrinsic Fatigue Mechanism of the Porcine Aortic Valve Extracellular Matrix - Jun Liao; Erinn M. Joyce; W. David Merryman; Hugh L. Jones; Mina Tahai; M. F. Horstemeyer; Lakiesha N. Williams; Richard A. Hopkins; Michael S. Sacks (Cardiovascular Engineering and Technology, 2012)

Non-cancer endpoints in BRCA1/2 carriers after risk-reducing salpingo-oophorectomy - J. V. Cohen; L. Chiel; L. Boghossian; M. Jones; J. E. Stopfer; J. Powers; T. R. Rebbeck; K. L. Nathanson; S. M. Domchek (Familial Cancer, 2012)

Fourteen novel microsatellite markers for the gopher frog, Lithobates capito (Amphibia: Ranidae) - Schyler O. Nunziata; Stephen C. Richter; Robert D. Denton; John M. Yeiser; Danielle E. Wells; Kenneth L. Jones; Cris Hagen; Stacey L. Lance (Conservation Genetics Resources, 2012)

Women’s self-perceived health and attractiveness predict their male vocal masculinity preferences in different directions across short- and long-term relationship contexts - D. R. Feinberg; L. M. DeBruine; B. C. Jones; A. C. Little; J. J. M. O’Connor; C. C. Tigue (Behavioral Ecology and Sociobiology, 2012)

Cylindrocarpon black foot in nurseries—two factors that can increase infection - C. Probst; E. E. Jones; H. J. Ridgway; M. V. Jaspers (Australasian Plant Pathology, 2012)

High-density genetic linkage maps with over 2,400 sequence-anchored DArT markers for genetic dissection in an F2 pseudo-backcross of Eucalyptus grandis × E. urophylla - Anand Raj Kumar Kullan; Maria M. van Dyk; Nicoletta Jones; Arnulf Kanzler; Arlene Bayley; Alexander A. Myburg (Tree Genetics & Genomes, 2012)

Erratum to: A system dynamics approach in LCA to account for temporal effects—a consequential energy LCI of car bodies-in-white - Peter Stasinopoulos; Paul Compston; Barry Newell; Haley M. Jones (The International Journal of Life Cycle Assessment, 2012)

A system dynamics approach in LCA to account for temporal effects—a consequential energy LCI of car body-in-whites - Peter Stasinopoulos; Paul Compston; Barry Newell; Haley M. Jones (The International Journal of Life Cycle Assessment, 2012)

Achieving consensus on current and future priorities for farmed fish welfare: a case study from the UK - I. K. Berrill; T. Cooper; C. M. MacIntyre; T. Ellis; T. G. Knowles; E. K. M. Jones; J. F. Turnbull (Fish Physiology and Biochemistry, 2012)

Mapping of earthworm distribution for the British Isles and Eire highlights the under-recording of an ecologically important group - Daniel Carpenter; Emma Sherlock; David T. Jones; Jim Chiminoides; Thomas Writer; Roy Neilson; Brian Boag; Aidan M. Keith; Paul Eggleton (Biodiversity and Conservation, 2012)

Parasites and hepatic lesions among pink salmon, Oncorhynchus gorbuscha (Walbaum), during early seawater residence - S M Saksida; G D Marty; S R M Jones; H A Manchester; C L Diamond; J Bidulka; S St‐Hilaire (Journal of Fish Diseases, 2012)
Juvenile pink salmon, Oncorhynchus gorbuscha (Walbaum), in the Broughton Archipelago region of western Canada were surveyed over 2 years for sea lice ( Lepeophtheirus salmonis and Caligus clemensi ), gross and microscopic lesions and evidence of infections with viruses and bacteria. The 1071 fish examined had an approximate ocean residence time no longer than 3 months. A high prevalence of degenerative liver lesions, renal myxosporean parasites and a low prevalence of skin lesions and sea lice were observed. No indications of viral or bacterial diseases were detected in either year. The monthly prevalence of sea lice in 2007 (18–51%) was higher than in 2008 (1–26%), and the infestation density exceeded the lethal threshold in only two fish. Degenerative hepatic lesions and renal myxosporean parasites occurred in approximately 40% of the pink salmon examined in June of both years, and the peak monthly prevalence of hepatocellular hydropic degeneration was greater in 2007 (32%, in May) than in 2008 (12%, in June). Logistic regression analysis found skin lesions and hepatocellular hydropic degeneration significantly associated with sea lice. Most parasites and lesions occurred during both years, but the prevalence was often higher in 2007. Fish weight was 35% less in June 2007 than in June 2008, but condition factor was not different. Further research is required to monitor inter‐annual variations and aetiology of the liver lesions and to assess their potential role on pink salmon survival.

Reflection impulsivity in adolescent cannabis users: a comparison with alcohol-using and non-substance-using adolescents - Nadia Solowij; Katy A. Jones; Megan E. Rozman; Sasha M. Davis; Joseph Ciarrochi; Patrick C.L. Heaven; Nicole Pesa; Dan I. Lubman; Murat Yücel (Psychopharmacology, 2012)

Homing ability of adult cardinalfish is affected by elevated carbon dioxide - Brynn M. Devine; Philip L. Munday; Geoffrey P. Jones (Oecologia, 2012)

Changes in the mRNA Levels of α2A and α2C Adrenergic Receptors in Rat Models of Parkinson’s Disease and l-DOPA-Induced Dyskinesia - Amal Alachkar; Jonathan M. Brotchie; Owen T. Jones (Journal of Molecular Neuroscience, 2012)

Increases in Australian cutaneous abscess hospitalisations: 1999–2008 - V. L. Vaska; G. R. Nimmo; M. Jones; K. Grimwood; D. L. Paterson (European Journal of Clinical Microbiology & Infectious Diseases, 2012)

Why are some biodiversity policies implemented and others ignored? Lessons from the uptake of the Global Strategy for Plant Conservation by botanic gardens - Sophie J. Williams; Julia P. G. Jones; Colin Clubbe; Suzanne Sharrock; James M. Gibbons (Biodiversity and Conservation, 2012)

The role of wax and resin in the nestmate recognition system of a stingless bee, Tetragonisca angustula - Sam M. Jones; Jelle S. van Zweden; Christoph Grüter; Cristiano Menezes; Denise A. Alves; Patrícia Nunes-Silva; Tomer Czaczkes; Vera L. Imperatriz-Fonseca; Francis L. W. Ratnieks (Behavioral Ecology and Sociobiology, 2012)

Verrucosispora maris sp. nov., a novel deep-sea actinomycete isolated from a marine sediment which produces abyssomicins - Michael Goodfellow; James E. M. Stach; Roselyn Brown; Avinash Naga Venkata Bonda; Amanda L. Jones; Joanne Mexson; Hans-Peter Fiedler; Tiago Domingues Zucchi; Alan T. Bull (Antonie van Leeuwenhoek, 2012)

The pathology of ‘scale drop syndrome’ in Asian seabass, Lates calcarifer Bloch, a first description - S Gibson‐Kueh; D Chee; J Chen; Y H Wang; S Tay; L N Leong; M L Ng; J B Jones; P K Nicholls; H W Ferguson (Journal of Fish Diseases, 2012)
This is the first pathological description of ‘scale drop syndrome’ (SDS) in Asian seabass, Lates calcarifer Bloch. Cumulative mortality was estimated at 40–50%. The vasculitis in all major organs including the skin and associated tissue necrosis was distinctive. The dermis overlying scale beds was often necrotic and associated with scale loss. Necrosis of splenic ellipsoids, renal glomeruli and choroid rete glands of eye were further hallmarks of a disease with systemic vascular involvement. The brain was not spared vascular damage, and the resulting multifocal encephalomalacia probably accounts for the spiral swimming behaviour in some affected fish. Other lesions included accentuated hepatic lobulation and gastric gland necrosis. Nuclear chromatin margination and karyolysis in hepatocytes, renal tubular epithelium and gastric and intestinal epithelium suggest specific targeting of cells. Basophilic cytoplasmic inclusions were present in spleen, kidney, liver, heart and choroid rete, but they were not prominent. Using transmission electron microscopy, two morphological forms of virions were observed: single‐ and double‐enveloped hexagonal virions. Based on size and morphology, these virions resemble iridovirus or herpesvirus. The cause of SDS is unknown, but the pathological changes, especially the vasculitis, suggest an infectious aetiology, possibly viral.

Hydrothermal mineral alteration patterns in the Mount Isa Inlier revealed by airborne hyperspectral data - C. Laukamp; T. Cudahy; M. Thomas; M. Jones; J. S. Cleverley; N. H.S. Oliver (Australian Journal of Earth Sciences, 2011)

Genetic control of flowering time in Eucalyptus globulus ssp. globulus - Rebecca C. Jones; René E. Vaillancourt; Peter L. Gore; Brad M. Potts (Tree Genetics & Genomes, 2011)

Transition zones in small lakes: the importance of dilution and biological uptake on lake-wide heterogeneity - Eleanor B. Mackay; Ian D. Jones; Andrew M. Folkard; Stephen J. Thackeray (Hydrobiologia, 2011)

Monocyclic and monoaromatic naphthenic acids: synthesis and characterisation - S. J. Rowland; C. E. West; A. G. Scarlett; D. Jones; M. Boberek; L. Pan; M. Ng; L. Kwong; A. Tonkin (Environmental Chemistry Letters, 2011)

Ontogenetic changes in responses to settlement cues by Anemonefish - D. L. Dixson; P. L. Munday; M. Pratchett; G. P. Jones (Coral Reefs, 2011)

Role of aluminum in red-to-blue color changes in Hydrangea macrophylla sepals - Henry D. Schreiber; Andrew H. Jones; Corinne M. Lariviere; Kelly M. Mayhew; Judith B. Cain (BioMetals, 2011)

Pacific Rim Forestry / Silviculture and Forest Ecology - Vishal Singh Negi; Archana Pal; Ratnesh Singh; Dulal Borthakur; Archana Pala; Vishal Singh Negi; Dulal Borthakur; Isabel Rushanaedy; Tyler Jones; Nicklos Dudley; Dulal Borthakur; Jannai Yafuso; et al. (Journal of Forestry, 2011)
Leucaena leucocephala (leucaena) is an important agroforestry tree of tropics and subtropics due to its protein rich foliages, ability to grow on poor soils, and high level of tolerance to various stresses including drought and diseases. We hypothesized that leucaena have a unique set of genes which confer tolerance to various abiotic and biotic stresses and these genes are either absent or not expressed in other legumes that are susceptible to these stress conditions. Interspecies suppression subtractive hybridization (iSSH) was performed to identify some unique genes from leucaena using cDNAs from leucaena and Acacia confusa (acacia) as the tester and driver, respectively. We identified 100 leucaena genes showing homology to various plant genes with known functions, of which 23 genes had homology to various stress-related proteins including chitinase, PR-10 protein, wound-stress protein, type-2 metallothionein, thaumatin-like protein, disease resistance response protein, cysteine proteinase, and kunitz trypsin inhibitor. We also identified 50 leucaena genes which either had homology to hypothetical proteins (HyPs) or had no homology at all. Putative functions of 15 HyPs were predicted using conserved domain and PSI-BLAST analyses. Linear motif analyses identified 17 HyPs with MAPK recognition motif, which is involved in signaling pathways, including stress responses. This study identified 23 known and some putative unique stress-related genes from leucaena which may serve as a useful source of stress-tolerance genes for tree and crop improvement in the future.

Zucchini yellow mosaic virus: biological properties, detection procedures and comparison of coat protein gene sequences - B. A. Coutts; M. A. Kehoe; C. G. Webster; S. J. Wylie; R. A. C. Jones (Archives of Virology, 2011)

Methane emissions from sheep pasture, measured with an open‐path eddy covariance system - Sigrid Dengel; Peter E. Levy; John Grace; Stephanie K. Jones; Ute M. Skiba (Global Change Biology, 2011)
Methane ( CH 4 ) is an important greenhouse gas, contributing 0.4–0.5 W m −2 to global warming. Methane emissions originate from several sources, including wetlands, rice paddies, termites and ruminating animals. Previous measurements of methane flux from farm animals have been carried out on animals in unnatural conditions, in laboratory chambers or fitted with cumbersome masks. This study introduces eddy covariance measurements of CH 4 , using the newly developed LI‐COR LI ‐7700 open‐path methane analyser, to measure field‐scale fluxes from sheep grazing freely on pasture. Under summer conditions, fluxes of methane in the morning averaged 30 nmol m −2 s −1 , whereas those in the afternoon were above 100 nmol m −2 s −1 , and were roughly two orders of magnitude larger than the small methane emissions from the soil. Methane emissions showed no clear relationship with air temperature or photosynthetically active radiation, but some diurnal pattern was apparent, probably linked to sheep grazing behaviour and metabolism. Over the measurement period (days 60–277, year 2010), cumulative methane fluxes were 0.34 mol CH 4 m −2 , equating to 134.3 g CO 2 equivalents m −2 . By comparison, a carbon dioxide ( CO 2 ) sink of 819 g CO 2 equivalents m −2 was measured over the same period, but it is likely that much of this would be released back to the atmosphere during the winter or as off‐site losses (through microbial and animal respiration). By dividing methane fluxes by the number of sheep in the field each day, we calculated CH 4 emissions per head of livestock as 7.4 kg CH 4 sheep −1 yr −1 , close to the published IPCC emission factor of 8 kg CH 4 sheep −1 yr −1 .

Mapping cell fate decisions that occur during soybean defense responses - Prachi D. Matsye; Ranjit Kumar; Parsa Hosseini; Christina M. Jones; Arianne Tremblay; Nadim W. Alkharouf; Benjamin F. Matthews; Vincent P. Klink (Plant Molecular Biology, 2011)

Erratum to: Are Tangles as Toxic as They Look? - Tara L. Spires-Jones; Katherine J. Kopeikina; Robert M. Koffie; Alix de Calignon; Bradley T. Hyman (Journal of Molecular Neuroscience, 2011)

Are Tangles as Toxic as They Look? - Tara L. Spires-Jones; Katherine J. Kopeikina; Robert M. Koffie; Alix de Calignon; Bradley T. Hyman (Journal of Molecular Neuroscience, 2011)

The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes - N. D. Gray; A. Sherry; R. J. Grant; A. K. Rowan; C. R. J. Hubert; C. M. Callbeck; C. M. Aitken; D. M. Jones; J. J. Adams; S. R. Larter; I. M. Head (Environmental Microbiology, 2011)
Summary Libraries of 16S rRNA genes cloned from methanogenic oil degrading microcosms amended with North Sea crude oil and inoculated with estuarine sediment indicated that bacteria from the genera Smithella ( Deltaproteobacteria, Syntrophaceace ) and Marinobacter sp. ( Gammaproteobacteria ) were enriched during degradation. Growth yields and doubling times (36 days for both Smithella and Marinobacter ) were determined using qPCR and quantitative data on alkanes, which were the predominant hydrocarbons degraded. The growth yield of the Smithella sp. [0.020 g (cell‐C) /g (alkane‐C) ], assuming it utilized all alkanes removed was consistent with yields of bacteria that degrade hydrocarbons and other organic compounds in methanogenic consortia. Over 450 days of incubation predominance and exponential growth of Smithella was coincident with alkane removal and exponential accumulation of methane. This growth is consistent with Smithella's occurrence in near surface anoxic hydrocarbon degrading systems and their complete oxidation of crude oil alkanes to acetate and/or hydrogen in syntrophic partnership with methanogens in such systems. The calculated growth yield of the Marinobacter sp., assuming it grew on alkanes, was [0.0005 g (cell‐C) /g (alkane‐C) ] suggesting that it played a minor role in alkane degradation. The dominant methanogens were hydrogenotrophs ( Methanocalculus spp. from the Methanomicrobiales ). Enrichment of hydrogen‐oxidizing methanogens relative to acetoclastic methanogens was consistent with syntrophic acetate oxidation measured in methanogenic crude oil degrading enrichment cultures. qPCR of the Methanomicrobiales indicated growth characteristics consistent with measured rates of methane production and growth in partnership with Smithella .

A model study of tidal distributions in the Celtic and Irish Sea regions determined with finite volume and finite element models - Alan M Davies; Jiuxing Xing; John Eric Jones (Ocean Dynamics, 2011)

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom - Edgar M. Medina; Gary W. Jones; David A. Fitzpatrick (Journal of Molecular Evolution, 2011)

Development and characterization of 12 microsatellite loci for the Dwarf Salamander, Eurycea quadridigitata - Anna M. Mckee; Stacey L. Lance; Kenneth L. Jones; Cris Hagen; Travis C. Glenn (Conservation Genetics Resources, 2011)

Erratum to: Establishment of Psyllaephagus parvus and P. perplexus as serendipitous biological control agents of Eucalyptus psyllids in southern California - Michele Eatough Jones; Kent M. Daane; Timothy D. Paine (BioControl, 2011)

Establishment of Psyllaephagus parvus and P. perplexans as serendipitous biological control agents of Eucalyptus psyllids in southern California - Michele Eatough Jones; Kent M. Daane; Timothy D. Paine (BioControl, 2011)

Total mercury in stranded marine mammals from the Oregon and southern Washington coasts - Nathan J. P. Wintle; Deborah A. Duffield; Nélio B. Barros (Deceased); Ronald D. Jones; James M. Rice (Marine Mammal Science, 2011)
Muscle samples from 105 marine mammals stranded along the Oregon and Washington coasts (2002–2009) were tested for levels of total mercury (THg) by Cold Vapor Atomic Fluorescence Spectrometry. The THg present is in the form of the highly toxic methylmercury. After normalizing tissue to 75% water weight, Steller sea lions and northern elephant seals exhibited the highest mean concentrations of THg followed by harbor seals, harbor porpoises, and California sea lions, 0.34 ± 0.278, 0.34 ± 0.485, 0.21 ± 0.216, 0.17 ± 0.169, and 0.15 ± 0.126 mg/kg normalized wet weight (ww), respectively. The mean normalized values demonstrate limited muscle methylmercury accumulation in these species in the Pacific Northwest. However, actual ww concentrations in some of the stranded carcasses may pose a risk to scavengers. Normalizing muscle mercury concentrations eliminated the variability from desiccation, and allowed for a clearer indication of the amount of mercury the animal accumulated before stranding.

Coral obligate filefish masquerades as branching coral - R. M. Brooker; P. L. Munday; G. P. Jones (Coral Reefs, 2011)

Tool use in the tuskfish Choerodon schoenleinii? - A. M. Jones; C. Brown; S. Gardner (Coral Reefs, 2011)

Carbon self‐utilization may assist Caulerpa taxifolia invasion - Joanne M. Oakes; Melissa D. Bautista; Damien Maher; W. Brian Jones; Bradley D. Eyre (Limnology and Oceanography, 2011)
Additions of 13 C‐labeled macroalgal detritus ( Caulerpa taxifolia ) and seagrass detritus ( Zostera capricorni ) to a vegetated intertidal mudflat in subtropical Australia provided insight into the mechanisms and ecosystem effects of C. taxifolia invasions in seagrass beds. Despite the high lability typical of macroalgae, carbon from seagrass detritus was removed from sediments and transferred to benthic compartments (microphytobenthos, bacteria, mud whelks, and live C. taxifolia and Z. capricorni ) at a faster rate than carbon from macroalgal detritus. This preference was more pronounced for live Z. capricorni than live C. taxifolia . Whereas rates of dissolved inorganic carbon production and utilization were similar for seagrass and macroalgal detritus, higher fluxes of dissolved organic carbon (DOC) from macroalgal detritus early in the experiment reflected the lower utilization of this carbon pool. Although both seagrass and algae can use DOC as a source of carbon, caulerpenyne may comprise part of the DOC pool leached from C. taxifolia detritus during early degradation. This compound can have allelopathic effects on seagrass and may, therefore, be inaccessible to Z. capricorni . The availability of an additional carbon source for C. taxifolia , generated from its own detritus, represents a competitive advantage for this invasive macroalga over existing seagrass, particularly because seagrass productivity can be carbon‐limited. A similar mechanism may exist for other species of invasive macroalga, particularly those that produce toxic secondary metabolites.

Modelling tide–surge interaction effects using finite volume and finite element models of the Irish Sea - Jiuxing Xing; Eric Jones; Alan M. Davies; Philip Hall (Ocean Dynamics, 2011)

Population genetic diversity and structure within and among disjunct populations of Alnus maritima (seaside alder) using microsatellites - James M. Jones; J. Phil Gibson (Conservation Genetics, 2011)

Verbal learning and memory in adolescent cannabis users, alcohol users and non-users - Nadia Solowij; Katy A. Jones; Megan E. Rozman; Sasha M. Davis; Joseph Ciarrochi; Patrick C. L. Heaven; Dan I. Lubman; Murat Yücel (Psychopharmacology, 2011)

Multiproxy summer and winter surface air temperature field reconstructions for southern South America covering the past centuries - R. Neukom; J. Luterbacher; R. Villalba; M. Küttel; D. Frank; P. D. Jones; M. Grosjean; H. Wanner; J.-C. Aravena; D. E. Black; D. A. Christie; R. D’Arrigo; et al. (Climate Dynamics, 2011)

The South American Monsoon System and the 1970s climate transition - Leila M. V. Carvalho; Charles Jones; Ana E. Silva; Brant Liebmann; Pedro L. Silva Dias (International Journal of Climatology, 2011)
The South American Monsoon System (SAMS) is characterised by intense convective activity and precipitation during austral summer. This study investigates changes in the onset, demise and duration of SAMS during 1948–2008. The results show a significant change in these characteristics in the early 1970s. Onset becomes steadily earlier from 1948 to early 1970s and has occurred earlier than 23–27 October after 1972–1973. Demise dates have remained later than 21–25 April after the mid‐to‐late 1970s. SAMS duration shows a statistical changepoint in the summer of 1971–1972 such that the mean duration was ∼170 days (1948–1972) and 195 days (1972–1982). Vertically integrated moisture flux is used to diagnose changes in mean state and reveal statistically significant increases over South America after 1971–1972. Copyright © 2010 Royal Meteorological Society

Red snapper management in the Gulf of Mexico: science- or faith-based? - J. H. Cowan; C. B. Grimes; W. F. Patterson; C. J. Walters; A. C. Jones; W. J. Lindberg; D. J. Sheehy; W. E. Pine; J. E. Powers; M. D. Campbell; K. C. Lindeman; S. L. Diamond; et al. (Reviews in Fish Biology and Fisheries, 2011)

Shotgun Proteomic Analysis of Emiliania huxleyi, a Marine Phytoplankton Species of Major Biogeochemical Importance - Bethan M. Jones; Richard J. Edwards; Paul J. Skipp; C. David O’Connor; M. Debora Iglesias-Rodriguez (Marine Biotechnology, 2011)

The influence of Holocene tree-line advance and retreat on an arctic lake ecosystem: a multi-proxy study from Kharinei Lake, North Eastern European Russia - V. J. Jones; N. Solovieva; A. E. Self; S. McGowan; P. Rosén; J. S. Salonen; H. Seppä; M. Väliranta; E. Parrott; S. J. Brooks (Journal of Paleolimnology, 2011)

An inter-continental comparison between the environmental histories of two lake catchment systems in montane environments of France and South West China - D. S. Crook; J. A. Dearing; R. T. Jones; M. Elvin (Water History, 2011)

Taxon-specific multiplex-PCR for quick, easy, and accurate identification of encyrtid and aphelinid parasitoid species attacking soft scale insects in California citrus groves - Paul F. Rugman-Jones; Lisa D. Forster; Emilio Guerrieri; Robert F. Luck; Joseph G. Morse; Maurilia M. Monti; Richard Stouthamer (BioControl, 2011)

Hovering guards of the stingless bee Tetragonisca angustula increase colony defensive perimeter as shown by intra- and inter-specific comparisons - Jelle S. van Zweden; Christoph Grüter; Sam M. Jones; Francis L.W. Ratnieks (Behavioral Ecology and Sociobiology, 2011)

The response of resistant kiwifruit (Actinidia chinensis) to armoured scale insect (Diaspididae) feeding - M. G. Hill; N. A. Mauchline; M. K. Jones; P. W. Sutherland (Arthropod-Plant Interactions, 2011)

Derivation of Mass Transfer Coefficients for Transient Uptake and Tissue Disposition of Soluble and Reactive Vapors in Lung Airways - B. Asgharian; O. T. Price; J. D. Schroeter; J. S. Kimbell; L. Jones; M. Singal (Annals of Biomedical Engineering, 2011)

The genetics and genomics of Syngnathidae: pipefishes, seahorses and seadragons - K. B. Mobley; C. M. Small; A. G. Jones (Journal of Fish Biology, 2011)
The goal of this review was to provide a historical overview of how molecular techniques have increased the understanding of the ecology and evolution of the family Syngnathidae (pipefishes, seahorses and seadragons). Molecular studies based primarily on mitochondrial DNA markers have proved their worth by elucidating complex phylogenetic relationships within the family. Phylogeographic studies, which have revealed how life‐history traits and past climatic events shape geographic distributions and patterns of genetic variation within syngnathid species, also provide interesting case studies for the conservation and management of threatened species. The application of microsatellite DNA markers has opened a floodgate of studies concerned with the breeding biology of these fishes, which are interesting due to their unique reproductive mode of male pregnancy. Research in this area has contributed significantly to the understanding of mating patterns and sexual selection. Molecular markers may also be employed in studies of demography, migration and local breeding population sizes. Genomic studies have identified genes that are probably involved in male pregnancy and promise additional insights into various aspects of syngnathid biology at the level of the gene. Despite these advances, much more remains to be explored. Goals for future research should include: (1) a more inclusive phylogeny to resolve outstanding issues concerning the relationships within the family and higher order taxa, (2) a broader use of molecular studies to aid management and conservation efforts, (3) the inclusion of more genera in comparative behavioural studies and (4) the continued development of genomic resources for syngnathids to facilitate comparative genomic work.

The Why, What, and How of Global Biodiversity Indicators Beyond the 2010 Target - JULIA P. G. JONES; BEN COLLEN; GILES ATKINSON; PETER W. J. BAXTER; PHILIP BUBB; JANINE B. ILLIAN; TODD E. KATZNER; AIDAN KEANE; JONATHAN LOH; EVE MCDONALD‐MADDEN; EMILY NICHOLSON; HENRIQUE M. PEREIRA; et al. (Conservation Biology, 2011)
The 2010 biodiversity target agreed by signatories to the Convention on Biological Diversity directed the attention of conservation professionals toward the development of indicators with which to measure changes in biological diversity at the global scale. We considered why global biodiversity indicators are needed, what characteristics successful global indicators have, and how existing indicators perform. Because monitoring could absorb a large proportion of funds available for conservation, we believe indicators should be linked explicitly to monitoring objectives and decisions about which monitoring schemes deserve funding should be informed by predictions of the value of such schemes to decision making. We suggest that raising awareness among the public and policy makers, auditing management actions, and informing policy choices are the most important global monitoring objectives. Using four well‐developed indicators of biological diversity (extent of forests, coverage of protected areas, Living Planet Index, Red List Index) as examples, we analyzed the characteristics needed for indicators to meet these objectives. We recommend that conservation professionals improve on existing indicators by eliminating spatial biases in data availability, fill gaps in information about ecosystems other than forests, and improve understanding of the way indicators respond to policy changes. Monitoring is not an end in itself, and we believe it is vital that the ultimate objectives of global monitoring of biological diversity inform development of new indicators.

Moisture transport and intraseasonal variability in the South America monsoon system - Leila M. V. Carvalho; Ana E. Silva; Charles Jones; Brant Liebmann; Pedro L. Silva Dias; Humberto R. Rocha (Climate Dynamics, 2011)

Evaluation of winter wheat breeding lines for traits related to nitrogen use under organic management - J. C. Dawson; K. M. Murphy; D. R. Huggins; S. S. Jones (Organic Agriculture, 2011)

The communicative potential of bat echolocation pulses - Gareth Jones; Björn M. Siemers (Journal of Comparative Physiology A, 2011)

Influence of training status and exercise modality on pulmonary O2 uptake kinetics in pubertal girls - Melitta A. McNarry; Joanne R. Welsman; Andrew M. Jones (European Journal of Applied Physiology, 2011)

Dairy Farm Age and Resistance to Antimicrobial Agents in Escherichia coli Isolated from Dairy Topsoil - Suzanna E. Jones; Jonathan M. Burgos; Marvin M. F. Lutnesky; Johnny A. Sena; Sanath Kumar; Lindsay M. Jones; Manuel F. Varela (Current Microbiology, 2011)

Ten novel microsatellite markers for the western mosquitofish Gambusia affinis - K. M. Purcell; S. L. Lance; K. L. Jones; C. A. Stockwell (Conservation Genetics Resources, 2011)

Development and characterization of 18 microsatellite loci for the Southern Leopard Frog, Rana sphenocephala - Anna M. McKee; Stacey L. Lance; Kenneth L. Jones; Cris Hagen; Travis C. Glenn (Conservation Genetics Resources, 2011)

The Role of Botanic Gardens in the Science and Practice of Ecological Restoration - KATE A. HARDWICK; PEGGY FIEDLER; LYNDON C. LEE; BRUCE PAVLIK; RICHARD J. HOBBS; JAMES ARONSON; MARTIN BIDARTONDO; ERIC BLACK; DAVID COATES; MATTHEW I. DAWS; KINGSLEY DIXON; STEPHEN ELLIOTT; et al. (Conservation Biology, 2011)
Many of the skills and resources associated with botanic gardens and arboreta, including plant taxonomy, horticulture, and seed bank management, are fundamental to ecological restoration efforts, yet few of the world's botanic gardens are involved in the science or practice of restoration. Thus, we examined the potential role of botanic gardens in these emerging fields. We believe a reorientation of certain existing institutional strengths, such as plant‐based research and knowledge transfer, would enable many more botanic gardens worldwide to provide effective science‐based support to restoration efforts. We recommend botanic gardens widen research to include ecosystems as well as species, increase involvement in practical restoration projects and training practitioners, and serve as information hubs for data archiving and exchange.

The mGluR2/3 agonist LY379268 reverses post-weaning social isolation-induced recognition memory deficits in the rat - Caitlin A. Jones; Angus M. Brown; Dorothee P. Auer; Kevin. C. F. Fone (Psychopharmacology, 2011)

Age estimation and lead–radium dating of Antarctic toothfish (Dissostichus mawsoni) in the Ross Sea - Cassandra M. Brooks; Allen H. Andrews; Julian R. Ashford; Nakul Ramanna; Christopher D. Jones; Craig C. Lundstrom; Gregor M. Cailliet (Polar Biology, 2011)

Changes in landscape and vegetation of coastal dunes in northwest Europe: a review - Sam Provoost; M. Laurence M. Jones; Sally E. Edmondson (Journal of Coastal Conservation, 2011)

Interpreting spatial language in image captions - Mark M. Hall; Philip D. Smart; Christopher B. Jones (Cognitive Processing, 2011)

Behavioral evidence for eavesdropping on prey song in two Palearctic sibling bat species - Patricia L. Jones; Rachel A. Page; Manfred Hartbauer; Björn M. Siemers (Behavioral Ecology and Sociobiology, 2011)

Warming increases the proportion of primary production emitted as methane from freshwater mesocosms - GABRIEL YVON‐DUROCHER; JOSÉ M. MONTOYA; GUY WOODWARD; J. IWAN JONES; MARK TRIMMER (Global Change Biology, 2011)
Methane (CH 4 ) and carbon dioxide (CO 2 ) are the dominant gaseous end products of the remineralization of organic carbon and also the two largest contributors to the anthropogenic greenhouse effect. We investigated whether warming altered the balance of CH 4 efflux relative to gross primary production (GPP) and ecosystem respiration (ER) in a freshwater mesocosm experiment. Whole ecosystem CH 4 efflux was strongly related to temperature with an apparent activation energy of 0.85 eV. Furthermore, CH 4 efflux increased faster than ER or GPP with temperature, with all three processes having sequentially lower activation energies. Warming of 4 °C increased the fraction of GPP effluxing as CH 4 by 20% and the fraction of ER as CH 4 by 9%, in line with the offset in their respective activation energies. Because CH 4 is 21 times more potent as a greenhouse gas, relative to CO 2 , these results suggest freshwater ecosystems could drive a previously unknown positive feedback between warming and the carbon cycle.

Oviposition Preferences of the African Wild Silkmoth, Gonometa postica Walker (Lepidoptera: Lasiocampidae) on Different Substrates - Ken O. Fening; Esther N. Kioko; Jones M. Mueke; Suresh K. Raina (Journal of Insect Behavior, 2011)

Stochastic simulations of the Madden–Julian oscillation activity - Charles Jones; Leila M. V. Carvalho (Climate Dynamics, 2011)

Notes on vocalisations of giant otters in the flooded Igapó forests of Jaú National Park, Amazonas, Brazil - B. M. Bezerra; A. S. Souto; N. Schiel; G. Jones (Journal of Ethology, 2011)

Molecular identification of the exotic slug Arion subfuscus sensu stricto (Gastropoda: Pulmonata) in California, with comments on the source location of introduced populations - R. J. Mc Donnell; P. Rugman-Jones; T. Backeljau; K. Breugelmans; K. Jordaens; R. Stouthamer; T. Paine; M. Gormally (Biological Invasions, 2011)

Effect of dietary ascorbic acid supplementation level on productivity, mortality, and carcass characteristics of Venda chickens - Ingrid M. Malebane; Jones Wilfred Ng’ambi; David Norris; Christian Mbajiorgu (Tropical Animal Health and Production, 2010)

Two mechanisms of aquatic and terrestrial habitat change along an Alaskan Arctic coastline - Christopher D. Arp; Benjamin M. Jones; Joel A. Schmutz; Frank E. Urban; M. Torre Jorgenson (Polar Biology, 2010)

Complications of Oral Exposure to Fentanyl Transdermal Delivery System Patches - Jane M. Prosser; Brent E. Jones; Lewis Nelson (Journal of Medical Toxicology, 2010)

Inter-individual variability in the adaptation of human muscle specific tension to progressive resistance training - Robert M. Erskine; David A. Jones; Alun G. Williams; Claire E. Stewart; Hans Degens (European Journal of Applied Physiology, 2010)

Otolith geochemistry does not reflect dispersal history of clownfish larvae - M. L. Berumen; H. J. Walsh; N. Raventos; S. Planes; G. P. Jones; V. Starczak; S. R. Thorrold (Coral Reefs, 2010)

Variation in the structure of epifaunal invertebrate assemblages among coral hosts - J. S. Stella; G. P. Jones; M. S. Pratchett (Coral Reefs, 2010)

Synergistic effects of habitat preference and gregarious behaviour on habitat use in coral reef cardinalfish - N. M. Gardiner; G. P. Jones (Coral Reefs, 2010)

Trophic level asynchrony in rates of phenological change for marine, freshwater and terrestrial environments - STEPHEN J. THACKERAY; TIMOTHY H. SPARKS; MORTEN FREDERIKSEN; SARAH BURTHE; PHILIP J. BACON; JAMES R. BELL; MARC S. BOTHAM; TOM M. BRERETON; PAUL W. BRIGHT; LAURENCE CARVALHO; TIM CLUTTON‐BROCK; ALISTAIR DAWSON; et al. (Global Change Biology, 2010)
Recent changes in the seasonal timing (phenology) of familiar biological events have been one of the most conspicuous signs of climate change. However, the lack of a standardized approach to analysing change has hampered assessment of consistency in such changes among different taxa and trophic levels and across freshwater, terrestrial and marine environments. We present a standardized assessment of 25 532 rates of phenological change for 726 UK terrestrial, freshwater and marine taxa. The majority of spring and summer events have advanced, and more rapidly than previously documented. Such consistency is indicative of shared large scale drivers. Furthermore, average rates of change have accelerated in a way that is consistent with observed warming trends. Less coherent patterns in some groups of organisms point to the agency of more local scale processes and multiple drivers. For the first time we show a broad scale signal of differential phenological change among trophic levels; across environments advances in timing were slowest for secondary consumers, thus heightening the potential risk of temporal mismatch in key trophic interactions. If current patterns and rates of phenological change are indicative of future trends, future climate warming may exacerbate trophic mismatching, further disrupting the functioning, persistence and resilience of many ecosystems and having a major impact on ecosystem services.

Identification of QTL associated with resistance to bacterial spot race T4 in tomato - Samuel F. Hutton; Jay W. Scott; Wencai Yang; Sung-Chur Sim; David M. Francis; Jeffrey B. Jones (Theoretical and Applied Genetics, 2010)

Endogenous cytokinins in Cocos nucifera L. in vitro cultures obtained from plumular explants - L. Sáenz; A. Azpeitia; C. Oropeza; L. H. Jones; K. Fuchsova; L. Spichal; M. Strnad (Plant Cell Reports, 2010)

Cadmium, Copper, Iron, and Zinc Concentrations in Kidneys of Grey Wolves, Canis lupus, from Alaska, Idaho, Montana (USA) and the Northwest Territories (Canada) - S. R. Hoffmann; S. A. Blunck; K. N. Petersen; E. M. Jones; J. C. Koval; R. Misek; J. A. Frick; H. D. Cluff; C. A. Sime; M. McNay; K. B. Beckman; M. W. Atkinson; et al. (Bulletin of Environmental Contamination and Toxicology, 2010)

Ecophysiological responses of salt cedar (Tamarix spp. L.) to the northern tamarisk beetle (Diorhabda carinulata Desbrochers) in a controlled environment - Keirith A. Snyder; Shauna M. Uselman; Timothy J. Jones; Sara Duke (Biological Invasions, 2010)

Validation and pharmacological characterisation of MK-801-induced locomotor hyperactivity in BALB/C mice as an assay for detection of novel antipsychotics - Andrea M. Bradford; Kevin M. Savage; Declan N. C. Jones; Mikhail Kalinichev (Psychopharmacology, 2010)

Responses of golden-backed uakaris, Cacajao melanocephalus, to call playback: implications for surveys in the flooded Igapó forest - Bruna M. Bezerra; Antonio S. Souto; Gareth Jones (Primates, 2010)

Epidemiology of non-multiresistant methicillin-resistant Staphylococcus aureus infection in Queensland, Australia: associations with indigenous populations and Panton–Valentine leukocidin - G. R. Nimmo; J. M. Schooneveldt; J. L. Sutherland; S. Power; D. Olesen; C. Selvey; F. Beard; M. Jones; D. L. Paterson (European Journal of Clinical Microbiology & Infectious Diseases, 2010)

Organic acids differ in enhancing phosphorus uptake by Triticum aestivum L.—effects of rhizosphere concentration and counterion - Z. Khademi; D. L. Jones; M. J. Malakouti; F. Asadi (Plant and Soil, 2010)

Tobacco Cessation Education for Dentists: An Evaluation of the Lecture Format - Kathleen Vendrell Rankin; Daniel L. Jones; Karen M. Crews (Journal of Cancer Education, 2010)

Research partnerships with local communities: two case studies from Papua New Guinea and Australia - G. R. Almany; R. J. Hamilton; D. H. Williamson; R. D. Evans; G. P. Jones; M. Matawai; T. Potuku; K. L. Rhodes; G. R. Russ; B. Sawynok (Coral Reefs, 2010)

The genetic location of the self-incompatibility locus in white clover (Trifolium repens L.) - Nora M. Casey; Dan Milbourne; Susanne Barth; Melanie Febrer; Glyn Jenkins; Michael T. Abberton; Charlotte Jones; Daniel Thorogood (Theoretical and Applied Genetics, 2010)

Modelling the influence of small-scale effects upon the larger scale: an oceanographic challenge - Alan M. Davies; John Eric Jones; Jiuxing Xing (Ocean Dynamics, 2010)

Education Effects on the International HIV Dementia Scale - Drenna Waldrop-Valverde; Ritu Nehra; Sunil Sharma; Ashima Malik; Deborah Jones; Adarsh M Kumar; Raymond L Ownby; Ajay Wanchu; Steve Weiss; Sudesh Prabhakar; Mahendra Kumar (Journal of NeuroVirology, 2010)

Do salmon lice, Lepeophtheirus salmonis , have a role in the epidemiology of amoebic gill disease caused by Neoparamoeba perurans ? - B F Nowak; J Bryan; S R M Jones (Journal of Fish Diseases, 2010)

Range expansion and hybridization in Round Island petrels (Pterodroma spp.): evidence from microsatellite genotypes - RUTH M. BROWN; RICHARD A. NICHOLS; CHRIS G. FAULKES; CARL G. JONES; LEANDRO BUGONI; VIKASH TATAYAH; DADA GOTTELLI; WILLIAM C. JORDAN (Molecular Ecology, 2010)

Haines Structure: a probable Eocene complex impact structure in the offshore Canning Basin, Western Australia - A. T. Jones; J. D. Gorter; J. M. Kennard (Australian Journal of Earth Sciences, 2010)

Narcissus late season yellows virus and Vallota speciosa virus found infecting domestic and wild populations of Narcissus species in Australia - S. J. Wylie; S. Nouri; B. A. Coutts; M. G. K. Jones (Archives of Virology, 2010)

Tetracapsuloides bryosalmonae in spawning pink salmon, Oncorhynchus gorbuscha (Walbaum), in the Quinsam River, British Columbia, Canada - L M Braden; G Prosperi‐Porta; E Kim; S R M Jones (Journal of Fish Diseases, 2010)

Population structure of the dusky pipefish ( Syngnathus floridae ) from the Atlantic and Gulf of Mexico, as revealed by mitochondrial DNA and microsatellite analyses - Kenyon B. Mobley; Clayton M. Small; Nathaniel K. Jue; Adam G. Jones (Journal of Biogeography, 2010)
Aim To elucidate the historical phylogeography of the dusky pipefish ( Syngnathus floridae ) in the North American Atlantic and Gulf of Mexico ocean basins. Location Southern Atlantic Ocean and northern Gulf of Mexico within the continental United States. Methods A 394‐bp fragment of the mitochondrial cytochrome b gene and a 235‐bp fragment of the mitochondrial control region were analysed from individuals from 10 locations. Phylogenetic reconstruction, haplotype network, mismatch distributions and analysis of molecular variance were used to infer population structure between ocean basins and time from population expansion within ocean basins. Six microsatellite loci were also analysed to estimate population structure and gene flow among five populations using genetic distance methods ( F ST , Nei’s genetic distance), isolation by distance (Mantel’s test), coalescent‐based estimates of genetic diversity and migration patterns, Bayesian cluster analysis and bottleneck simulations. Results Mitochondrial analyses revealed significant structuring between ocean basins in both cytochrome b ( Φ ST = 0.361, P 0.0001; Φ CT = 0.312, P 0.02) and control region ( Φ ST = 0.166, P 0.0001; Φ CT = 0.128, P 0.03) sequences. However, phylogenetic reconstructions failed to show reciprocal monophyly in populations between ocean basins. Microsatellite analyses revealed significant population substructuring between all locations sampled except for the two locations that were in closest proximity to each other (global F ST value = 0.026). Bayesian analysis of microsatellite data also revealed significant population structuring between ocean basins. Coalescent‐based analyses of microsatellite data revealed low migration rates among all sites. Mismatch distribution analysis of mitochondrial loci supports a sudden population expansion in both ocean basins in the late Pleistocene, with the expansion of Atlantic populations occurring more recently. Main conclusions Present‐day populations of S. floridae do not bear the mitochondrial DNA signature of the strong phylogenetic discontinuity between the Atlantic and Gulf coasts of North America commonly observed in other species. Rather, our results suggest that Atlantic and Gulf of Mexico populations of S. floridae are closely related but nevertheless exhibit local and regional population structure. We conclude that the present‐day phylogeographic pattern is the result of a recent population expansion into the Atlantic in the late Pleistocene, and that life‐history traits and ecology may play a pivotal role in shaping the realized geographical distribution pattern of this species.

Are species–area relationships from entire archipelagos congruent with those of their constituent islands? - Ana M. C. Santos; Robert J. Whittaker; Kostas A. Triantis; Paulo A. V. Borges; Owen R. Jones; Donald L. J. Quicke; Joaquín Hortal (Global Ecology and Biogeography, 2010)
Aim To establish the extent to which archipelagos follow the same species–area relationship as their constituent islands and to explore the factors that may explain departures from the relationship. Location Thirty‐eight archipelagos distributed worldwide. Methods We used ninety‐seven published datasets to create island species–area relationships (ISARs) using the Arrhenius logarithmic form of the power model. Observed and predicted species richness of an archipelago and of each of its islands were used to calculate two indices that determined whether the archipelago followed the ISAR. Archipelagic residuals ( ArcRes ) were calculated as the residual of the prediction provided by the ISAR using the total area of the archipelago, standardized by the total richness observed in the archipelago. We also tested whether any characteristic of the archipelago (geological origin and isolation) and/or taxon accounts for whether an archipelago fits into the ISAR or not. Finally, we explored the relationship between ArcRes and two metrics of nestedness. Results The archipelago was close to the ISAR of its constituent islands in most of the cases analysed. Exceptions arose for archipelagos where (i) the slopes of the ISAR are low, (ii) observed species richness is higher than expected by the ISAR and/or (iii) distance to the mainland is small. The archipelago's geological origin was also important; a higher percentage of oceanic archipelagos fit into their ISAR than continental ones. ArcRes indicated that the ISAR underpredicts archipelagic richness in the least isolated archipelagos. Different types of taxon showed no differences in ArcRes . Nestedness and ArcRes appear to be related, although the form of the relationship varies between metrics. Main conclusions Archipelagos, as a rule, follow the same ISAR as their constituent islands. Therefore, they can be used as distinct units themselves in large‐scale biogeographical and macroecological studies. Departure from the ISAR can be used as a crude indicator of richness‐ordered nestedness, responsive to factors such as isolation, environmental heterogeneity, number and age of islands.

Elucidation of antimicrobial susceptibility profiles and genotyping of Salmonella enterica isolates from clinical cases of salmonellosis in New Mexico in 2008 - Kenneth P. Smith; Jeffy George; Kathleen M. Cadle; Sanath Kumar; Steven J. Aragon; Ricardo L. Hernandez; Suzanna E. Jones; Jody L. Floyd; Manuel F. Varela (World Journal of Microbiology and Biotechnology, 2010)

Population genetic structuring in a rare tropical plant: Idiospermum australiense (Diels) S.T. Blake - Lynne M. Jones; Paul A. Gadek; Mark G. Harrington (Plant Systematics and Evolution, 2010)

Topsoil inversion as a restoration measure in sand dunes, early results from a UK field-trial - M. Laurence M. Jones; Kim Norman; Peter M. Rhind (Journal of Coastal Conservation, 2010)

Factors affecting vegetation establishment and development in a sand dune chronosequence at Newborough Warren, North Wales - M. Laurence M. Jones; Alwyn Sowerby; Peter M. Rhind (Journal of Coastal Conservation, 2010)

The long-term (1979–2005) effects of the North Atlantic Oscillation on wind-induced wave mixing in Loch Leven (Scotland) - Bryan M. Spears; Ian D. Jones (Hydrobiologia, 2010)

Five hundred microsatellite loci for Peromyscus - Jesse N. Weber; Maureen B. Peters; Olga V. Tsyusko; Catherine R. Linnen; Cris Hagen; Nancy A. Schable; Tracey D. Tuberville; Anna M. McKee; Stacey L. Lance; Kenneth L. Jones; Heidi S. Fisher; Michael J. Dewey; et al. (Conservation Genetics, 2010)

The population genetic structure of a common tropical damselfish on the Great Barrier Reef and eastern Papua New Guinea - D. B. Jones; D. R. Jerry; M. I. McCormick; L. K. Bay (Coral Reefs, 2010)

The importance of ship log data: reconstructing North Atlantic, European and Mediterranean sea level pressure fields back to 1750 - M. Küttel; E. Xoplaki; D. Gallego; J. Luterbacher; R. García-Herrera; R. Allan; M. Barriendos; P. D. Jones; D. Wheeler; H. Wanner (Climate Dynamics, 2010)

Adventitious shoot regeneration from cotyledonary explants of rapid-cycling fast plants of Brassica rapa L - S. Cogbill; T. Faulcon; G. Jones; M. McDaniel; G. Harmon; R. Blackmon; M. Young (Plant Cell, Tissue and Organ Culture (PCTOC), 2010)

Variability in drug metabolizing enzyme activity in HIV-infected patients - Amanda E. Jones; Kevin C. Brown; Rebecca E. Werner; Karl Gotzkowsky; Andrea Gaedigk; Mike Blake; David W. Hein; Charles van der Horst; Angela D. M. Kashuba (European Journal of Clinical Pharmacology, 2010)

Estimation of global temperature trends: what’s important and what isn’t - Phil D. Jones; T. M. L. Wigley (Climatic Change, 2010)

Conventional myosins – unconventional functions - Peter D. Chantler; Steven R. Wylie; Caroline P. Wheeler-Jones; Imelda M. McGonnell (Biophysical Reviews, 2010)

Development of delivery methods for carbohydrate-based drugs: controlled release of biologically-active short chain fatty acid-hexosamine analogs - Udayanath Aich; M. Adam Meledeo; Srinivasa-Gopalan Sampathkumar; Jie Fu; Mark B. Jones; Christopher A. Weier; Sung Yun Chung; Benjamin C. Tang; Ming Yang; Justin Hanes; Kevin J. Yarema (Glycoconjugate Journal, 2010)

PKC inhibition increases gap junction intercellular communication and cell adhesion in human neuroblastoma - Melissa Morley; Claire Jones; Mandeep Sidhu; Vishal Gupta; Suzanne M. Bernier; Walter J. Rushlow; Daniel J. Belliveau (Cell and Tissue Research, 2010)

Genetic support for random mating between left and right‐mouth morphs in the dimorphic scale‐eating cichlid fish Perissodus microlepis from Lake Tanganyika - H. J. Lee; S. Pittlik; J. C. Jones; W. Salzburger; M. Barluenga; A. Meyer (Journal of Fish Biology, 2010)
Population genetic analyses were conducted to investigate whether random mating occurs between left and right‐mouth morphs of the dimorphic scale‐eating cichlid fish Perissodus microlepis from two geographical sites in southern Lake Tanganyika. The mitochondrial and nuclear DNA markers (13 microsatellite loci) revealed no genetic differentiation between left and right morphs ( i.e. widespread interbreeding). The observed lack of genetic divergence between the different morphs allowed for the exclusion of the possibility of assortative mating between same morph types. The microsatellite data showed no significant departures of heterozygosity from Hardy–Weinberg equilibrium, suggesting purely random mating between the morphs. Overall, this study indicated no genetic evidence for either assortative or disassortative mating, but it did provide support for the random mating hypothesis. Highly significant, albeit weak, spatial population structure was also found when samples of different morphs were pooled according to geographical sites. An additional analysis of two microsatellite loci that were recently suggested to be putatively linked to the genetic locus that determines the laterality of these mouth morphs did not show any such association.

Effect of seasons and larval food plants on the quality of Gonometa postica cocoons - Ken O. Fening; Esther N. Kioko; Suresh K. Raina; Jones M. Mueke (Phytoparasitica, 2010)

Influence of training status and exercise modality on pulmonary O2 uptake kinetics in pre-pubertal girls - Melitta A. Winlove; Andrew M. Jones; Joanne R. Welsman (European Journal of Applied Physiology, 2010)

Evaluation of the skill and added value of a reanalysis‐driven regional simulation for Alpine temperature - Kerstin Prömmel; Beate Geyer; Julie M. Jones; Martin Widmann (International Journal of Climatology, 2010)
To determine whether the use of regional climate models improves the representation of climate is a crucial topic in climate modelling. An improvement over coarser scale models is expected especially in areas with complex orography or along coastlines. However, some studies have shown no clear added value for regional climate models. In this study a high‐resolution regional climate simulation performed with REMO 5.0 (regional model) over the whole of Europe over the period 1958–1998 is analysed for 2‐m temperature over the European Alps and their surroundings called the Greater Alpine region (GAR). The simulation is driven by perfect boundary conditions at the lateral boundaries provided by the ERA40 reanalysis and spectral nudging of the large‐scale wind fields towards ERA40 values for the upper layers inside the model domain. The added value of the regional simulation (1/6° resolution) is analysed with respect to the driving reanalysis (1.125° resolution). Both the REMO simulation and the ERA40 reanalysis are validated against different station datasets of monthly and daily mean 2‐m temperature. Correlation analysis shows that the temporal variability of temperature is well represented by both REMO and ERA40, whereas both show considerable biases. The REMO bias reaches 3 K in summer in regions known to experience a problem with summer drying in a number of regional models. The comparison of REMO and ERA40 shows that an added value of the former exists for all regions in winter. For the regions surrounding the Alps, the added value is absent in summer, whereas in the inner Alpine subregions with most complex orography, REMO performs better than ERA40 during the whole year. The only moderate value added by REMO in this hindcast set‐up may be partly explicable by the fact that meteorological measurements are assimilated in the ERA40 reanalysis but not in the REMO simulation. Copyright © 2009 Royal Meteorological Society

Seven years of recent European net terrestrial carbon dioxide exchange constrained by atmospheric observations - W. PETERS; M. C. KROL; G. R. Van Der WERF; S. HOUWELING; C. D. JONES; J. HUGHES; K. SCHAEFER; K. A. MASARIE; A. R. JACOBSON; J. B. MILLER; C. H. CHO; M. RAMONET; et al. (Global Change Biology, 2010)
We present an estimate of net ecosystem exchange (NEE) of CO 2 in Europe for the years 2001–2007. It is derived with a data assimilation that uses a large set of atmospheric CO 2 mole fraction observations (∼70 000) to guide relatively simple descriptions of terrestrial and oceanic net exchange, while fossil fuel and fire emissions are prescribed. Weekly terrestrial sources and sinks are optimized (i.e., a flux inversion) for a set of 18 large ecosystems across Europe in which prescribed climate, weather, and surface characteristics introduce finer scale gradients. We find that the terrestrial biosphere in Europe absorbed a net average of −165 Tg C yr −1 over the period considered. This uptake is predominantly in non‐EU countries, and is found in the northern coniferous (−94 Tg C yr −1 ) and mixed forests (−30 Tg C yr −1 ) as well as the forest/field complexes of eastern Europe (−85 Tg C yr −1 ). An optimistic uncertainty estimate derived using three biosphere models suggests the uptake to be in a range of −122 to −258 Tg C yr −1 , while a more conservative estimate derived from the a‐posteriori covariance estimates is −165±437 Tg C yr −1 . Note, however, that uncertainties are hard to estimate given the nature of the system and are likely to be significantly larger than this. Interannual variability in NEE includes a reduction in uptake due to the 2003 drought followed by 3 years of more than average uptake. The largest anomaly of NEE occurred in 2005 concurrent with increased seasonal cycles of observed CO 2 . We speculate these changes to result from the strong negative phase of the North Atlantic Oscillation in 2005 that lead to favorable summer growth conditions, and altered horizontal and vertical mixing in the atmosphere. All our results are available through http://www.carbontracker.eu

Shewanella oneidensis MR‐1 mutants selected for their inability to produce soluble organic‐Fe(III) complexes are unable to respire Fe(III) as anaerobic electron acceptor - Morris E. Jones; Christine M. Fennessey; Thomas J. DiChristina; Martial Taillefert (Environmental Microbiology, 2010)
Summary Recent voltammetric analyses indicate that Shewanella putrefaciens strain 200 produces soluble organic‐Fe(III) complexes during anaerobic respiration of sparingly soluble Fe(III) oxides. Results of the present study expand the range of Shewanella species capable of producing soluble organic‐Fe(III) complexes to include Shewanella oneidensis MR‐1. Soluble organic‐Fe(III) was produced by S. oneidensis cultures incubated anaerobically with Fe(III) oxides, or with Fe(III) oxides and the alternate electron acceptor fumarate, but not in the presence of O 2 , nitrate or trimethylamine‐ N ‐oxide. Chemical mutagenesis procedures were combined with a novel MicroElectrode Screening Array (MESA) to identify four (designated Sol) mutants with impaired ability to produce soluble organic‐Fe(III) during anaerobic respiration of Fe(III) oxides. Two of the Sol mutants were deficient in anaerobic growth on both soluble Fe(III)‐citrate and Fe(III) oxide, yet retained the ability to grow on a suite of seven alternate electron acceptors. The rates of soluble organic‐Fe(III) production were proportional to the rates of iron reduction by the S. oneidensis wild‐type and Sol mutant strains, and all four Sol mutants retained wild‐type siderophore production capability. Results of this study indicate that the production of soluble organic‐Fe(III) may be an important intermediate step in the anaerobic respiration of both soluble and sparingly soluble forms of Fe(III) by S. oneidensis .

Propafenone Poisoning—A Case Report with Plasma Propafenone Concentrations - Hanna Ovaska; Andrew Ludman; Edgar P. Spencer; David M. Wood; Alison L. Jones; Paul I. Dargan (Journal of Medical Toxicology, 2010)

Influence of exercise variation on the retention of a pacing strategy - Alexis R. Mauger; Andrew M. Jones; Craig Anthony Williams (European Journal of Applied Physiology, 2010)

Microbial ecological response of the intestinal flora of Peromyscus maniculatus and P. leucopus to heavy metal contamination - JOSEPH D. COOLON; KENNETH L. JONES; SANJEEV NARAYANAN; SAMANTHA M. WISELY (Molecular Ecology, 2010)
Heavy metal contamination negatively affects natural systems including plants, birds, fish and bacteria by reducing biodiversity at contaminated sites. At the Tri‐State Mining District, efforts have been made to remediate sites to mitigate the detrimental effects that contamination has caused on human health. While the remediation effort has returned the site to within federal safety standards, it is unclear if this effort is sufficient to restore floral and faunal communities. Intrinsic to ecosystem and organism health is the biodiversity and composition of microbial communities. We have taken advantage of recent advances in sequencing technology and surveyed the bacterial community of remediated and reference soils as well as the intestinal microbial community of two ubiquitous rodent species to provide insight on the impacts of residual heavy metal contamination on the ecosystem. Rodents found on the remediated site had reduced body mass, smaller body size and lower body fat than animals on reference sites. Using bar‐coded, massively parallel sequencing, we found that bacterial communities in both the soil and Peromyscus spp. gastrointestinal tracts had no difference in diversity between reference and remediated sites but assemblages differed in response to contamination. These results suggest that niche voids left by microbial taxa that were unable to deal with the remnant levels of heavy metals on remediated sites were replaced by taxa that could persist in this environment. Whether this replacement provided similar ecosystem services as ancestral bacterial communities is unknown.

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes - K. R. ELMER; S. FAN; H. M. GUNTER; J. C. JONES; S. BOEKHOFF; S. KURAKU; A. MEYER (Molecular Ecology, 2010)
Crater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next‐generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthic Amphilophus astorquii and limnetic Amphilophus zaliosus . We obtained 24 174 A. astorquii and 21 382 A. zaliosus high‐quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of nonsynonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection ( K a / K s > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on K s ratios and p‐distances between 3′‐untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome‐wide substitutional mutation rate of ∼1.25 × 10 −6 per site per year. We conclude that next‐generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water - THORSTEN STOECK; DAVID BASS; MARKUS NEBEL; RICHARD CHRISTEN; MEREDITH D. M. JONES; HANS‐WERNER BREINER; THOMAS A. RICHARDS (Molecular Ecology, 2010)
Sequencing of ribosomal DNA clone libraries amplified from environmental DNA has revolutionized our understanding of microbial eukaryote diversity and ecology. The results of these analyses have shown that protist groups are far more genetically heterogeneous than their morphological diversity suggests. However, the clone library approach is labour‐intensive, relatively expensive, and methodologically biased. Therefore, even the most intensive rDNA library analyses have recovered only small samples of much larger assemblages, indicating that global environments harbour a vast array of unexplored biodiversity. High‐throughput parallel tag 454 sequencing offers an unprecedented scale of sampling for molecular detection of microbial diversity. Here, we report a 454 protocol for sampling and characterizing assemblages of eukaryote microbes. We use this approach to sequence two SSU rDNA diversity markers—the variable V4 and V9 regions—from 10 L of anoxic Norwegian fjord water. We identified 38 116 V4 and 15 156 V9 unique sequences. Both markers detect a wide range of taxonomic groups but in both cases the diversity detected was dominated by dinoflagellates and close relatives. Long‐tailed rank abundance curves suggest that the 454 sequencing approach provides improved access to rare genotypes. Most tags detected represent genotypes not currently in GenBank, although many are similar to database sequences. We suggest that current understanding of the ecological complexity of protist communities, genetic diversity, and global species richness are severely limited by the sequence data hitherto available, and we discuss the biological significance of this high amplicon diversity.

Corallivory in tubelip wrasses: diet, feeding and trophic importance - A. J. Cole; M. S. Pratchett; G. P. Jones (Journal of Fish Biology, 2010)
This paper describes a 2 month study of the patterns of abundance, feeding pressure, diet and feeding selectivity in corallivorous tubelip wrasses (Labridae), rarely studied, yet widespread and abundant group of corallivores on Indo‐Pacific coral reefs. The relative abundance and feeding pressure of corallivorous wrasses and butterflyfishes (Chaetodontidae) in Kimbe Bay, Papua New Guinea, were compared. Overall, tubelip wrasses were more than twice as abundant as corallivorous butterflyfishes and accounted for three times as many feeding bites on corals. The three most abundant tubelip wrasses (yellowtail tubelip Diproctacanthus xanthurus , Allen's tubelip Labropsis alleni and the tubelip wrasse Labrichthys unilineatus ) were all obligate corallivores taking > 97% of bites from the surface of live corals. Labropsis alleni and D. xanthurus were highly selective, consuming preferred prey species in proportions significantly higher than expected given their availability. In contrast, L. unilineatus was fairly non‐selective and consumed most corals in direct accordance with their availability. As coral predators, tubelip wrasses are highly comparable to coral‐feeding butterflyfishes in the coral species consumed, range of dietary specialization and their reliance on live coral. Tubelip wrasses, however, may supersede butterflyfishes as the predominant corallivorous family in some Indo‐Pacific locations, and coral‐feeding tubelip wrasses are likely to be severely affected by coral decline.

Historical changes in the distributions of invasive and endemic marine invertebrates are contrary to global warming predictions: the effects of decadal climate oscillations - Thomas J. Hilbish; Pamela M. Brannock; Karlie R. Jones; Allison B. Smith; Brooke N. Bullock; David S. Wethey (Journal of Biogeography, 2010)
Aim We tested whether a hybrid zone that has formed between an endemic and an invasive species of marine mussel has shifted poleward as expected under a general hypothesis of global warming or has responded instead to decadal climate oscillations. Location We sampled 15 locations on the coast of California, USA, that span the distributions of the two species of marine mussels and their hybrids. Methods Mussels were sampled in 2005–08 and analysed at three nuclear gene loci using methods identical to those used in a study a decade earlier in order to document the genetic architecture of this system. Change in the system was determined by comparing the frequency of species‐specific alleles and multi‐locus genotypes over the intervening decade. Climate variation over the same period was examined by comparing the Pacific Decadal Oscillation (PDO), El Niño/Southern Oscillation (ENSO), upwelling indices and sea surface temperature (SST) during and prior to the study period. Results Contrary to the general expectations of global warming we show that the highly invasive warm‐water mussel Mytilus galloprovincialis and the hybrid zone formed with the endemic species Mytilus trossulus has rapidly contracted southwards. Mytilus galloprovincialis declined in abundance over the northern third of its geographic range ( c . 540 km) and has become rare or absent across the northern 200 km of the range it previously colonized during its initial invasion. The distribution of the native species M. trossulus has remained unchanged over the same time period. Main conclusions The large‐scale range shift in the warm‐water invasive species M. galloprovincialis and the hybrid zone it forms with M. trossulus has been exceptionally rapid and is in the opposite direction to that predicted by the global warming hypotheses. This shift, however, is consistent with decadal climate variation associated with the ENSO and the PDO. Since the biogeography of this system was first described in 1999, the PDO has shifted from a warm phase, dominated by frequent and large El Niño events, to a cold‐phase period, with minimal ENSO activity. Thus recent decadal climate variation can oppose global trends in average temperature and this study illustrates the need to integrate the effects of climate change across multiple time‐scales.

A UK scheme for reporting serious adverse events and reactions associated with ocular tissue transplantation - Stephen Kaye; Andrew Baddon; Mark Jones; W. John Armitage; Deirdre Fehily; Ruth M. Warwick (Cell and Tissue Banking, 2010)

Roles of human disturbance, precipitation, and a pathogen on the survival and reproductive probabilities of deer mice - M. Andrea Previtali; Erin M. Lehmer; Jessica M. C. Pearce-Duvet; Jeremy D. Jones; Christine A. Clay; Britta A. Wood; Patrick W. Ely; Sean M. Laverty; M. Denise Dearing (Ecology, 2010)
Climate change, human disturbance, and disease can have large impacts on the dynamics of a species by affecting the likelihood of survival and reproduction of individuals. We investigated the roles of precipitation, off‐road vehicle (ORV) alteration of habitat, and infection with Sin Nombre virus on the survival and reproductive probabilities of deer mice ( Peromyscus maniculatus ). We used generalized linear mixed models to estimate the effects of these factors and their interactions by fitting capture–recapture data collected seasonally from 2002 to 2007 at 17 sites in the Great Basin Desert of central Utah, USA. During periods with high precipitation, we found no difference in survival and reproductive probabilities between seasons, but during drier periods, we found a reduction of overwinter survival and fall reproductive activity. Precipitation also interacted with disturbance to affect survival probabilities and female reproduction; in periods with low precipitation, deer mice on highly disturbed sites had extremely low survival probabilities and low reproductive probabilities of females compared to those of individuals from low‐disturbance sites. However, high precipitation ameliorated the effect of disturbance on both parameters. Deer mice from sites with high impact of ORV disturbance also had low survival over summer. Additionally, male reproductive probabilities were diminished on highly disturbed sites in both seasons; in contrast, they were reduced only in the fall on low‐disturbance sites. Density had an overall negative effect on survival and reproductive probabilities of deer mice. For females, the negative effect on reproductive activity was amplified in highly disturbed sites. We found no effect of hantavirus infection on survival probabilities of deer mice. Overall, this study revealed complexity in the determinants of deer mouse survival and reproduction given by the effects of a number of significant interactions among explanatory variables. Thus, factors that may not appear to have a strong effect when investigated alone can still be influential by modulating the effect of a different factor.

Emissions of nitrous oxide from Irish arable soils: effects of tillage and reduced N input - M. Abdalla; M. Jones; P. Ambus; M. Williams (Nutrient Cycling in Agroecosystems, 2010)

Emissions of nitrous oxide from Irish arable soils: effects of tillage and reduced N input - M. Abdalla; M. Jones; P. Ambus; M. Williams (Nutrient Cycling in Agroecosystems, 2010)

Time course of changes in immuneoendocrine markers following an international rugby game - Brian Cunniffe; Andrew J. Hore; Dean M. Whitcombe; Ken P. Jones; Julien S. Baker; Bruce Davies (European Journal of Applied Physiology, 2010)

Gamma irradiation of dried plant material: implications for the identification of plant pathogens employing molecular techniques - L. M. Jones; K. R. E. Grice; R. I. Davis (Australasian Plant Pathology, 2010)

Genome sequences and phylogenetic placement of two isolates of Bean common mosaic virus from Macroptilium atropurpureum in north-west Australia - M. Saqib; S. Nouri; B. Cayford; R. A. C. Jones; M. G. K. Jones (Australasian Plant Pathology, 2010)

Generation of Arabidopsis Mutants by Heterologous Expression of a Full-Length cDNA Library from Tomato Fruits - Yi-Hong Wang; Chris M. Mosebach; Abraham S. Kibbey; Marcie K. Ryhal; Angelica D. Jones; Julie A. Palmer; Leon V. Kochian (Plant Molecular Biology Reporter, 2009)

An inter-comparison of tidal solutions computed with a range of unstructured grid models of the Irish and Celtic Sea Regions - John Eric Jones; Philip Hall; Alan M. Davies (Ocean Dynamics, 2009)

Coral-feeding fishes slow progression of black-band disease - Andrew J. Cole; Karen M. Chong Seng; Morgan S. Pratchett; Geoffrey P. Jones (Coral Reefs, 2009)

Telomere dynamics during replicative senescence are not directly modulated by conditions of oxidative stress in IMR90 fibroblast cells - Bethan Britt-Compton; Fiona Wyllie; Jan Rowson; Rebecca Capper; Rhiannon E. Jones; Duncan M. Baird (Biogerontology, 2009)

Diets of eight fish species from the upper slope off the Wairarapa coast, North Island, New Zealand, with notes on the diets of others - M. R. L. Jones (New Zealand Journal of Marine and Freshwater Research, 2009)
The diets of eight demersal fish species from the upper continental slope (c. 24CM‐50 m) were determined from samples taken during late January and early February 2004, off the Wairarapa coast, North Island, New Zealand. Diets were from a combination of benthopelagic and benthic sources, with most species exhibiting ontogenetic shifts in diet, in that larger‐bodied food (fish and/or natant decapod prawns) was more important in the diets of larger fish. Javelinfish ( Lepidorhynchus denticulatus ), silver roughy ( Hoplostethus mediterraneus ), and capro dory ( Capromimus abbreviatus ) had predominantly benthopelagic diets, whereas the diets of sea perch ( Helicolenus percoides ), Bollons’ rattail ( Caelorinchus bollonsi ), two‐banded rattail (C. biclinozonalis ), and silverside ( Argentina elongata ) were predominantly benthic, with the crab Carcinoplax victoriensis an important food item. The diet of Oliver's rattail (C. oliverianus ) was a mix of benthopelagic and benthic organisms. Generally, levels of dietary overlap between the eight species were low. Overall, the diets of these fish probably reflect regional and seasonal levels of food availability. Notes on food observed in the stomachs of a further 18 species, for which there were fewer than 10 stomach samples per species are also provided.

Future change of temperature and precipitation extremes in South America as derived from the PRECIS regional climate modeling system - J. A. Marengo; R. Jones; L. M. Alves; M. C. Valverde (International Journal of Climatology, 2009)
Using the PRECIS regional climate modeling system this study analyses the distribution of extremes of temperature and precipitation in South America in the recent past (1961–1990) and in a future (2071–2100) climate under the IPCC SRES A2 and B2 emissions scenarios. The results show that for the present climate the model simulates well the spatial distribution of extreme temperature and rainfall events when compared with observations, with temperature the more realistic. The observations over the region are far from comprehensive which compromises the assessment of model quality. In all the future climate scenarios considered all parts of the region would experience significant and often different changes in rainfall and temperature extremes. In the future, the occurrence of warm nights is projected to be more frequent in the entire tropical South America while the occurrence of cold night events is likely to decrease. Significant changes in rainfall extremes and dry spells are also projected. These include increased intensity of extreme precipitation events over most of Southeastern South America and western Amazonia consistent with projected increasing trends in total rainfall in these regions. In Northeast Brazil and eastern Amazonia smaller or no changes are seen in projected rainfall intensity though significant changes are seen in the frequency of consecutive dry days. Copyright © 2009 Royal Meteorological Society

The influence of flow cell geometry related shear stresses on the distribution, structure and susceptibility of Pseudomonas aeruginosa 01 biofilms - M. Mehdi Salek; Steven M. Jones; Robert J. Martinuzzi (Biofouling, 2009)

Access to mycorrhizal networks and roots of trees: importance for seedling survival and resource transfer - François P. Teste; Suzanne W. Simard; Daniel M. Durall; Robert D. Guy; Melanie D. Jones; Amanda L. Schoonmaker (Ecology, 2009)
Mycorrhizal networks (MNs) are fungal hyphae that connect roots of at least two plants. It has been suggested that these networks are ecologically relevant because they may facilitate interplant resource transfer and improve regeneration dynamics. This study investigated the effects of MNs on seedling survival, growth and physiological responses, interplant resource (carbon and nitrogen) transfer, and ectomycorrhizal (EM) fungal colonization of seedlings by trees in dry interior Douglas‐fir ( Pseudotsuga menziesii var. glauca ) forests. On a large, recently harvested site that retained some older trees, we established 160 isolated plots containing pairs of older Douglas‐fir “donor” trees and either manually sown seed or planted Douglas‐fir “receiver” seedlings. Seed‐ and greenhouse‐grown seedlings were sown and planted into four mesh treatments that served to restrict MN access (i.e., planted into mesh bags with 0.5‐, 35‐, 250‐μm pores, or without mesh). Older trees were pulse labeled with carbon ( 13 CO 2 ) and nitrogen ( 15 NH 4 15 NO 3 ) to quantify resource transfer. After two years, seedlings grown from seed in the field had the greatest survival and received the greatest amounts of transferred carbon (0.0063% of donor photo‐assimilates) and nitrogen (0.0018%) where they were grown without mesh; however, planted seedlings were not affected by access to tree roots and hyphae. Size of “donor” trees was inversely related to the amount of carbon transferred to seedlings. The potential for MNs to form was high (based on high similarity of EM communities between hosts), and MN‐mediated colonization appeared only to be important for seedlings grown from seed in the field. These results demonstrate that MNs and mycorrhizal roots of trees may be ecologically important for natural regeneration in dry forests, but it is still uncertain whether resource transfer is an important mechanism underlying seedling establishment.

PanTHERIA: a species‐level database of life history, ecology, and geography of extant and recently extinct mammals - Kate E. Jones; Jon Bielby; Marcel Cardillo; Susanne A. Fritz; Justin O'Dell; C. David L. Orme; Kamran Safi; Wes Sechrest; Elizabeth H. Boakes; Chris Carbone; Christina Connolly; Michael J. Cutts; et al. (Ecology, 2009)
Analyses of life‐history, ecological, and geographic trait differences among species, their causes, correlates, and likely consequences are increasingly important for understanding and conserving biodiversity in the face of rapid global change. Assembling multispecies trait data from diverse literature sources into a single comprehensive data set requires detailed consideration of methods to reliably compile data for particular species, and to derive single estimates from multiple sources based on different techniques and definitions. Here we describe PanTHERIA, a species‐level data set compiled for analysis of life history, ecology, and geography of all known extant and recently extinct mammals. PanTHERIA is derived from a database capable of holding multiple geo‐referenced values for variables within a species containing 100 740 lines of biological data for extant and recently extinct mammalian species, collected over a period of three years by 20 individuals. PanTHERIA also includes spatial databases of mammalian geographic ranges and global climatic and anthropogenic variables. Here we detail how the data fields are extracted and defined for PanTHERIA using a customized data input format (MammalForm); how data were collected from the literature, species names and sources tracked, error‐checking and validation procedures applied, and how data were consolidated into species‐level values for each variable. Tables of the consolidated species‐level values are made available for each of two recent species‐level taxonomic classifications of mammals, as well as associated taxonomic synonymy conversion and data‐input files. This study provides a useful guide to prospective researchers on how to structure and codify life‐history, ecological, geographic, and taxonomic data and methods to extract meaningful species‐level traits. It also provides comprehensive information on traits like size, diet, environmental conditions, and ecology to permit macroecological and macroevolutionary analyses of this important clade. The complete data sets corresponding to abstracts published in the Data Papers section of the journal are published electronically in Ecological Archives at 〈 http://esapubs.org/archive 〉. (The accession number for each Data Paper is given directly beneath the title.)

In vivo specific tension of the human quadriceps femoris muscle - Robert M. Erskine; David A. Jones; Constantinos N. Maganaris; Hans Degens (European Journal of Applied Physiology, 2009)

What can the Viviparous-1 gene tell us about wheat pre-harvest sprouting? - L. Q. Xia; Y. Yang; Y. Z. Ma; X. M. Chen; Z. H. He; M. S. Röder; H. D. Jones; P. R. Shewry (Euphytica, 2009)

Evaluating the role of environmental quality in the sustainable rural economic development of England - J. R. Park; M. J. Stabler; P. J. Jones; S. R. Mortimer; J. R. Tiffin; R. B. Tranter (Environment, Development and Sustainability, 2009)

Fluid expulsion features associated with sand waves on Australia’s central North West Shelf - A. T. Jones; J. M. Kennard; G. A. Logan; E. Grosjean; J. Marshall (Geo-Marine Letters, 2009)

Sensitivity of striped trumpeter, Latris lineata, embryos to mechanical shock and simulated transport - M. Jones; S. C. Battaglene; P. M. Pankhurst (Aquaculture International, 2009)

High-resolution array comparative genomic hybridization analysis reveals unanticipated complexity of genetic deficiencies on chromosome V in Caenorhabditis elegans - Martin R. Jones; Shu Yi Chua; Nigel J. O’Neil; Robert C. Johnsen; Ann M. Rose; David L. Baillie (Molecular Genetics and Genomics, 2009)

Visualisation of hrp gene expression in Xanthomonas euvesicatoria in the tomato phyllosphere - Yongxiang Zhang; Ewen M. Callaway; Jeffrey B. Jones; Mark Wilson (European Journal of Plant Pathology, 2009)

Mass deposition event of Pyrosoma atlanticum carcasses off Ivory Coast (West Africa) - M. Lebrato; D. O. B. Jones (Limnology and Oceanography, 2009)
Thousands of moribund thaliacean carcasses ( Pyrosoma atlanticum ) were deposited between February and March 2006 at the seafloor in the Ivory Coast area (West Africa). Remotely operated vehicle surveys were conducted in a continuous depth gradient between 20 and 1275 m along an oil pipeline. Video and still photography were used to estimate the carcass distribution, density, and size on the seabed, as well as recording the local megafauna interactions with the gelatinous material. Large patches of dead pyrosomids covered extensive areas on the continental slope, whereas minor aggregations were found on the shelf. The carcasses were in many instances trapped along the pipelines, accumulating extensively in troughs and furrows in the slope, and especially in soft sediment channels. Pyrosoma atlanticum dried samples were used to calculate the carbon content, enabling the extrapolation to the densities and sizes recorded in the video surveys. The average standing stock of organic carbon associated with the carcasses was >5 g C m −2 in the whole slope and canyon, with values as high as 22 g C m −2 in certain areas. Eight megafaunal species from three different phyla were observed 63 times directly feeding on the decomposing carcasses. The gelatinous carbon may have contributed substantially to the detrital food web including microbes at the seabed, and certainly to the diet of larger benthic organisms. The organism‐level carbon measurements and documented fate of pyrosomid organic carbon is new evidence of the importance of gelatinous material in large‐scale processes and elemental cycling.

Arctic Lake Physical Processes and Regimes with Implications for Winter Water Availability and Management in the National Petroleum Reserve Alaska - Benjamin M. Jones; Christopher D. Arp; Kenneth M. Hinkel; Richard A. Beck; Joel A. Schmutz; Barry Winston (Environmental Management, 2009)

Connectivity, biodiversity conservation and the design of marine reserve networks for coral reefs - G. R. Almany; S. R. Connolly; D. D. Heath; J. D. Hogan; G. P. Jones; L. J. McCook; M. Mills; R. L. Pressey; D. H. Williamson (Coral Reefs, 2009)

Larval retention and connectivity among populations of corals and reef fishes: history, advances and challenges - G. P. Jones; G. R. Almany; G. R. Russ; P. F. Sale; R. S. Steneck; M. J. H. van Oppen; B. L. Willis (Coral Reefs, 2009)

Management under uncertainty: guide-lines for incorporating connectivity into the protection of coral reefs - L. J. McCook; G. R. Almany; M. L. Berumen; J. C. Day; A. L. Green; G. P. Jones; J. M. Leis; S. Planes; G. R. Russ; P. F. Sale; S. R. Thorrold (Coral Reefs, 2009)

Connectivity and resilience of coral reef metapopulations in marine protected areas: matching empirical efforts to predictive needs - L. W. Botsford; J. W. White; M.- A. Coffroth; C. B. Paris; S. Planes; T. L. Shearer; S. R. Thorrold; G. P. Jones (Coral Reefs, 2009)

Influence of soil nutrients on ectomycorrhizal communities in a chronosequence of mixed temperate forests - Brendan D. Twieg; Daniel M. Durall; Suzanne W. Simard; Melanie D. Jones (Mycorrhiza, 2009)