Social behaviour in sharks and rays: analysis, patterns and implications for conservation - David M P Jacoby; Darren P Croft; David W Sims (Fish and Fisheries, 2012)
There are widespread records of grouping behaviour in both adult and juvenile sharks and rays (Class Chondrichthyes, Subclass Elasmobranchii). Yet despite burgeoning descriptions of these events, many of the proximate and ultimate causes of group living in these top predators remain elusive. Given the documented negative anthropogenic effects on many shark populations globally, there is an increasing need to understand how behaviourally mediated grouping influences population distributions and abundance, and the role this plays in exacerbating vulnerability to fishing mortality. Here, we analyse group living in elasmobranchs: we describe our current understanding of the patterns, mechanisms and functions of both aggregation (where grouping is not driven by social mechanisms) and social grouping (where grouping is influenced by social interaction) and discuss some of the current methods used to study social behaviour in this taxa. In particular, social preferences in elasmobranchs have received relatively little attention. We propose that the study of shark aggregations may benefit from a more fine‐scale analytical approach offered by detailed exploration of social interactions using social network analysis. Better understanding of the frequency and longevity of social relations, in conjunction with current long‐term data on habitat use and site philopatry, will likely serve for a more informed approach to coastal and pelagic elasmobranch conservation initiatives.

An allosteric enhancer of M4 muscarinic acetylcholine receptor function inhibits behavioral and neurochemical effects of cocaine - Ditte Dencker; Pia Weikop; Gunnar Sørensen; David P. D. Woldbye; Gitta Wörtwein; Jürgen Wess; Anders Fink-Jensen (Psychopharmacology, 2012)

Catchment land use and trophic state impacts on phytoplankton composition: a case study from the Rotorua lakes’ district, New Zealand - Wendy J. Paul; David P. Hamilton; Ilia Ostrovsky; Steven D. Miller; Austin Zhang; Kohji Muraoka (Hydrobiologia, 2012)

Predicting the spatiotemporal expression of local and referred acute muscle pain in individual subjects - Troy K. Rubin; Sally Lake; Saskia van der Kooi; Nicholas P. Lucas; David A. Mahns; Luke A. Henderson; Vaughan G. Macefield (Experimental Brain Research, 2012)

Inheritance of resistance to root-lesion nematodes (Pratylenchus thornei and P. neglectus) in five doubled-haploid populations of wheat - John P. Thompson; Rebecca S. Zwart; David Butler (Euphytica, 2012)

Osmium isotope systematics of historical lavas from Piton de la Fournaise (Réunion Island, Indian Ocean) - P. Schiano; K. David; I. Vlastélic; A. Gannoun; M. Klein; F. Nauret; P. Bonnand (Contributions to Mineralogy and Petrology, 2012)

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

Experimental infection of laboratory-bred bank voles (Myodes glareolus) with murid herpesvirus 4 - David J. Hughes; Anja Kipar; Gail Leeming; Jeffery T. Sample; James P. Stewart (Archives of Virology, 2012)

A Status Report on Manuscript Submissions in the Journal of Aquatic Food Product Technology - David P. Green (Journal of Aquatic Food Product Technology, 2012)

Blueberry supplementation induces spatial memory improvements and region-specific regulation of hippocampal BDNF mRNA expression in young rats - Catarina Rendeiro; David Vauzour; Rebecca J. Kean; Laurie T. Butler; Marcus Rattray; Jeremy P. E. Spencer; Claire M. Williams (Psychopharmacology, 2012)

Probabilistic assessment of wildfire hazard and municipal watershed exposure - Joe Scott; Don Helmbrecht; Matthew P. Thompson; David E. Calkin; Kate Marcille (Natural Hazards, 2012)

The mammalian gene function resource: the international knockout mouse consortium - Allan Bradley; Konstantinos Anastassiadis; Abdelkader Ayadi; James F. Battey; Cindy Bell; Marie-Christine Birling; Joanna Bottomley; Steve D. Brown; Antje Bürger; Carol J. Bult; Wendy Bushell; Francis S. Collins; et al. (Mammalian Genome, 2012)

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

Sources of uncertainty in future changes in local precipitation - David P. Rowell (Climate Dynamics, 2012)

Lymphatics, lymph nodes and the immune system: barriers and gateways for cancer spread - Robert L. Ferris; Michael T. Lotze; Stanley P. L. Leong; David S. B. Hoon; Donald L. Morton (Clinical & Experimental Metastasis, 2012)

Preoperative sentinel lymph node mapping of the prostate using PET/CT fusion imaging and Ga-68-labeled tilmanocept in an animal model - Sean P. Stroup; Christopher J. Kane; Salman Farchshchi-Heydari; Claude M. James; Christopher H. Davis; Anne M. Wallace; Carl K. Hoh; David R. Vera (Clinical & Experimental Metastasis, 2012)

Cigarette smoking, alcohol intake, and thyroid cancer risk: a pooled analysis of five prospective studies in the United States - Cari M. Kitahara; Martha S. Linet; Laura E. Beane Freeman; David P. Check; Timothy R. Church; Yikyung Park; Mark P. Purdue; Catherine Schairer; Amy Berrington de González (Cancer Causes & Control, 2012)

CTCF and Sp1 interact with the Murine gammaherpesvirus 68 internal repeat elements - Hannah C. Stevens; Kevin S-W Cham; David J. Hughes; Ren Sun; Jeffery T. Sample; Vivien J. Bubb; James P. Stewart; John P. Quinn (Virus Genes, 2012)

Intracellular-signaling tumor-regression modeling of the pro-apoptotic receptor agonists dulanermin and conatumumab - Brittany P. Kay; Cheng-Pang Hsu; Jian-Feng Lu; Yu-Nien Sun; Shuang Bai; Yan Xin; David Z. D’Argenio (Journal of Pharmacokinetics and Pharmacodynamics, 2012)

Chemical Composition of Metapleural Gland Secretions of Fungus-Growing and Non-fungus-growing Ants - Alexsandro S. Vieira; E. David Morgan; Falko P. Drijfhout; Maria I. Camargo-Mathias (Journal of Chemical Ecology, 2012)

A suggested new bacteriophage genus: “Viunalikevirus” - Evelien M. Adriaenssens; Hans-Wolfgang Ackermann; Hany Anany; Bob Blasdel; Ian F. Connerton; David Goulding; Mansel W. Griffiths; Steven P. Hooton; Elizabeth M. Kutter; Andrew M. Kropinski; Ju-Hoon Lee; Martine Maes; et al. (Archives of Virology, 2012)
We suggest a bacteriophage genus, “Viunalikevirus”, as a new genus within the family Myoviridae . To date, this genus includes seven sequenced members: Salmonella phages ViI, SFP10 and ΦSH19; Escherichia phages CBA120 and PhaxI; Shigella phage phiSboM-AG3; and Dickeya phage LIMEstone1. Their shared myovirus morphology, with comparable head sizes and tail dimensions, and genome organization are considered distinguishing features. They appear to have conserved regulatory sequences, a horizontally acquired tRNA set and the probable substitution of an alternate base for thymine in the DNA. A close examination of the tail spike region in the DNA revealed four distinct tail spike proteins, an arrangement which might lead to the umbrella-like structures of the tails visible on electron micrographs. These properties set the suggested genus apart from the recently ratified subfamily Tevenvirinae , although a significant evolutionary relationship can be observed.

Methods for reactive oxygen species (ROS) detection in aqueous environments - Justina M. Burns; William J. Cooper; John L. Ferry; D. Whitney King; Brian P. DiMento; Kristopher McNeill; Christopher J. Miller; William L. Miller; Barrie M. Peake; Steven A. Rusak; Andrew L. Rose; T. David Waite (Aquatic Sciences, 2012)

Collaborative Gaze Channelling for Improved Cooperation During Robotic Assisted Surgery - Ka-Wai Kwok; Loi-Wah Sun; George P. Mylonas; David R. C. James; Felipe Orihuela-Espina; Guang-Zhong Yang (Annals of Biomedical Engineering, 2012)

Invasion history of North American Canada thistle, Cirsium arvense - Alessia Guggisberg; Erik Welk; René Sforza; David P. Horvath; James V. Anderson; Michael E. Foley; Loren H. Rieseberg (Journal of Biogeography, 2012)
Aim Canada thistle ( Cirsium arvense – Cardueae, Asteraceae) is one of the worst invasive plants world‐wide. Native to Eurasia, its unintentional introduction into North America now threatens the native flora and is responsible for enormous agricultural losses. The goals of this study are to: (1) reconstruct the evolutionary history of C. arvense and estimate how often it may have colonized North America, (2) compare the genetic diversity between European and North American populations to detect signs of demographic bottlenecks and/or patterns of population admixture, and (3) conduct bioclimatic comparisons to infer eventual niche shifts following this species’ introduction into North America. Location Europe and North America. Methods A total of 1522 individuals from 58 populations were investigated with six microsatellite markers. Estimates of heterozygosity ( H E ) and allelic richness ( R S ) were quantified for each population, and population structure was inferred via analyses of molecular variance (AMOVAs), principal components analyses (PCAs), Mantel tests and Bayesian clustering analyses. Climatic niche spaces were based on 19 bioclimatic variables extracted from approximately 32,000 locations covering the entire range, and compared using PCA and hierarchical cluster analysis. Results Although there is evidence of multiple introductions from divergent European lineages, North American populations of C. arvense exhibited significantly lower levels of genetic diversity than their putative ancestors. Bioclimatic comparisons pointed to a high degree of niche conservatism during invasion, but indicated that genotypes from the former USSR and Central European mountain chains were probably best adapted to invade North America upon entry into the continent. Main conclusions Genetic and historical data suggest that C. arvense first entered North America from Western Europe with the first European settlers, and was later introduced from Eastern Europe into the prairie states during the agricultural boom. The species went through a significant bottleneck following its introduction into the New World, but the level of genetic diversity remained high owing to admixture between genetically differentiated lineages and to a highly efficient outcrossing breeding system.

Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC–MS/MS based protein quantification and metabolic flux analysis - Jack P. Wang; Christopher M. Shuford; Quanzi Li; Jina Song; Ying-Chung Lin; Ying-Hsuan Sun; Hsi-Chuan Chen; Cranos M. Williams; David C. Muddiman; Ronald R. Sederoff; Vincent L. Chiang (Planta, 2012)

Contrasting bud bank dynamics of two co-occurring grasses in tallgrass prairie: implications for grassland dynamics - Jacqueline P. Ott; David C. Hartnett (Plant Ecology, 2012)

Documenting measurement sensitivity and bias of field-measured parameters in water quality monitoring programs - David P. Thoma; Roy J. Irwin; Pete E. Penoyer (Environmental Monitoring and Assessment, 2012)

Clinical correlation and molecular evaluation confirm that the MLH1 p.Arg182Gly (c.544A>G) mutation is pathogenic and causes Lynch syndrome - Michael P. Farrell; David J. Hughes; Ian R. Berry; David J. Gallagher; Emily A. Glogowski; Stewart J. Payne; Michael J. Kennedy; Róisín M. Clarke; Susan A. White; Cian B. Muldoon; Fiona Macdonald; Pauline Rehal; et al. (Familial Cancer, 2012)

The Measurement of Local Variation in Shape - Eladio J. Márquez; Ryan Cabeen; Roger P. Woods; David Houle (Evolutionary Biology, 2012)

Variation in stem radial growth of the Australian conifer, Callitris columellaris, across the world’s driest and least fertile vegetated continent - Lynda D. Prior; Pauline F. Grierson; W. Lachlan McCaw; David Y. P. Tng; Scott C. Nichols; David M. J. S. Bowman (Trees, 2012)

Neuropeptide Y Y5 receptor antagonism attenuates cocaine-induced effects in mice - Gunnar Sørensen; Morten Jensen; Pia Weikop; Ditte Dencker; Søren H. Christiansen; Claus Juul Loland; Cecilie Hee Bengtsen; Jørgen Holm Petersen; Anders Fink-Jensen; Gitta Wörtwein; David P. D. Woldbye (Psychopharmacology, 2012)

Migration as an escape from parasitism in New Zealand galaxiid fishes - Robert Poulin; Gerard P. Closs; Adrian W. T. Lill; Andy S. Hicks; Kristin K. Herrmann; David W. Kelly (Oecologia, 2012)

Erratum to: Febrile response induced by cecal ligation and puncture (CLP) in rats: involvement of prostaglandin E2 and cytokines - Maria José Figueiredo; Denis Melo Soares; Juliano Manvailer Martins; Renes de Resende Machado; Carlos Arterio Sorgi; Lucia Helena Faccioli; Miriam Cristina Contin de Melo; David do Carmo Malvar; Glória E. P. Souza (Medical Microbiology and Immunology, 2012)

Impacts of logging and rehabilitation on invertebrate communities in tropical rainforests of northern Borneo - David P. Edwards; Amy R. Backhouse; Charlotte Wheeler; Chey Vun Khen; Keith C. Hamer (Journal of Insect Conservation, 2012)

Auxin and ABA act as central regulators of developmental networks associated with paradormancy in Canada thistle (Cirsium arvense) - James V. Anderson; Münevver Doğramacı; David P. Horvath; Michael E. Foley; Wun S. Chao; Jeffrey C. Suttle; Jyothi Thimmapuram; Alvaro G. Hernandez; Shahjahan Ali; Mark A. Mikel (Functional & Integrative Genomics, 2012)

Application of a single-objective, hybrid genetic algorithm approach to pharmacokinetic model building - Eric A. Sherer; Mark E. Sale; Bruce G. Pollock; Chandra P. Belani; Merrill J. Egorin; Percy S. Ivy; Jeffrey A. Lieberman; Stephen B. Manuck; Stephen R. Marder; Matthew F. Muldoon; Howard I. Scher; David B. Solit; et al. (Journal of Pharmacokinetics and Pharmacodynamics, 2012)

Increased cortical expression of FK506 binding protein-51 in HIV-associated neurocognitive disorders - Virawudh Soontornniyomkij; Ian P. Everall; David J. Moore; Ben Gouaux; Erick T. Tatro; Vadim Gospodarev; Eliezer Masliah; Nicole S. Yin; Harry V. Vinters; Cristian L. Achim (Journal of NeuroVirology, 2012)

Nomenclature report on the major histocompatibility complex genes and alleles of Great Ape, Old and New World monkey species - Natasja G. de Groot; Nel Otting; James Robinson; Antoine Blancher; Bernard A. P. Lafont; Steven G. E. Marsh; David H. O’Connor; Takashi Shiina; Lutz Walter; David I. Watkins; Ronald E. Bontrop (Immunogenetics, 2012)

Trophic Transfer Efficiency of Methylmercury and Inorganic Mercury to Lake Trout Salvelinus namaycush from Its Prey - C. P. Madenjian; S. R. David; D. P. Krabbenhoft (Archives of Environmental Contamination and Toxicology, 2012)

The biogeography of mitochondrial and nuclear discordance in animals - DAVID P. L. TOEWS; ALAN BRELSFORD (Molecular Ecology, 2012)
Combining nuclear (nuDNA) and mitochondrial DNA (mtDNA) markers has improved the power of molecular data to test phylogenetic and phylogeographic hypotheses and has highlighted the limitations of studies using only mtDNA markers. In fact, in the past decade, many conflicting geographic patterns between mitochondrial and nuclear genetic markers have been identified (i.e. mito‐nuclear discordance). Our goals in this synthesis are to: (i) review known cases of mito‐nuclear discordance in animal systems, (ii) to summarize the biogeographic patterns in each instance and (iii) to identify common drivers of discordance in various groups. In total, we identified 126 cases in animal systems with strong evidence of discordance between the biogeographic patterns obtained from mitochondrial DNA and those observed in the nuclear genome. In most cases, these patterns are attributed to adaptive introgression of mtDNA, demographic disparities and sex‐biased asymmetries, with some studies also implicating hybrid zone movement, human introductions and Wolbachia infection in insects. We also discuss situations where divergent mtDNA clades seem to have arisen in the absence of geographic isolation. For those cases where foreign mtDNA haplotypes are found deep within the range of a second taxon, data suggest that those mtDNA haplotypes are more likely to be at a high frequency and are commonly driven by sex‐biased asymmetries and/or adaptive introgression. In addition, we discuss the problems with inferring the processes causing discordance from biogeographic patterns that are common in many studies. In many cases, authors presented more than one explanation for discordant patterns in a given system, which indicates that likely more data are required. Ideally, to resolve this issue, we see important future work shifting focus from documenting the prevalence of mito‐nuclear discordance towards testing hypotheses regarding the drivers of discordance. Indeed, there is great potential for certain cases of mitochondrial introgression to become important natural systems within which to test the effect of different mitochondrial genotypes on whole‐animal phenotypes.

Synoptic forcing of wave states in the southeast Chukchi Sea, Alaska, at an offshore location - Oceana P. Francis; David E. Atkinson (Natural Hazards, 2012)

Synoptic forcing of wave states in the southeast Chukchi Sea, Alaska, at nearshore locations - Oceana P. Francis; David E. Atkinson (Natural Hazards, 2012)

Photobiology of corals from Brazil’s near-shore marginal reefs of Abrolhos - David J. Suggett; Ruy K. P. Kikuchi; Marília D. M. Oliveira; Saulo Spanó; Rafael Carvalho; David J. Smith (Marine Biology, 2012)

Molecular ecology and adaptation of visual photopigments in craniates - WAYNE I. L. DAVIES; SHAUN P. COLLIN; DAVID M. HUNT (Molecular Ecology, 2012)
In craniates, opsin‐based photopigments expressed in the eye encode molecular ‘light sensors’ that constitute the initial protein in photoreception and the activation of the phototransduction cascade. Since the cloning and sequencing of the first vertebrate opsin gene (bovine rod opsin) nearly 30 years ago (Ovchinnikov Yu 1982, FEBS Letters , 148, 179–191; Hargrave et al. 1983, Biophysics of Structure & Mechanism , 9, 235–244; Nathans & Hogness 1983, Cell , 34, 807–814), it is now well established that variation in the subtypes and spectral properties of the visual pigments that mediate colour and dim‐light vision is a prevalent mechanism for the molecular adaptation to diverse light environments. In this review, we discuss the origins and spectral tuning of photopigments that first arose in the agnathans to sample light within the ancient aquatic landscape of the Early Cambrian, detailing the molecular changes that subsequently occurred in each of the opsin classes independently within the main branches of extant jawed gnathostomes. Specifically, we discuss the adaptive changes that have occurred in the photoreceptors of craniates as they met the ecological challenges to survive in quite differing photic niches, including brightly lit aquatic surroundings; the deep sea; the transition to and from land; diurnal, crepuscular and nocturnal environments; and light‐restricted fossorial settings. The review ends with a discussion of the limitations inherent to the ‘nocturnal‐bottleneck’ hypothesis relevant to the evolution of the mammalian visual system and a proposition that transition through a ‘mesopic‐bottleneck’ may be a more appropriate model.

Using aerial photography to investigate evidence of feeding by bowhead whales - Julie A. Mocklin; David J. Rugh; Sue E. Moore; Robyn P. Angliss (Marine Mammal Science, 2012)
Aerial photographs were analyzed to investigate the feeding habits of the Bering‐Chukchi‐Beaufort (BCB) population of bowhead whales ( Balaena mysticetus ), particularly epibenthic feeding near Barrow, Alaska. Evidence of epibenthic feeding was based on mud visible on the dorsal surface of whales, resulting from feeding near the seafloor. Other cues used to assess feeding were an open mouth or the presence of feces in photographs. Over 3,600 photographs were analyzed including photos from surveys in spring and late summer and in both the western and eastern Beaufort Sea. Of all the photographs analyzed, 64% were scored as definitively muddy. In spring, ratios ranged from a low of 27% in 2003 to a high of 76% in 2004. When all May sample sets off Barrow were combined (1985, 1986, 2003, 2004), there was a significant difference ( t ‐test, P

Erratum: Differential effects of ocean acidification on growth and photosynthesis among phylotypes of Symbiodinium (Dinophyceae) - Patrick Brading; Mark E. Warner; Phillip Davey; David J. Smith; Eric P. Achterberg; David J. Suggett (Limnology and Oceanography, 2012)

Towards an integrated global framework to assess the impacts of land use and management change on soil carbon: current capability and future vision - Pete Smith; Christian A. Davies; Stephen Ogle; Giuliana Zanchi; Jessica Bellarby; Neil Bird; Robert M. Boddey; Niall P. McNamara; David Powlson; Annette Cowie; Meine van Noordwijk; Sarah C. Davis; et al. (Global Change Biology, 2012)
I ntergovernmental P anel on C limate C hange ( IPCC ) T ier 1 methodologies commonly underpin project‐scale carbon accounting for changes in land use and management and are used in frameworks for L ife C ycle A ssessment and carbon footprinting of food and energy crops. These methodologies were intended for use at large spatial scales. This can introduce error in predictions at finer spatial scales. There is an urgent need for development and implementation of higher tier methodologies that can be applied at fine spatial scales (e.g. farm/project/plantation) for food and bioenergy crop greenhouse gas (GHG) accounting to facilitate decision making in the land‐based sectors. Higher tier methods have been defined by IPCC and must be well evaluated and operate across a range of domains (e.g. climate region, soil type, crop type, topography), and must account for land use transitions and management changes being implemented. Furthermore, the data required to calibrate and drive the models used at higher tiers need to be available and applicable at fine spatial resolution, covering the meteorological, soil, cropping system and management domains, with quantified uncertainties. Testing the reliability of the models will require data either from sites with repeated measurements or from chronosequences. We review current global capability for estimating changes in soil carbon at fine spatial scales and present a vision for a framework capable of quantifying land use change and management impacts on soil carbon, which could be used for addressing issues such as bioenergy and biofuel sustainability, food security, forest protection, and direct/indirect impacts of land use change. The aim of this framework is to provide a globally accepted standard of carbon measurement and modelling appropriate for GHG accounting that could be applied at project to national scales (allowing outputs to be scaled up to a country level), to address the impacts of land use and land management change on soil carbon.

What controls the distribution of tropical forest and savanna? - Brett P. Murphy; David M.J.S. Bowman (Ecology Letters, 2012)
Ecology Letters (2012) 15 : 748–758 Abstract Forest and savanna biomes dominate the tropics, yet factors controlling their distribution remain poorly understood. Climate is clearly important, but extensive savannas in some high rainfall areas suggest a decoupling of climate and vegetation. In some situations edaphic factors are important, with forest often associated with high nutrient availability. Fire also plays a key role in limiting forest, with fire exclusion often causing a switch from savanna to forest. These observations can be captured by a broad conceptual model with two components: (1) forest and savanna are alternative stable states, maintained by tree cover‐fire feedbacks, (2) the interaction between tree growth rates and fire frequency limits forest development; any factor that increases growth (e.g. elevated availability of water, nutrients, CO 2 ), or decreases fire frequency, will favour canopy closure. This model is consistent with the range of environmental variables correlated with forest distribution, and with the current trend of forest expansion, likely driven by increasing CO 2 concentrations. Resolving the drivers of forest and savanna distribution has moved beyond simple correlative studies that are unlikely to establish ultimate causation. Experiments using Dynamic Global Vegetation Models, parameterised with measurements from each continent, provide an important tool for understanding the controls of these systems.

Sucrose Mobilisation in Sugarcane Stalk Induced by Heterotrophic Axillary Bud Growth - Brian P. O’Neill; Matthew P. Purnell; David J. Anderson; Lars K. Nielsen; Stevens M. Brumbley (Tropical Plant Biology, 2012)

Are executive function and impulsivity antipodes? A conceptual reconstruction with special reference to addiction - Warren K. Bickel; David P. Jarmolowicz; E. Terry Mueller; Kirstin M. Gatchalian; Samuel M. McClure (Psychopharmacology, 2012)

Comparison of wintertime eukaryotic community from sea ice and open water in the Baltic Sea, based on sequencing of the 18S rRNA gene - Markus Majaneva; Janne-Markus Rintala; Maria Piisilä; David P. Fewer; Jaanika Blomster (Polar Biology, 2012)

Exploring warm-season cover crops as carbon sources for anaerobic soil disinfestation (ASD) - David M. Butler; Erin N. Rosskopf; Nancy Kokalis-Burelle; Joseph P. Albano; Joji Muramoto; Carol Shennan (Plant and Soil, 2012)

Mice Chronically Infected with Chimeric HIV Resist Peripheral and Brain Superinfection: A Model of Protective Immunity to HIV - Jennifer L. Kelschenbach; Manisha Saini; Eran Hadas; Chao-jiang Gu; Wei Chao; Galina Bentsman; Jessie P. Hong; Tomas Hanke; Leroy R. Sharer; Mary Jane Potash; David J. Volsky (Journal of Neuroimmune Pharmacology, 2012)

Genetic effects of habitat fragmentation and population isolation on Etheostoma raneyi (Percidae) - Ken A. Sterling; David H. Reed; Brice P. Noonan; Melvin L. Warren (Conservation Genetics, 2012)

Analysis of climate policy targets under uncertainty - Mort Webster; Andrei P. Sokolov; John M. Reilly; Chris E. Forest; Sergey Paltsev; Adam Schlosser; Chien Wang; David Kicklighter; Marcus Sarofim; Jerry Melillo; Ronald G. Prinn; Henry D. Jacoby (Climatic Change, 2012)

A cross-sectional analysis of the association between diet and insulin-like growth factor (IGF)-I, IGF-II, IGF-binding protein (IGFBP)-2, and IGFBP-3 in men in the United Kingdom - Nicholas J. Young; Chris Metcalfe; David Gunnell; Mari-Anne Rowlands; J. Athene Lane; Rebecca Gilbert; Kerry N. L. Avery; Michael Davis; David E. Neal; Freddie C. Hamdy; Jenny Donovan; Richard M. Martin; et al. (Cancer Causes & Control, 2012)

A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC molecules - Alessandro Sette; John Sidney; Scott Southwood; Carrie Moore; Jessica Berry; Courtney Dow; Kate Bradley; Ilka Hoof; Mark G. Lewis; William H. Hildebrand; Curtis P. McMurtrey; Nancy A. Wilson; et al. (Immunogenetics, 2012)

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

Tumors and proliferative lesions in adult offspring after maternal exposure to methylarsonous acid during gestation in CD1 mice - Erik J. Tokar; Bhalchandra A. Diwan; David J. Thomas; Michael P. Waalkes (Archives of Toxicology, 2012)

Microbial biodiversity in a Malaysian oil field and a systematic comparison with oil reservoirs worldwide - Dongmei Li; David J. Midgley; Jason P. Ross; Yalchin Oytam; Guy C. J. Abell; Herbert Volk; Wan Ata Wan Daud; Philip Hendry (Archives of Microbiology, 2012)

New evidence for jute (Corchorus capsularis L.) in the Indus civilization - Rita P. Wright; David L. Lentz; Harriet F. Beaubien; Christine K. Kimbrough (Archaeological and Anthropological Sciences, 2012)

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA - DAVID M. LODGE; CAMERON R. TURNER; CHRISTOPHER L. JERDE; MATTHEW A. BARNES; LINDSAY CHADDERTON; SCOTT P. EGAN; JEFFREY L. FEDER; ANDREW R. MAHON; MICHAEL E. PFRENDER (Molecular Ecology, 2012)
Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology , Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next‐generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.

Soil organic matter turnover is governed by accessibility not recalcitrance - Jennifer A. J. Dungait; David W. Hopkins; Andrew S. Gregory; Andrew P. Whitmore (Global Change Biology, 2012)
Mechanisms to mitigate global climate change by sequestering carbon ( C ) in different ‘sinks' have been proposed as at least temporary measures. Of the major global C pools, terrestrial ecosystems hold the potential to capture and store substantially increased volumes of C in soil organic matter ( SOM ) through changes in management that are also of benefit to the multitude of ecosystem services that soils provide. This potential can only be realized by determining the amount of SOM stored in soils now, with subsequent quantification of how this is affected by management strategies intended to increase SOM concentrations, and used in soil C models for the prediction of the roles of soils in future climate change. An apparently obvious method to increase C stocks in soils is to augment the soil C pools with the longest mean residence times ( MRT ). Computer simulation models of soil C dynamics, e.g. RothC and Century, partition these refractory constituents into slow and passive pools with MRT s of centuries to millennia. This partitioning is assumed to reflect: (i) the average biomolecular properties of SOM in the pools with reference to their source in plant litter, (ii) the accessibility of the SOM to decomposer organisms or catalytic enzymes, or (iii) constraints imposed on decomposition by environmental conditions, including soil moisture and temperature. However, contemporary analytical approaches suggest that the chemical composition of these pools is not necessarily predictable because, despite considerable progress with understanding decomposition processes and the role of decomposer organisms, along with refinements in simulation models, little progress has been made in reconciling biochemical properties with the kinetically defined pools. In this review, we will explore how advances in quantitative analytical techniques have redefined the new understanding of SOM dynamics and how this is affecting the development and application of new modelling approaches to soil C .

The impact of extra-pair mating behavior on hybridization and genetic introgression - Patricia J. Hartman; Daniel P. Wetzel; Philip H. Crowley; David F. Westneat (Theoretical Ecology, 2012)

Febrile response induced by cecal ligation and puncture (CLP) in rats: involvement of prostaglandin E2 and cytokines - Maria José Figueiredo; Denis de Melo Soares; Juliano Manvailer Martins; Renes de Resende Machado; Carlos Arterio Sorgi; Lucia Helena Faccioli; Miriam Cristina Contin de Melo; David do Carmo Malvar; Glória E. P. Souza (Medical Microbiology and Immunology, 2012)

A global view of the OCA2-HERC2 region and pigmentation - Michael P. Donnelly; Peristera Paschou; Elena Grigorenko; David Gurwitz; Csaba Barta; Ru-Band Lu; Olga V. Zhukova; Jong-Jin Kim; Marcello Siniscalco; Maria New; Hui Li; Sylvester L. B. Kajuna; et al. (Human Genetics, 2012)

Does life in unstable environments favour facultative selfing? A case study in the freshwater snail Drepanotrema depressissimum (Basommatophora: Planorbidae) - T. Lamy; L. Lévy; J. P. Pointier; P. Jarne; P. David (Evolutionary Ecology, 2012)

Spatial and trophic overlap of marked and unmarked Columbia River Basin spring Chinook salmon during early marine residence with implications for competition between hatchery and naturally produced fish - Elizabeth A. Daly; Richard D. Brodeur; Joseph P. Fisher; Laurie A. Weitkamp; David J. Teel; Brian R. Beckman (Environmental Biology of Fishes, 2012)

Breeding success of four male life history types of spring Chinook Salmon spawning in an artificial stream - Steve L. Schroder; Curtis M. Knudsen; Todd N. Pearsons; Todd W. Kassler; Edward P. Beall; Sewall F. Young; David E. Fast (Environmental Biology of Fishes, 2012)

Extreme events, trends, and variability in Northern Hemisphere lake-ice phenology (1855–2005) - Barbara J. Benson; John J. Magnuson; Olaf P. Jensen; Virginia M. Card; Glenn Hodgkins; Johanna Korhonen; David M. Livingstone; Kenton M. Stewart; Gesa A. Weyhenmeyer; Nick G. Granin (Climatic Change, 2012)

Climate change projections and stratosphere–troposphere interaction - Adam A. Scaife; Thomas Spangehl; David R. Fereday; Ulrich Cubasch; Ulrike Langematz; Hideharu Akiyoshi; Slimane Bekki; Peter Braesicke; Neal Butchart; Martyn P. Chipperfield; Andrew Gettelman; Steven C. Hardiman; et al. (Climate Dynamics, 2012)

Reduced investment in immune function in invasion-front populations of the cane toad (Rhinella marina) in Australia - David Llewellyn; Michael B. Thompson; Gregory P. Brown; Benjamin L. Phillips; Richard Shine (Biological Invasions, 2012)

Efficacy of fungicides on mycelial growth of diatrypaceous fungi associated with grapevine trunk disease - David Gramaje; Matthew R. Ayres; Florent P. Trouillas; Mark R. Sosnowski (Australasian Plant Pathology, 2012)

Methane emissions from soils: synthesis and analysis of a large UK data set - Peter E. Levy; Annette Burden; Mark D. A. Cooper; Kerry J. Dinsmore; Julia Drewer; Chris Evans; David Fowler; Jenny Gaiawyn; Alan Gray; Stephanie K. Jones; Timothy Jones; Niall P. McNamara; et al. (Global Change Biology, 2012)
Nearly 5000 chamber measurements of CH 4 flux were collated from 21 sites across the U nited K ingdom, covering a range of soil and vegetation types, to derive a parsimonious model that explains as much of the variability as possible, with the least input requirements. Mean fluxes ranged from −0.3 to 27.4 nmol CH 4 m −2 s −1 , with small emissions or low rates of net uptake in mineral soils (site means of −0.3 to 0.7 nmol m −2 s −1 ) and much larger emissions from organic soils (site means of −0.3 to 27.4 nmol m −2 s −1 ). Less than half of the observed variability in instantaneous fluxes could be explained by independent variables measured. The reasons for this include measurement error, stochastic processes and, probably most importantly, poor correspondence between the independent variables measured and the actual variables influencing the processes underlying methane production, transport and oxidation. When temporal variation was accounted for, and the fluxes averaged at larger spatial scales, simple models explained up to ca. 75% of the variance in CH 4 fluxes. Soil carbon, peat depth, soil moisture and pH together provided the best sub‐set of explanatory variables. However, where plant species composition data were available, this provided the highest explanatory power. Linear and nonlinear models generally fitted the data equally well, with the exception that soil moisture required a power transformation. To estimate the impact of changes in peatland water table on CH 4 emissions in the U nited K ingdom, an emission factor of +0.4 g CH 4 m −2 yr −1 per cm increase in water table height was derived from the data.

Accelerators of Innovation and Discovery - David P. Green (Journal of Aquatic Food Product Technology, 2012)

Chemical and physical factors associated with yellow perch abundance in Great Lakes coastal wetlands: patterns within and among wetland types - Aaron D. Parker; Matthew J. Cooper; Carl R. Ruetz; David P. Coulter; Donald G. Uzarski (Wetlands Ecology and Management, 2012)

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

MDMA induces Per1, Per2 and c-fos gene expression in rat suprachiasmatic nuclei - Rowan P. Ogeil; David J. Kennaway; Mark D. Salkeld; Shantha M. W. Rajaratnam; Jillian H. Broadbear (Psychopharmacology, 2012)

Galanin negatively modulates opiate withdrawal via galanin receptor 1 - Fiona E. Holmes; Athena Armenaki; Tiina P. Iismaa; Emily B. Einstein; John Shine; Marina R. Picciotto; David Wynick; Venetia Zachariou (Psychopharmacology, 2012)

Genetic variants associated with the white blood cell count in 13,923 subjects in the eMERGE Network - David R. Crosslin; Andrew McDavid; Noah Weston; Sarah C. Nelson; Xiuwen Zheng; Eugene Hart; Mariza de Andrade; Iftikhar J. Kullo; Catherine A. McCarty; Kimberly F. Doheny; Elizabeth Pugh; Abel Kho; et al. (Human Genetics, 2012)

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

The reliability of the intermittent critical velocity test and assessment of critical rest interval in men and women - David H. Fukuda; Abbie E. Smith; Kristina L. Kendall; Robert P. Hetrick; Ryan L. Hames; Joel T. Cramer; Jeffrey R. Stout (European Journal of Applied Physiology, 2012)

Aspiration of alendronic acid leading to localized bronchiectasis - Gordon I. A. MacDonald; Graeme P. Currie; David M. Reid (European Journal of Clinical Pharmacology, 2012)

Erratum to: A survey-based evaluation of community-based co-management of forest resources: a case study of Baishuijiang National Natural Reserve in China - Zhu Ting; Ganesh P. Shivakoti; Chen Haiyun; David Maddox (Environment, Development and Sustainability, 2012)

A survey-based evaluation of community-based co-management of forest resources: a case study of Baishuijiang National Natural Reserve in China - Zhu Ting; Ganesh P. Shivakoti; Chen Haiyun; David Maddox (Environment, Development and Sustainability, 2012)

Species designation of the Bruneau Dune tiger beetle (Cicindela waynei) is supported by phylogenetic analysis of mitochondrial DNA sequence data - Caren S. Goldberg; David C. Tank; Simon Uribe-Convers; William R. Bosworth; Hannah E. Marx; Lisette P. Waits (Conservation Genetics, 2012)

Predictors of survival among patients diagnosed with adenocarcinoma of the esophagus and gastroesophageal junction - Aaron P. Thrift; Christina M. Nagle; Paul P. Fahey; Bernard M. Smithers; David I. Watson; David C. Whiteman (Cancer Causes & Control, 2012)

Change and stasis in marine hybrid zones in response to climate warming - Thomas J. Hilbish; Fernando P. Lima; Pamela M. Brannock; Elizabeth K. Fly; Rhiannon L. Rognstad; David S. Wethey (Journal of Biogeography, 2012)
Aim We test the prediction that hybrid zones between warm‐ and cold‐adapted species will move towards the territory formerly occupied by the cold‐adapted species in response to a warming climate. We use multiple tests of this prediction to distinguish amongst potential mechanistic hypotheses of responses to climate change. Location We sampled 97 locations on the Atlantic coast of Spain and France and the English Channel that span three hybrid zones formed between two species of marine mussels ( Mytilus galloprovincialis and M. edulis ). Methods Mussels were sampled in 2005–07 and analysed at a nuclear gene ( Glu‐5′ ) that is diagnostically differentiated between the subject species. Results were compared to those of studies made in the same region over the past two decades. Historical change in sea surface temperature (SST) was analysed using National Oceanic and Atmospheric Administration (NOAA) Optimum Interpolation Daily SST. Species distribution models (random forest and maximum entropy) of the current distribution of mussels were constructed and validated by hindcasting the historical distributions of these species. Validated models were used in combination with forecasts of SST to predict changes in mussel distribution to 2050 and 2100. Results We show that over the past two decades two of the hybrid zones in France have not changed in either position or shape. The third hybrid zone, however, has shifted in the predicted direction, c . 100 km eastward into the warming English Channel. Species distribution modelling strongly implicates changes in winter cold SST as driving this change in the position of one of the hybrid zones. Forecasts of future SST indicate that rapid changes in distribution will occur over the next century. Main conclusions Hybrid zones can be used to conduct repeated tests of ecological responses to climate change and can be valuable in sorting among prospective mechanistic hypotheses that underlie that change. Winter temperatures, but not seasonal high temperature, appear to control the distribution of both species. Species distribution modelling indicates that the collapse of these hybrid zones is imminent, with the rapid expansion of the subtropical species in response to continuing SST warming.

Reconciling estimates of the contemporary North American carbon balance among terrestrial biosphere models, atmospheric inversions, and a new approach for estimating net ecosystem exchange from inventory‐based data - Daniel J. Hayes; David P. Turner; Graham Stinson; A. David McGuire; Yaxing Wei; Tristram O. West; Linda S. Heath; Bernardus de Jong; Brian G. McConkey; Richard A. Birdsey; Werner A. Kurz; Andrew R. Jacobson; et al. (Global Change Biology, 2012)
We develop an approach for estimating net ecosystem exchange ( NEE ) using inventory‐based information over North America ( NA ) for a recent 7‐year period (ca. 2000–2006). The approach notably retains information on the spatial distribution of NEE , or the vertical exchange between land and atmosphere of all non‐fossil fuel sources and sinks of CO 2 , while accounting for lateral transfers of forest and crop products as well as their eventual emissions. The total NEE estimate of a −327 ± 252 TgC yr −1 sink for NA was driven primarily by CO 2 uptake in the Forest Lands sector (−248 TgC yr −1 ), largely in the Northwest and Southeast regions of the US, and in the Crop Lands sector (−297 TgC yr −1 ), predominantly in the Midwest US states. These sinks are counteracted by the carbon source estimated for the Other Lands sector (+218 TgC yr −1 ), where much of the forest and crop products are assumed to be returned to the atmosphere (through livestock and human consumption). The ecosystems of Mexico are estimated to be a small net source (+18 TgC yr −1 ) due to land use change between 1993 and 2002. We compare these inventory‐based estimates with results from a suite of terrestrial biosphere and atmospheric inversion models, where the mean continental‐scale NEE estimate for each ensemble is −511 TgC yr −1 and −931 TgC yr −1 , respectively. In the modeling approaches, all sectors, including Other Lands, were generally estimated to be a carbon sink, driven in part by assumed CO 2 fertilization and/or lack of consideration of carbon sources from disturbances and product emissions. Additional fluxes not measured by the inventories, although highly uncertain, could add an additional −239 TgC yr −1 to the inventory‐based NA sink estimate, thus suggesting some convergence with the modeling approaches.

Effects of Planting Configuration and In-Row Plant Spacing on Photosynthetically Active Radiation Interception for Three Irrigated Potato Cultivars - David D. Tarkalson; Bradley A. King; David L. Bjorneberg; John P. Taberna (Potato Research, 2012)

Biogeographical patterns and co-occurrence of pathogenic infection across island populations of Berthelot’s pipit (Anthus berthelotii) - Lewis G. Spurgin; Juan Carlos Illera; David P. Padilla; David S. Richardson (Oecologia, 2012)

C5a Receptor (CD88) Inhibition Improves Hypothermia-Induced Neuroprotection in an In Vitro Ischemic Model - John Thundyil; Dale Pavlovski; Yu-Hsuan Hsieh; Mathias Gelderblom; Tim Magnus; David P. Fairlie; Thiruma V. Arumugam (NeuroMolecular Medicine, 2012)

Changing patterns of carbon allocation in lake phytoplankton: an FTIR analysis - Andrew P. Dean; James M. Nicholson; David C. Sigee (Hydrobiologia, 2012)

A community-based framework for aquatic ecosystem models - Dennis Trolle; David P. Hamilton; Matthew R. Hipsey; Karsten Bolding; Jorn Bruggeman; Wolf M. Mooij; Jan H. Janse; Anders Nielsen; Erik Jeppesen; J. Alex Elliott; Vardit Makler-Pick; Thomas Petzoldt; et al. (Hydrobiologia, 2012)

The Potential Role for Management of U.S. Public Lands in Greenhouse Gas Mitigation and Climate Policy - Lydia P. Olander; David M. Cooley; Christopher S. Galik (Environmental Management, 2012)

The Effects of Permafrost Thaw on Soil Hydrologic, Thermal, and Carbon Dynamics in an Alaskan Peatland - Jonathan A. O’Donnell; M. Torre Jorgenson; Jennifer W. Harden; A. David McGuire; Mikhail Z. Kanevskiy; Kimberly P. Wickland (Ecosystems, 2012)

New constraints on fluid sources in orogenic gold deposits, Victoria, Australia - Bin Fu; Mark A. Kendrick; Alison M. Fairmaid; David Phillips; Christopher J. L. Wilson; Terrence P. Mernagh (Contributions to Mineralogy and Petrology, 2012)

Phylogenetic assessment of culture collection strains of Thiobacillus thioparus, and definitive 16S rRNA gene sequences for T. thioparus, T. denitrificans, and Halothiobacillus neapolitanus - Rich Boden; David Cleland; Peter N. Green; Yoko Katayama; Yoshihito Uchino; J. Colin Murrell; Donovan P. Kelly (Archives of Microbiology, 2012)

Testing metapopulation dynamics using genetic, demographic and ecological data - T. LAMY; J. P. POINTIER; P. JARNE; P. DAVID (Molecular Ecology, 2012)
The metapopulation concept is a cornerstone in the recent history of ecology and evolution. However, determining whether a natural system fits a metapopulation model is a complex issue. Extinction‐colonization dynamics are indeed often difficult to quantify because species detectability is not always 100%, resulting in an imperfect record of extinctions. Here, we explore whether combining population genetics with demographic and ecological surveys can yield more realistic estimates of metapopulation dynamics. We apply this approach to the freshwater snail Drepanotrema depressissimum in a fragmented landscape of tropical ponds. In addition to studying correlations between genetic diversity and demographical or ecological characteristics, we undertake, for the first time, a detailed search for genetic signatures of extinction–recolonization events using temporal changes in allele frequencies within sites. Surprisingly, genetic data indicate that extinction is much rarer than suggested by demographic surveys. Consequently, this system is better described as a set of populations with different sizes and immigration rates than as a true metapopulation. We identify several cases of apparent extinction owing to nondetection of low‐density populations, and of aestivating individuals in desiccated ponds. More generally, we observed a frequent mismatch between genetic and demographical/ecological information at small spatial and temporal scales. We discuss the causes of these discrepancies and show how these two types of data provide complementary information on population dynamics and history, especially when temporal genetic samples are available.

A dynamic explanation of size–density scaling in carnivores - John P. DeLong; David A. Vasseur (Ecology, 2012)
Population abundance is negatively related to body size for many types of organisms. Despite the ubiquity of size–density scaling relationships, we lack a general understanding of the underlying mechanisms. Although dynamic models suggest that it is possible to predict the intercept and slope of the scaling relationship from prior observations, this has never been empirically attempted. Here we fully parameterize a set of consumer–resource models for mammalian carnivores and successfully predict the size–density scaling relationship for this group without the use of free parameters. All models produced similar predictions, but comparison of nested models indicated that the primary factors generating size–density scaling in mammalian carnivores are prey productivity, predator–prey size ratios, and consumer area of capture.

ATPace™: injectable adenosine 5′-triphosphate - Amir Pelleg; Steven P. Kutalek; Daniel Flammang; David Benditt (Purinergic Signalling, 2012)

Functional groups show distinct differences in nitrogen cycling during early stand development: implications for forest management - Doug P. Aubrey; David R. Coyle; Mark D. Coleman (Plant and Soil, 2012)

Aluminum resistance mechanisms in oat (Avena sativa L.) - Lorien Radmer; Mesfin Tesfaye; David A. Somers; Stephen J. Temple; Carroll P. Vance; Deborah A. Samac (Plant and Soil, 2012)

Canine models of Duchenne muscular dystrophy and their use in therapeutic strategies - Joe N. Kornegay; Janet R. Bogan; Daniel J. Bogan; Martin K. Childers; Juan Li; Peter Nghiem; David A. Detwiler; C. Aaron Larsen; Robert W. Grange; Ratna K. Bhavaraju-Sanka; Sandra Tou; Bruce P. Keene; et al. (Mammalian Genome, 2012)

Carbon and nitrogen stable isotope ratios in surface sediments from lakes of western Ireland: implications for inferring past lake productivity and nitrogen loading - Craig A. Woodward; Aaron P. Potito; David W. Beilman (Journal of Paleolimnology, 2012)

Extending the range of an ancient crop, Salvia hispanica L.—a new ω3 source - Watchareewan Jamboonsri; Timothy D. Phillips; Robert L. Geneve; Joseph P. Cahill; David F. Hildebrand (Genetic Resources and Crop Evolution, 2012)

An experimental test and models of drift and dispersal processes of pallid sturgeon (Scaphirhynchus albus) free embryos in the Missouri River - Patrick J. Braaten; David B. Fuller; Ryan D. Lott; Michael P. Ruggles; Tyrel F. Brandt; Robert G. Legare; Robert J. Holm (Environmental Biology of Fishes, 2012)

Serum insulin-like growth factors and mortality in localised and advanced clinically detected prostate cancer - Mari-Anne Rowlands; Jeff M. P. Holly; Freddie Hamdy; Joshua Phillips; Louise Goodwin; Gemma Marsden; David Gunnell; Jenny Donovan; David E. Neal; Richard M. Martin (Cancer Causes & Control, 2012)

Spatially explicit capture–recapture methods to estimate minke whale density from data collected at bottom-mounted hydrophones - Tiago A. Marques; Len Thomas; Stephen W. Martin; David K. Mellinger; Susan Jarvis; Ronald P. Morrissey; Carroll-Anne Ciminello; Nancy DiMarzio (Journal of Ornithology, 2012)

Plant phylogeny as a surrogate for turnover in beetle assemblages - David A. Nipperess; Andrew J. Beattie; Daniel P. Faith; Scott G. Ginn; Roger L. Kitching; Chris A. M. Reid; Tracey Russell; Lesley Hughes (Biodiversity and Conservation, 2012)

Did central Australian megafaunal extinction coincide with abrupt ecosystem collapse or gradual climate change? - Brett P. Murphy; Grant J. Williamson; David M. J. S. Bowman (Global Ecology and Biogeography, 2012)
Aim In central Australia, the giant flightless bird Genyornis newtoni disappeared about 45–50 thousand years ago (ka). It has been reported that coincident with this extinction the carbon isotopic composition of preserved eggshells of the extant emu ( Dromaius novaehollandiae ) shows an abrupt dietary shift from tropical grasses (C 4 photosynthesis) to temperate grasses and/or woody browse (C 3 photosynthesis). This abrupt shift has been interpreted as signalling ‘ecosystem collapse’ due to landscape burning by humans. We evaluate an alternative interpretation, that the shift in diet was not abrupt, but gradual, and caused by the weakening of the Australian monsoon. Location Lake Eyre, central Australia. Methods We re‐analysed a large, published dataset of emu diet δ 13 C (inferred from δ 13 C of preserved eggshells) spanning the last 140,000 years, using time‐series analysis. Using Akaike's information criterion, we compared two contrasting models: (1) there was an abrupt shift in δ 13 C coincident with the extinction of Genyornis , assumed 47.5 ka; and (2) there was a gradual shift in δ 13 C, correlated with reconstructed water level in Lake Eyre, a proxy for monsoon intensity. Results There was little evidence of an abrupt shift in emu diet δ 13 C about 45–50 ka, but δ 13 C appeared to steadily decrease between about 80 and 30 ka. Indeed, the model representing a correlation between δ 13 C and lake level was more than seven times more likely than the model representing an abrupt shift at 47.5 ka. Main conclusions The emu eggshell isotopic record from Lake Eyre does not support the hypothesis that landscape burning by humans transformed a savanna−grassland mosaic into the modern desert scrub, contributing to the extinction of Genyornis . While our findings cast strong doubt on the foremost line of evidence that landscape burning by humans caused the megafaunal extinctions, and suggest that central Australia was becoming increasingly arid in the Late Pleistocene, the relative roles of hunting by humans and climate change in the megafaunal extinctions remain unresolved.

Happy New Year and Best Wishes for 2012! - David P. Green (Journal of Aquatic Food Product Technology, 2012)

Impulsive behaviour induced by both NMDA receptor antagonism and GABAA receptor activation in rat ventromedial prefrontal cortex - Emily R. Murphy; Anushka B. P. Fernando; Gonzalo P. Urcelay; Emma S. J. Robinson; Adam C. Mar; David E. H. Theobald; Jeffrey W. Dalley; Trevor W. Robbins (Psychopharmacology, 2012)

Modulation of high impulsivity and attentional performance in rats by selective direct and indirect dopaminergic and noradrenergic receptor agonists - Anushka B. P. Fernando; Daina Economidou; David E. Theobald; Mu-Fa Zou; Amy H. Newman; Marcia Spoelder; Daniele Caprioli; Margarita Moreno; Lucia Hipόlito; Albert T. Aspinall; Trevor W. Robbins; Jeffrey W. Dalley (Psychopharmacology, 2012)

Does genetic introgression improve female reproductive performance? A test on the endangered Florida panther - Jeffrey A. Hostetler; David P. Onorato; Benjamin M. Bolker; Warren E. Johnson; Stephen J. O’Brien; Deborah Jansen; Madan K. Oli (Oecologia, 2012)

The inability of tegaserod to affect platelet aggregation and coronary artery tone at supratherapeutic concentrations - Deborah L. Higgins; Mike P. Ero; Michelle Loeb; Kathryn Kersey; Alan Hopkins; David T. Beattie (Naunyn-Schmiedeberg's Archives of Pharmacology, 2012)

Histologic, immunologic and endocrine biomarkers indicate contaminant effects in fishes of the Ashtabula River - Luke R. Iwanowicz; Vicki S. Blazer; Nathaniel P. Hitt; Stephen D. McCormick; David S. DeVault; Christopher A. Ottinger (Ecotoxicology, 2012)

An assessment and interpretation of the observed warming of West Antarctica in the austral spring - David P. Schneider; Clara Deser; Yuko Okumura (Climate Dynamics, 2012)

Managing dependencies in forest offset projects: toward a more complete evaluation of reversal risk - David M. Cooley; Christopher S. Galik; Thomas P. Holmes; Carolyn Kousky; Roger M. Cooke (Mitigation and Adaptation Strategies for Global Change, 2012)

Adjusting age at first breeding of albatrosses and petrels for emigration and study duration - Peter W. Dillingham; Graeme P. Elliott; Kath J. Walker; David Fletcher (Journal of Ornithology, 2012)

A reassessment of historical records of avian introductions to Australia: no case for propagule pressure - Michael P. Moulton; Wendell P. Cropper; Linda E. Moulton; Michael L. Avery; David Peacock (Biodiversity and Conservation, 2012)

Dynamic Changes in Neural Circuit Topology Following Mild Mechanical Injury In Vitro - Tapan P. Patel; Scott C. Ventre; David F. Meaney (Annals of Biomedical Engineering, 2012)

Heterozygosity predicts clutch and egg size but not plasticity in a house sparrow population with no evidence of inbreeding - DANIEL P. WETZEL; IAN R. K. STEWART; DAVID F. WESTNEAT (Molecular Ecology, 2012)
We investigated the link between heterozygosity and the reaction norm attributes of reproductive performance in female house sparrows ( Passer domesticus ). We collected data on clutch size, egg size, hatching success and nestling survival in 2816 nesting attempts made by 791 marked individuals over a 16‐year period. Pedigree analysis revealed no evidence of inbreeding. Neither parent–offspring regression nor an animal model revealed significant heritability in clutch or egg size. We selected 42 females that laid at least seven clutches at our study site and used a survey of 21 autosomal microsatellite loci to estimate heterozygosity for each female. We controlled for phenotypic plasticity and found that both clutch and egg size showed significant positive correlations with heterozygosity. We found no evidence that heterozygosity influenced the slope of individual reaction norms. Further analysis suggested that clutch size was affected by heterozygosity across the genome, but egg size had more complex relationships, with evidence favouring the influence of multiple loci. Given the apparent lack of inbreeding and large population size, our results suggest associative overdominance as the likely mechanism for the impact of heterozygosity, but also created a puzzle about the process producing associations between neutral markers and the genes affecting clutch size or egg size. One possible explanation is a long‐term residual effect of the historical bottleneck that occurred when house sparrows were introduced into North America. The existence of heterozygosity‐fitness correlations in a population with considerable phenotypic plasticity and little inbreeding implies that the effects of heterozygosity may be more significant than previously thought.

Carbon (δ 13 C ) and nitrogen (δ 15 N ) stable isotope composition in plant and soil in S outhern P atagonia's native forests - Pablo L. Peri; Brenton Ladd; David A. Pepper; Stephen P. Bonser; Shawn W. Laffan; Wulf Amelung (Global Change Biology, 2012)
Stable isotope natural abundance measurements integrate across several biogeochemical processes in ecosystem N and C dynamics. Here, we report trends in natural isotope abundance (δ 13 C and δ 15 N in plant and soil) along a climosequence of 33 N othofagus forest stands located within P atagonia, S outhern A rgentina. We measured 28 different abiotic variables (both climatic variables and soil properties) to characterize environmental conditions at each of the 33 sites. Foliar δ 13 C values ranged from −35.4‰ to −27.7‰, and correlated positively with foliar δ 15 N values, ranging from −3.7‰ to 5.2‰. Soil δ 13 C and δ 15 N values reflected the isotopic trends of the foliar tissues and ranged from −29.8‰ to −25.3‰, and −4.8‰ to 6.4‰, respectively, with no significant differences between N othofagus species ( N othofagus pumilio , N othofagus antarctica , N othofagus betuloides ). Principal component analysis and multiple regressions suggested that mainly water availability variables (mean annual precipitation), but not soil properties, explained between 42% and 79% of the variations in foliar and soil δ 13 C and δ 15 N natural abundance, which declined with increased moisture supply. We conclude that a decline in water use efficiency at wetter sites promotes both the depletion of heavy C and N isotopes in soil and plant biomass. Soil δ 13 C values were higher than those of the plant tissues and this difference increased as annual precipitation increased. No such differences were apparent when δ 15 N values in soil and plant were compared, which indicates that climatic differences contributed more to the overall C balance than to the overall N balance in these forest ecosystems.

Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll‐based photoheterotroph belonging to the phylum Acidobacteria - Amaya M. Garcia Costas; Zhenfeng Liu; Lynn P. Tomsho; Stephan C. Schuster; David M. Ward; Donald A. Bryant (Environmental Microbiology, 2012)
Summary Candidatus Chloracidobacterium thermophilum, which naturally inhabits microbial mats of alkaline siliceous hot springs in Yellowstone National Park, is the only known chlorophototroph in the phylum Acidobacteria . The Ca . C . thermophilum genome was composed of two chromosomes (2 683 362 bp and 1 012 010 bp), and both encoded essential genes. The genome included genes to produce chlorosomes, the Fenna‐Matthews‐Olson protein, bacteriochlorophylls a and c as principal pigments, and type‐1, homodimeric reaction centres. Ca . C. thermophilum is an aerobic photoheterotroph that lacks the ability to synthesize several essential nutrients. Key genes of all known carbon fixation pathways were absent, as were genes for assimilatory nitrate and sulfate reduction and vitamin B 12 synthesis. Genes for the synthesis of branched‐chain amino acids (valine, isoleucine and leucine) were also absent, but genes for catabolism of these compounds were present. This observation suggested that Ca . C. thermophilum may synthesize branched‐chain amino acids from an intermediate(s) of the catabolic pathway by reversing these reactions. The genome encoded an aerobic respiratory electron transport chain that included NADH dehydrogenase, alternative complex III and cytochrome oxidase. The chromosomes of the laboratory isolate were compared with assembled, metagenomic scaffolds from the major Ca . C. thermophilum population in hot‐spring mats. The larger chromosomes of the two populations were highly syntenous but significantly divergent (∼13%) in sequence. In contrast, the smaller chromosomes have undergone numerous rearrangements, contained many transposases, and might be less constrained by purifying selection than the large chromosomes. Some transposases were homologous to those of mat community members from other phyla.

A specialist root herbivore exploits defensive metabolites to locate nutritious tissues - Christelle A. M. Robert; Nathalie Veyrat; Gaétan Glauser; Guillaume Marti; Gwladys R. Doyen; Neil Villard; Mickaël D. P. Gaillard; Tobias G. Köllner; David Giron; Mélanie Body; Benjamin A. Babst; Richard A. Ferrieri; et al. (Ecology Letters, 2012)
Ecology Letters (2011) 14 : 55–64 Abstract The most valuable organs of plants are often particularly rich in essential elements, but also very well defended. This creates a dilemma for herbivores that need to maximise energy intake while minimising intoxication. We investigated how the specialist root herbivore Diabrotica virgifera solves this conundrum when feeding on wild and cultivated maize plants. We found that crown roots of maize seedlings were vital for plant development and, in accordance, were rich in nutritious primary metabolites and contained higher amounts of the insecticidal 2,4‐dihydroxy‐7‐methoxy‐1,4‐benzoxazin‐3‐one (DIMBOA) and the phenolic compound chlorogenic acid. The generalist herbivores Diabrotica balteata and Spodoptera littoralis were deterred from feeding on crown roots, whereas the specialist D. virgifera preferred and grew best on these tissues. Using a 1,4‐benzoxazin‐3‐one‐deficient maize mutant, we found that D. virgifera is resistant to DIMBOA and other 1,4‐benzoxazin‐3‐ones and that it even hijacks these compounds to optimally forage for nutritious roots.

Experimental and environmental factors affect spurious detection of ecological thresholds - Jonathan P. Daily; Nathaniel P. Hitt; David R. Smith; Craig D. Snyder (Ecology, 2012)
Threshold detection methods are increasingly popular for assessing nonlinear responses to environmental change, but their statistical performance remains poorly understood. We simulated linear change in stream benthic macroinvertebrate communities and evaluated the performance of commonly used threshold detection methods based on model fitting (piecewise quantile regression [PQR]), data partitioning (nonparametric change point analysis [NCPA]), and a hybrid approach (significant zero crossings [SiZer]). We demonstrated that false detection of ecological thresholds (type I errors) and inferences on threshold locations are influenced by sample size, rate of linear change, and frequency of observations across the environmental gradient (i.e., sample–environment distribution, SED). However, the relative importance of these factors varied among statistical methods and between inference types. False detection rates were influenced primarily by user‐selected parameters for PQR (τ) and SiZer (bandwidth) and secondarily by sample size (for PQR) and SED (for SiZer). In contrast, the location of reported thresholds was influenced primarily by SED. Bootstrapped confidence intervals for NCPA threshold locations revealed strong correspondence to SED. We conclude that the choice of statistical methods for threshold detection should be matched to experimental and environmental constraints to minimize false detection rates and avoid spurious inferences regarding threshold location.

Factors Influencing the Occurrence of Inundated Playa Wetlands During Winter on the Texas High Plains - William P. Johnson; Mindy B. Rice; David A. Haukos; Philip P. Thorpe (Wetlands, 2011)

MicroRNA-101 Inhibits Growth of Epithelial Ovarian Cancer by Relieving Chromatin-Mediated Transcriptional Repression of p21waf1/cip1 - Assaad Semaan; Aamer M. Qazi; Shelly Seward; Sreedhar Chamala; Christopher S. Bryant; Sanjeev Kumar; Robert Morris; Christopher P. Steffes; David L. Bouwman; Adnan R Munkarah; Donald W. Weaver; Scott A. Gruber; et al. (Pharmaceutical Research, 2011)

Interventricular differences in myofilament function in experimental congestive heart failure - Rashad J. Belin; Marius P. Sumandea; Gail A. Sievert; Laura A. Harvey; David L. Geenen; R. John Solaro; Pieter P. de Tombe (Pflügers Archiv - European Journal of Physiology, 2011)

Alternating temperature breaks dormancy in leafy spurge seeds and impacts signaling networks associated with HY5 - Wun S. Chao; Michael E. Foley; Münevver Doğramacı; James V. Anderson; David P. Horvath (Functional & Integrative Genomics, 2011)

Dehydration and vernalization treatments identify overlapping molecular networks impacting endodormancy maintenance in leafy spurge crown buds - Münevver Doğramacı; David P. Horvath; Michael J. Christoffers; James V. Anderson (Functional & Integrative Genomics, 2011)

Evaluation of limited sampling strategies for total and free prednisolone in adult kidney transplant recipients - Katherine A. Barraclough; Nicole M. Isbel; Brett C. McWhinney; Jacobus P. J. Ungerer; Gregory Medley; David W. Johnson; Carmel M. Hawley; Diana R. Leary; Scott B. Campbell; Christine E. Staatz (European Journal of Clinical Pharmacology, 2011)

The twentieth century contiguous US temperature changes indicated by daily data and higher statistical moments - Samuel S. P. Shen; Ai B. Gurung; Hee-S. Oh; T. Shu; David R. Easterling (Climatic Change, 2011)

How weather impacts the forced climate response - Ben P. Kirtman; Edwin K. Schneider; David M. Straus; Dughong Min; Robert Burgman (Climate Dynamics, 2011)

New Choices and Challenges for Regulated Private Forests: The “Alternate Plan” Option - Roje S. Gootee; Keith A. Blatner; Matthew S. Carroll; David M. Baumgartner; Edward P. Weber (Journal of Forestry, 2011)
The state of Washington has developed a policy instrument that substantially amends traditional “top-down” private forest regulation. Called the “Alternate Plan” option, it gives landowners unusual new flexibility in designing forest management projects for their property. Projects may depart from any of the state's established Forest Practices Rules, if the property owner can satisfactorily show that a customized proposal would provide equivalent environmental protection. The state provides a prompt review and decision and then supervises project implementation and monitors compliance with the approved project specifications. We interviewed 109 stakeholders involved in the design, use, and implementation of this innovative program. From this data we evaluate the functional advantages and challenges inherent in this new regulatory approach, suggest modifications to improve its effectiveness, and discuss policymaking implications.

The role of MHC class I allele Mamu-A*07 during SIVmac239 infection - Jason S. Reed; John Sidney; Shari M. Piaskowski; Chrystal E. Glidden; Enrique J. León; Benjamin J. Burwitz; Holly L. Kolar; Christopher M. Eernisse; Jessica R. Furlott; Nicholas J. Maness; Andrew D. Walsh; Richard A. Rudersdorf; et al. (Immunogenetics, 2011)

Sympatric Divergence and Performance Trade-Offs of Bluegill Ecomorphs - David J. Ellerby; Shannon P. Gerry (Evolutionary Biology, 2011)

Multiple Effects of Changes in Arctic Snow Cover - Terry V. Callaghan; Margareta Johansson; Ross D. Brown; Pavel Ya. Groisman; Niklas Labba; Vladimir Radionov; Raymond S. Bradley; Sylvie Blangy; Olga N. Bulygina; Torben R. Christensen; Jonathan E. Colman; Richard L. H. Essery; et al. (Ambio, 2011)

Equivalent water thickness in savanna ecosystems: MODIS estimates based on ground and EO-1 Hyperion data - Laerte Guimaraes Ferreira; Gregory P. Asner; David E. Knapp; Eric A. Davidson; Michael Coe; Mercedes M. C. Bustamante; Eddie Lenza de Oliveira (International Journal of Remote Sensing, 2011)

Equitable regulation of private forests - Roje S. Gootee; Keith A. Blatner; David M. Baumgartner; Matthew S. Carroll; Edward P. Weber (Small-scale Forestry, 2011)

Soils, crop nutrient status and nutrient dynamics on small-holder farms in central Tibet, China - Nicholas G. Paltridge; Samantha P. P. Grover; Liu Gouyi; Jin Tao; Murray J. Unkovich; Nyima Tashi; David R. Coventry (Plant and Soil, 2011)

Gold Nanoparticle Penetration and Reduced Metabolism in Human Skin by Toluene - Hagar I. Labouta; David C. Liu; Lynlee L. Lin; Margaret K. Butler; Jeffrey E. Grice; Anthony P. Raphael; Tobias Kraus; Labiba K. El-Khordagui; H. Peter Soyer; Michael S. Roberts; Marc Schneider; Tarl W. Prow (Pharmaceutical Research, 2011)

Effects of composition of labile organic matter on biogenic production of methane in the coastal sediments of the Arabian Sea - Maria-Judith Gonsalves; Christabelle E. G. Fernandes; Sheryl Oliveira Fernandes; David L. Kirchman; P. A. Loka Bharathi (Environmental Monitoring and Assessment, 2011)

Mercury in breeding saltmarsh sparrows (Ammodramus caudacutus caudacutus) - Oksana P. Lane; Kathleen M. O’Brien; David C. Evers; Thomas P. Hodgman; Andrew Major; Nancy Pau; Mark J. Ducey; Robert Taylor; Deborah Perry (Ecotoxicology, 2011)

Teleconnections in a warmer climate: the pliocene perspective - Sonali P. Shukla; Mark A. Chandler; David Rind; Linda E. Sohl; Jeff Jonas; Jean Lerner (Climate Dynamics, 2011)

Hippocampal pyramidal cells: the reemergence of cortical lamination - Lutz Slomianka; Irmgard Amrein; Irene Knuesel; Jens Christian Sørensen; David P. Wolfer (Brain Structure and Function, 2011)

Continental-scale climatic drivers of growth ring variability in an Australian conifer - David M. J. S. Bowman; Lynda D. Prior; David Y. P. Tng; Quan Hua; Timothy J. Brodribb (Trees, 2011)

Pre-clinical characterization of CX-4945, a potent and selective small molecule inhibitor of CK2 for the treatment of cancer - Fabrice Pierre; Peter C. Chua; Sean E. O’Brien; Adam Siddiqui-Jain; Pauline Bourbon; Mustapha Haddach; Jerome Michaux; Johnny Nagasawa; Michael K. Schwaebe; Eric Stefan; Anne Vialettes; Jeffrey P. Whitten; et al. (Molecular and Cellular Biochemistry, 2011)

Regulation of caspase pathways by protein kinase CK2: identification of proteins with overlapping CK2 and caspase consensus motifs - Jacob P. Turowec; James S. Duncan; Greg B. Gloor; David W. Litchfield (Molecular and Cellular Biochemistry, 2011)

Spatial ecology and residency patterns of adult great barracuda (Sphyraena barracuda) in coastal waters of The Bahamas - Amanda C. O’Toole; Andy J. Danylchuk; Tony L. Goldberg; Cory D. Suski; David P. Philipp; Edd Brooks; Steven J. Cooke (Marine Biology, 2011)

Bovine IFNGR2, IL12RB1, IL12RB2, and IL23R polymorphisms and MAP infection status - Sameer D. Pant; Chris P. Verschoor; Alicia M. Skelding; Flavio S. Schenkel; Qiumei You; Graham A. Biggar; David F. Kelton; Niel A. Karrow (Mammalian Genome, 2011)

Extracts of the marine brown macroalga, Ascophyllum nodosum, induce jasmonic acid dependent systemic resistance in Arabidopsis thaliana against Pseudomonas syringae pv. tomato DC3000 and Sclerotinia sclerotiorum - Sowmyalakshmi Subramanian; Jatinder Singh Sangha; Bruce A. Gray; Rudra P. Singh; David Hiltz; Alan T. Critchley; Balakrishnan Prithiviraj (European Journal of Plant Pathology, 2011)

MercNet: a national monitoring network to assess responses to changing mercury emissions in the United States - David Schmeltz; David C. Evers; Charles T. Driscoll; Richard Artz; Mark Cohen; David Gay; Richard Haeuber; David P. Krabbenhoft; Robert Mason; Kristi Morris; James G. Wiener (Ecotoxicology, 2011)

Spatiotemporal trends of mercury in walleye and largemouth bass from the Laurentian Great Lakes Region - Bruce A. Monson; David F. Staples; Satyendra P. Bhavsar; Thomas M. Holsen; Candy S. Schrank; Sara K. Moses; Daryl J. McGoldrick; Sean M. Backus; Kathryn A. Williams (Ecotoxicology, 2011)

Podophyllotoxin and other aryltetralin lignans from Eriope latifolia and Eriope blanchetii - Edlene O. Santos; Luciano S. Lima; Jorge M. David; Lidiane C. Martins; Maria Lenise S. Guedes; Juceni P. David (Natural Product Research, 2011)

Precipitation Changes in High Southern Latitudes from Global Reanalyses: A Cautionary Tale - Julien P. Nicolas; David H. Bromwich (Surveys in Geophysics, 2011)

Determining the mechanism by which fish diversity influences production - Michael P. Carey; David H. Wahl (Oecologia, 2011)

Aggregations and offshore movements as indicators of spawning activity of bonefish (Albula vulpes) in The Bahamas - Andy J. Danylchuk; Steven J. Cooke; Tony L. Goldberg; Cory D. Suski; Karen J. Murchie; Sascha E. Danylchuk; Aaron D. Shultz; Christopher R. Haak; Edd J. Brooks; Annabelle Oronti; Jeff B. Koppelman; David P. Philipp (Marine Biology, 2011)

Differential Acute Toxicity of Tetrachlorobenzene Isomers to Oligochaetes in Soil and Water: Application of the Critical Body Residue Concept - Christopher M. Hurdzan; Roman P. Lanno; David M. Sovic (Bulletin of Environmental Contamination and Toxicology, 2011)

To boldly go: individual differences in boldness influence migratory tendency - Ben B. Chapman; Kaj Hulthén; David R. Blomqvist; Lars‐Anders Hansson; Jan‐Åke Nilsson; Jakob Brodersen; P. Anders Nilsson; Christian Skov; Christer Brönmark (Ecology Letters, 2011)
Ecology Letters (2011) 14 : 871–876 Abstract Partial migration, whereby only a fraction of the population migrates, is thought to be the most common type of migration in the animal kingdom, and can have important ecological and evolutionary consequences. Despite this, the factors that influence which individuals migrate and which remain resident are poorly understood. Recent work has shown that consistent individual differences in personality traits in animals can be ecologically important, but field studies integrating personality traits with migratory behaviour are extremely rare. In this study, we investigate the influence of individual boldness, an important personality trait, upon the migratory propensity of roach, a freshwater fish, over two consecutive migration seasons. We assay and individually tag 460 roach and show that boldness influences migratory propensity, with bold individuals being more likely to migrate than shy fish. Our data suggest that an extremely widespread personality trait in animals can have significant ecological consequences via influencing individual‐level migratory behaviour.

Environmental stress and disease in pearl oysters, focusing on the Akoya pearl oyster ( Pinctada fucata Gould 1850) - Rhiannon P. Kuchel; Wayne A. O’Connor; David A. Raftos (Reviews in Aquaculture, 2011)
Pinctada fucata Gould 1850 was first commercially cultivated in Japan in the early 1920s. Japan dominated this market until the proliferation of Akoya viral disease (AVD) in 1996. Since that time the Japanese industry has struggled. In 2000, Japanese production of Akoya pearls represented only 13% of the total world market value. A number of investigations into this downturn have concluded that the proliferation of AVD was a result of stress associated with increasing urbanization and industrialization. This relationship between environmental stress and altered immunological activity is well documented in a number of oyster species. The decline in Japanese pearl production has led to interest in Akoya cultivation in Australia. Commercial Akoya pearl oyster ventures are now in operation in the Australian states of New South Wales, Queensland and Western Australia. The development of a robust and lucrative Akoya pearl industry in Australia will rely on the cultivation and maintenance of healthy oysters. Oyster health is associated with immunological status, which can be jeopardized by both stress and disease. This review details the relationship between the oyster immune system, environmental stress and disease outbreaks in the genus Pinctada , with implications for P. fucata and the fledgling Australian industry.

Integrated national-scale assessment of wildfire risk to human and ecological values - Matthew P. Thompson; David E. Calkin; Mark A. Finney; Alan A. Ager; Julie W. Gilbertson-Day (Stochastic Environmental Research and Risk Assessment, 2011)

Increased cocaine self-administration in M4 muscarinic acetylcholine receptor knockout mice - Lene S. Schmidt; Morgane Thomsen; Pia Weikop; Ditte Dencker; Jürgen Wess; David P. D. Woldbye; Gitta Wortwein; Anders Fink-Jensen (Psychopharmacology, 2011)

Synthesis and characterization of an unsymmetrical cobalt(III) active site analogue of nitrile hydratase - Jennifer K. Angelosante; Lauren M. Schopp; Breia J. Lewis; Amber D. Vitalo; Dustin T. Titus; Rebecca A. Swanson; April N. Stanley; Brendan P. Abolins; Michelle J. Frome; Lisa E. Cooper; David L. Tierney; Curtis Moore; et al. (JBIC Journal of Biological Inorganic Chemistry, 2011)

Advancing effects analysis for integrated, large-scale wildfire risk assessment - Matthew P. Thompson; David E. Calkin; Julie W. Gilbertson-Day; Alan A. Ager (Environmental Monitoring and Assessment, 2011)

Landscape-Scale Simulation of Heterogeneous Fire Effects on Pyrogenic Carbon Emissions, Tree Mortality, and Net Ecosystem Production - Garrett W. Meigs; David P. Turner; William D. Ritts; Zhiqiang Yang; Beverly E. Law (Ecosystems, 2011)

Analyzing Variability and the Rate of Decline of Migratory Shorebirds in Moreton Bay, Australia - HOWARD B. WILSON; BRUCE E. KENDALL; RICHARD A. FULLER; DAVID A. MILTON; HUGH P. POSSINGHAM (Conservation Biology, 2011)
Estimating the abundance of migratory species is difficult because sources of variability differ substantially among species and populations. Recently developed state‐space models address this variability issue by directly modeling both environmental and measurement error, although their efficacy in detecting declines is relatively untested for empirical data. We applied state‐space modeling, generalized least squares (with autoregression error structure), and standard linear regression to data on abundance of wetland birds (shorebirds and terns) at Moreton Bay in southeast Queensland, Australia. There are internationally significant numbers of 8 species of waterbirds in the bay, and it is a major terminus of the large East Asian‐Australasian Flyway. In our analyses, we considered 22 migrant and 8 resident species. State‐space models identified abundances of 7 species of migrants as significantly declining and abundance of one species as significantly increasing. Declines in migrant abundance over 15 years were 43–79%. Generalized least squares with an autoregressive error structure showed abundance changes in 11 species, and standard linear regression showed abundance changes in 15 species. The higher power of the regression models meant they detected more declines, but they also were associated with a higher rate of false detections. If the declines in Moreton Bay are consistent with trends from other sites across the flyway as a whole, then a large number of species are in significant decline.

Use of Fatty Acid Analysis to Determine Dispersal of Caspian Terns in the Columbia River Basin, U.S.A. - CHRISTINA J. MARANTO; JULIA K. PARRISH; DAVID P. HERMAN; ANDRÉ E. PUNT; JULIAN D. OLDEN; MICHAEL T. BRETT; DANIEL D. ROBY (Conservation Biology, 2011)
Lethal control, which has been used to reduce local abundances of animals in conflict with humans or with endangered species, may not achieve management goals if animal movement is not considered. In populations with emigration and immigration, lethal control may induce compensatory immigration, if the source of attraction remains unchanged. Within the Columbia River Basin (Washington, U.S.A.), avian predators forage at dams because dams tend to reduce rates of emigration of juvenile salmonids ( Oncorhynchus spp. ), artificially concentrating these prey. We used differences in fatty acid profiles between Caspian Terns ( Hydroprogne caspia ) at coastal and inland breeding colonies and terns culled by a lethal control program at a mid‐Columbia River dam to infer dispersal patterns. We modeled the rate of loss of fatty acid biomarkers, which are fatty acids that can be traced to a single prey species or groups of species, to infer whether and when terns foraging at dams had emigrated from the coast. Nonmetric multidimensional scaling showed that coastal terns had high levels of C 20 and C 22 monounsaturated fatty acids, whereas fatty acids of inland breeders were high in C18:3n3, C20:4n6, and C22:5n3. Models of the rate of loss of fatty acid showed that approximately 60% of the terns collected at Rock Island Dam were unlikely to have bred successfully at local (inland) sites, suggesting that terns foraging at dams come from an extensive area. Fatty acid biomarkers may provide accurate information about patterns of dispersal in animal populations and may be extremely valuable in cases where populations differ demonstrably in prey base.

Consequences of long-distance swimming and travel over deep-water pack ice for a female polar bear during a year of extreme sea ice retreat - George M. Durner; John P. Whiteman; Henry J. Harlow; Steven C. Amstrup; Eric V. Regehr; Merav Ben-David (Polar Biology, 2011)

Submarine hydrothermal activity and gold-rich mineralization at Brothers Volcano, Kermadec Arc, New Zealand - Cornel E. J. de Ronde; Gary J. Massoth; David A. Butterfield; Bruce W. Christenson; Junichiro Ishibashi; Robert G. Ditchburn; Mark D. Hannington; Robert L. Brathwaite; John E. Lupton; Vadim S. Kamenetsky; Ian J. Graham; Georg F. Zellmer; et al. (Mineralium Deposita, 2011)

Genetic Variation in the Common Reed, Phragmites australis, in the Mississippi River Delta Marshes: Evidence for Multiple Introductions - Donald P. Hauber; Kristin Saltonstall; David A. White; Craig S. Hood (Estuaries and Coasts, 2011)

Marine Macrophyte Wrack Inputs and Dissolved Nutrients in Beach Sands - Jenifer E. Dugan; David M. Hubbard; Henry M. Page; Joshua P. Schimel (Estuaries and Coasts, 2011)

North Atlantic climate responses to perturbations in Antarctic Intermediate Water - Jennifer A. Graham; David P. Stevens; Karen J. Heywood; Zhaomin Wang (Climate Dynamics, 2011)

Planetary-scale variability in the northern winter and the impact of land–sea thermal contrast - Franco Molteni; Martin P. King; Fred Kucharski; David M. Straus (Climate Dynamics, 2011)

Rossby wave dynamics of the North Pacific extra-tropical response to El Niño: importance of the basic state in coupled GCMs - Andrew Dawson; Adrian J. Matthews; David P. Stevens (Climate Dynamics, 2011)

Dietary carbohydrate, glycemic index, glycemic load, and risk of prostate cancer in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) cohort - James M. Shikany; Andrew P. Flood; Cari M. Kitahara; Ann W. Hsing; Tamra E. Meyer; Bradley J. Willcox; David T. Redden; Regina G. Ziegler (Cancer Causes & Control, 2011)

A Real-Time Risk Assessment Tool Supporting Wildland Fire Decisionmaking - David E. Calkin; Matthew P. Thompson; Mark A. Finney; Kevin D. Hyde (Journal of Forestry, 2011)
Development of appropriate management strategies for escaped wildland fires is complex. Fire managers need the ability to identify, in real time, the likelihood that wildfire will affect valuable developed and natural resources (e.g., private structures, public infrastructure, and natural and cultural resources). These determinations help guide where and when aggressive suppression is required to protect values and when fire may be allowed to burn to enhance ecosystem conditions. This article describes the primary components of the Wildland Fire Decision Support System (WFDSS), a geospatial decision support system developed by the US Forest Service. WFDSS provides state-of-the-art wildfire risk analysis, decision documentation, and long-term implementation planning. In particular, we describe how the two primary decision support analysis components of WFDSS, Fire Spread Probability (fire behavior) and Rapid Assessment of Values at Risk (resource assessment), fit into the current state of risk assessment tools for wildfire suppression decisionmaking.

Seabed foraging by Antarctic krill: Implications for stock assessment, bentho‐pelagic coupling, and the vertical transfer of iron - Katrin Schmidt; Angus Atkinson; Sebastian Steigenberger; Sophie Fielding; Margaret C. M. Lindsay; David W. Pond; Geraint A. Tarling; Thor A. Klevjer; Claire S. Allen; Stephen Nicol; Eric P. Achterberg (Limnology and Oceanography, 2011)
A compilation of more than 30 studies shows that adult Antarctic krill ( Euphausia superba ) may frequent benthic habitats year‐round, in shelf as well as oceanic waters and throughout their circumpolar range. Net and acoustic data from the Scotia Sea show that in summer 2‐20% of the population reside at depths between 200 and 2000 m, and that large aggregations can form above the seabed. Local differences in the vertical distribution of krill indicate that reduced feeding success in surface waters, either due to predator encounter or food shortage, might initiate such deep migrations and results in benthic feeding. Fatty acid and microscopic analyses of stomach content confirm two different foraging habitats for Antarctic krill: the upper ocean, where fresh phytoplankton is the main food source, and deeper water or the seabed, where detritus and copepods are consumed. Krill caught in upper waters retain signals of benthic feeding, suggesting frequent and dynamic exchange between surface and seabed. Krill contained up to 260 nmol iron per stomach when returning from seabed feeding. About 5% of this iron is labile, i.e., potentially available to phytoplankton. Due to their large biomass, frequent benthic feeding, and acidic digestion of particulate iron, krill might facilitate an input of new iron to Southern Ocean surface waters. Deep migrations and foraging at the seabed are significant parts of krill ecology, and the vertical fluxes involved in this behavior are important for the coupling of benthic and pelagic food webs and their elemental repositories.

The interaction of La3+ complexes of DOTA/DTPA glycoconjugates with the RCA120 lectin: a saturation transfer difference NMR spectroscopic study - João M. C. Teixeira; David M. Dias; F. Javier Cañada; José A. Martins; João P. André; Jesús Jiménez-Barbero; Carlos F. G. C. Geraldes (JBIC Journal of Biological Inorganic Chemistry, 2011)

Comparative Feeding Ecology of Two Communities of Chimpanzees (Pan troglodytes) in Kibale National Park, Uganda - Kevin B. Potts; David P. Watts; Richard W. Wrangham (International Journal of Primatology, 2011)

Workshop Approach for Developing Climate Change Adaptation Strategies and Actions for Natural Resource Management Agencies in the United States - Jessica E. Halofsky; David L. Peterson; Michael J. Furniss; Linda A. Joyce; Constance I. Millar; Ronald P. Neilson (Journal of Forestry, 2011)
Concrete ways to adapt to climate change are needed to help land-management agencies take steps to incorporate climate change into management and take advantage of opportunities to balance the negative effects of climate change. Because the development of adaptation tools and strategies is at an early stage, it is important that ideas and strategies are disseminated quickly to advance thinking and practice. Here, we offer an example of a successful workshop, focused on National Forests in the United States, which allowed quick dissemination of ideas and strategies for climate change adaptation in resource management through an interaction between scientists and managers. We share both the process used in the workshop and the outcome of facilitated dialogue at the workshop. By presenting concrete adaptation methods and showing the value of a focused scientist–manager dialogue, we hope to motivate the US Forest Service and other natural resource agencies to emulate our approach and begin the process of adapting to climate change.

Linkage to chromosome 2q32.2-q33.3 in familial serrated neoplasia (Jass syndrome) - Aedan Roberts; Derek Nancarrow; Mark Clendenning; Daniel D. Buchanan; Mark A. Jenkins; David Duggan; Darin Taverna; Diane McKeone; Rhiannon Walters; Michael D. Walsh; Bruce W. Young; Jeremy R. Jass; et al. (Familial Cancer, 2011)

Evaluation of In-Row Plant Spacing and Planting Configuration for Three Irrigated Potato Cultivars - David D. Tarkalson; Bradley A. King; Dave L. Bjorneberg; John P. Taberna (American Journal of Potato Research, 2011)

Source Identification of Florida Bay's Methylmercury Problem: Mainland Runoff Versus Atmospheric Deposition and In situ Production - Darren G. Rumbold; David W. Evans; Sharon Niemczyk; Larry E. Fink; Krysten A. Laine; Nicole Howard; David P. Krabbenhoft; Mark Zucker (Estuaries and Coasts, 2011)

Oropharyngeal cancer incidence trends: diminishing racial disparities - Linda Morris Brown; David P. Check; Susan S. Devesa (Cancer Causes & Control, 2011)

Genomics of the NF-κB signaling pathway: hypothesized role in ovarian cancer - Kristin L. White; David N. Rider; Kimberly R. Kalli; Keith L. Knutson; Gail P. Jarvik; Ellen L. Goode (Cancer Causes & Control, 2011)

The significance of the sub-Antarctic Kerguelen Islands for the assessment of the vulnerability of native communities to climate change, alien insect invasions and plant viruses - M. Lebouvier; M. Laparie; M. Hullé; A. Marais; Y. Cozic; L. Lalouette; P. Vernon; T. Candresse; Y. Frenot; David Renault (Biological Invasions, 2011)

Bioreactor System Using Noninvasive Imaging and Mechanical Stretch for Biomaterial Screening - Jonathan A. Kluge; Gary G. Leisk; Robyn D. Cardwell; Alexander P. Fernandes; Michael House; Andrew Ward; A. Luis Dorfmann; David L. Kaplan (Annals of Biomedical Engineering, 2011)

Heterozygosity–fitness correlations among wild populations of European tree frog ( Hyla arborea ) detect fixation load - E. LUQUET; P. DAVID; J.‐P. LENA; P. JOLY; L. KONECNY; C. DUFRESNES; N. PERRIN; S. PLENET (Molecular Ecology, 2011)
Quantifying the impacts of inbreeding and genetic drift on fitness traits in fragmented populations is becoming a major goal in conservation biology. Such impacts occur at different levels and involve different sets of loci. Genetic drift randomly fixes slightly deleterious alleles leading to different fixation load among populations. By contrast, inbreeding depression arises from highly deleterious alleles in segregation within a population and creates variation among individuals. A popular approach is to measure correlations between molecular variation and phenotypic performances. This approach has been mainly used at the individual level to detect inbreeding depression within populations and sometimes at the population level but without consideration about the genetic processes measured. For the first time, we used in this study a molecular approach considering both the interpopulation and intrapopulation level to discriminate the relative importance of inbreeding depression vs. fixation load in isolated and non‐fragmented populations of European tree frog ( Hyla arborea ), complemented with interpopulational crosses. We demonstrated that the positive correlations observed between genetic heterozygosity and larval performances on merged data were mainly caused by co‐variations in genetic diversity and fixation load among populations rather than by inbreeding depression and segregating deleterious alleles within populations. Such a method is highly relevant in a conservation perspective because, depending on how populations lose fitness (inbreeding vs. fixation load), specific management actions may be designed to improve the persistence of populations.

Differential effects of ocean acidification on growth and photosynthesis among phylotypes of Symbiodinium (Dinophyceae) - Patrick Brading; Mark E. Warner; Phillip Davey; David J. Smith; Eric P. Achterberg; David J. Suggett (Limnology and Oceanography, 2011)
We investigated the effect of elevated partial pressure of CO 2 (pCO 2 ) on the photosynthesis and growth of four phylotypes (ITS2 types A1, A13, A2, and B1) from the genus Symbiodinium , a diverse dinoflagellate group that is important, both free‐living and in symbiosis, for the viability of cnidarians and is thus a potentially important model dinoflagellate group. The response of Symbiodinium to an elevated pCO 2 was phylotype‐specific. Phylotypes A1 and B1 were largely unaffected by a doubling in pCO 2 ; in contrast, the growth rate of A13 and the photosynthetic capacity of A2 both increased by ~ 60%. In no case was there an effect of ocean acidification (OA) upon respiration (dark‐ or light‐dependent) for any of the phylotypes examined. Our observations suggest that OA might preferentially select among free‐living populations of Symbiodinium, with implications for future symbioses that rely on algal acquisition from the environment (i.e., horizontal transmission). Furthermore, the carbon environment within the host could differentially affect the physiology of different Symbiodinium phylotypes. The range of responses we observed also highlights that the choice of species is an important consideration in OA research and that further investigation across phylogenetic diversity, for both the direction of effect and the underlying mechanism(s) involved, is warranted.

Molecular characterization of an allelic series of mutations in the mouse Nox3 gene - John P. Flaherty; Heather E. Fairfield; Catrina A. Spruce; Christopher M. McCarty; David E. Bergstrom (Mammalian Genome, 2011)

Assessment of quantitative food web metrics for investigating the influence of land use on warm water fish diets - Derek P. Crane; Thomas H. Johengen; J. David Allan (Hydrobiologia, 2011)

HIV gp41 six-helix bundle constructs induce rapid vesicle fusion at pH 3.5 and little fusion at pH 7.0: understanding pH dependence of protein aggregation, membrane binding, and electrostatics, and implications for HIV-host cell fusion - Kelly Sackett; Allan TerBush; David P. Weliky (European Biophysics Journal, 2011)

Denitrification Potential in Lake Sediment Increases Across a Gradient of Catchment Agriculture - Denise A. Bruesewitz; David P. Hamilton; Louis A. Schipper (Ecosystems, 2011)

Small-scale mineralogical heterogeneity from variations in phase assemblages in the transition zone and D″ layer predicted by convection modelling - Arie P. van den Berg; David A. Yuen; Michael H. G. Jacobs; Maarten V. de Hoop (Journal of Earth Science, 2011)

Development of 10 microsatellite loci in the wolf spider Arctosa sancterosae (Araneae: Lycosidae) - Robert A. Hataway; David H. Reed; Brice P. Noonan (Conservation Genetics Resources, 2011)

Integration of invasive Opuntia spp. by native and alien seed dispersers in the Mediterranean area and the Canary Islands - Benigno Padrón; Manuel Nogales; Anna Traveset; Montserrat Vilà; Alejandro Martínez-Abraín; David P. Padilla; Patricia Marrero (Biological Invasions, 2011)

Planting System Effect on Yield Response of Russet Norkotah to Irrigation and Nitrogen under High Intensity Sprinkler Irrigation - Bradley A. King; David D. Tarkalson; David L. Bjorneberg; John P. Taberna (American Journal of Potato Research, 2011)

Critical Nitrogen Deposition Loads in High-elevation Lakes of the Western US Inferred from Paleolimnological Records - Jasmine E. Saros; David W. Clow; Tamara Blett; Alexander P. Wolfe (Water, Air, & Soil Pollution, 2011)