bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation
Authors: Yu Pengfei , Xiao Shu , Xin Xiaoyun , Song Chun-Xiao , Huang Wei , McDee Darina , Tanaka Tetsuya , Wang Ting , He Chuan , Zhong Sheng
Published: October 2012

Spatial organization of different epigenomic marks was used to infer functions of the epigenome. It remains unclear what can be learned from the temporal changes of the epigenome. Here, we developed a probabilistic model to cluster genomic sequences based on the similarity of temporal changes of multiple epigenomic marks during a cellular differentiation process. We differentiated mouse embryonic stem (ES) cells into mesendoderm cells. At three time points during this differentiation process, we used high-throughput sequencing to measure seven histone modifications and variants—H3K4me1/2/3, H3K27ac, H3K27me3, H3K36me3, and H2A.Z; two DNA modifications—5-mC and 5-hmC; and transcribed mRNAs and noncoding RNAs (ncRNAs). Genomic sequences were clustered based on the spatiotemporal epigenomic information. These clusters not only clearly distinguished gene bodies, promoters, and enhancers, but also were predictive of bidirectional promoters, miRNA promoters, and piRNAs. This suggests specific epigenomic patterns exist on piRNA genes much earlier than germ cell development. Temporal changes of H3K4me2, unmethylated CpG, and H2A.Z were predictive of 5-hmC changes, suggesting unmethylated CpG and H3K4me2 as potential upstream signals guiding TETs to specific sequences. Several rules on combinatorial epigenomic changes and their effects on mRNA expression and ncRNA expression were derived, including a simple rule governing the relationship between 5-hmC and gene expression levels. A Sox17 enhancer containing a FOXA2 binding site and a Foxa2 enhancer containing a SOX17 binding site were identified, suggesting a positive feedback loop between the two mesendoderm transcription factors. These data illustrate the power of using epigenome dynamics to investigate regulatory functions.
Steady-State Phosphorylation of Light-Harvesting Complex II Proteins Preserves Photosystem I under Fluctuating White Light
Authors: Grieco Michele , Tikkanen Mikko , Paakkarinen Virpi , Kangasjärvi Saijaliisa , Aro Eva-Mari
Published: October 2012

According to the “state transitions” theory, the light-harvesting complex II (LHCII) phosphorylation in plant chloroplasts is essential to adjust the relative absorption cross section of photosystem II (PSII) and PSI upon changes in light quality. The role of LHCII phosphorylation upon changes in light intensity is less thoroughly investigated, particularly when changes in light intensity are too fast to allow the phosphorylation/dephosphorylation processes to occur. Here, we demonstrate that the Arabidopsis (Arabidopsis thaliana) stn7 (for state transition7) mutant, devoid of the STN7 kinase and LHCII phosphorylation, shows a growth penalty only under fluctuating white light due to a low amount of PSI. Under constant growth light conditions, stn7 acquires chloroplast redox homeostasis by increasing the relative amount of PSI centers. Thus, in plant chloroplasts, the steady-state LHCII phosphorylation plays a major role in preserving PSI upon rapid fluctuations in white light intensity. Such protection of PSI results from LHCII phosphorylation-dependent equal distribution of excitation energy to both PSII and PSI from the shared LHCII antenna and occurs in cooperation with nonphotochemical quenching and the proton gradient regulation5-dependent control of electron flow, which are likewise strictly regulated by white light intensity. LHCII phosphorylation is concluded to function both as a stabilizer (in time scales of seconds to minutes) and a dynamic regulator (in time scales from tens of minutes to hours and days) of redox homeostasis in chloroplasts, subject to modifications by both environmental and metabolic cues. Exceeding the capacity of LHCII phosphorylation/dephosphorylation to balance the distribution of excitation energy between PSII and PSI results in readjustment of photosystem stoichiometry.
Angiotensin‐(1–7) treatment ameliorates angiotensin II‐induced apoptosis of human umbilical vein endothelial cells
Authors: Yang Hui‐Yu , Bian Yun‐Fei , Zhang Hua‐Ping , Gao Fen , Xiao Chuan‐Shi , Liang Bin , Li Jin , Zhang Na‐Na , Yang Zhi‐Ming
Published: October 2012

Angiotensin (Ang)‐(1–7), a metabolite of AngI and AngII, is a counter‐regulatory mediator of AngII. In the present study, we investigated the effects of Ang‐(1–7) on AngII‐induced apoptosis in human umbilical vein endothelial cells (HUVEC). To this end, HUVEC were pretreated with 10−9, 10−8, 10−7 or 10−6 mol/L Ang‐(1–7) at for 30 min before being stimulated with 10−6 mol/L Ang‐II for another 24 h. Acridine orange/ethidium bromide and propidium iodide staining were used to analyse the effects of Ang‐(1–7) on AngII‐induced apoptosis.

Alone, 10−6 mol/L Ang‐(1–7) had no effect on the apoptosis of HUVEC following exposure of cells for 30 min, whereas AngII (10−6 mol/L, 24 h) significantly enhanced the number of apoptotic cells (P < 0.01). The AngII‐induced apoptosis of HUVEC was suppressed by 10−9–10−6 mol/L Ang‐(1–7). The anti‐apoptotic effects of Ang‐(1–7) were almost completely abolished by A‐779 (10−6 mol/L, 30 min), a specific Mas receptor antagonist.

In addition, Ang‐(1–7) inhibited AngII‐induced accumulation of cleaved caspase 3 and enhanced the expression of the anti‐apoptotic factor Bcl‐2 at both the mRNA and protein levels.

Angiotensin II upregulated the expression of lectin‐like oxidized low‐density lipoprotein receptor‐1 (LOX‐1), which is involved in endothelial apoptosis, at both the mRNA and protein levels. This effect was blocked by Ang‐(1–7) in a concentration‐dependent manner, although A‐779 almost completely reversed Ang‐(1–7)‐mediated inhibition of AngII‐induced upregulation of LOX‐1.

Silencing of LOX‐1 using short interference RNA enhanced the protective effects of Ang‐(1–7) against AngII‐induced apoptosis in HUVEC.

Together, the results suggest that Ang‐(1–7) ameliorates AngII‐induced apoptosis of HUVEC at least in part by suppressing LOX‐1 expression.
Continuing decline of a keystone tree species in the Kruger National Park, South Africa
Authors: Helm Chantal V. , Witkowski Ed T. F.
Published: October 2012

Sclerocarya birrea subsp. caffra (marula), a keystone large tree species in southern Africa and heavily utilized by people and herbivores, is declining at an unprecedented rate in the Kruger National Park (KNP), South Africa. Due to increasing concerns over large tree declines in the KNP, mirroring those in eastern Africa over the last 50 years, and local extinctions of marula populations in the north‐western KNP, adult trees in the southern KNP were monitored between 2001 and 2010. Annual mortality rates across all adult size classes ranged between 3.2 and 4.6%. Loss of adult marula trees in some areas over the last decade exceeded 25%. Rainfall had a strong influence on mortality rates temporally and spatially, but the distance to the nearest perennial river had little influence. Overall, marula populations continue to decline and further local extinctions are possible. Given the clearly unacceptable trends of decline, the next step is to utilize this information (i) to develop predictive models for the future dynamics of marula populations incorporating all drivers; (ii) to advocate active management of refugia within the park where marula populations are protected from elephant impacts; and in combination with (iii) continued monitoring.
Cerebrospinal fluid kynurenic acid is associated with manic and psychotic features in patients with bipolar I disorder
Authors: Olsson Sara K , Sellgren Carl , Engberg Göran , Landén Mikael , Erhardt Sophie
Published: October 2012

Olsson SK, Sellgren C, Engberg G, Landén M, Erhardt S. Cerebrospinal fluid kynurenic acid is associated with manic and psychotic features in patients with bipolar I disorder. Bipolar Disord 2012: 14: 719–726. © 2012 The Authors. Journal compilation © 2012 John Wiley & Sons A/S.

Objectives:  Kynurenic acid (KYNA), an end metabolite of tryptophan degradation, antagonizes glutamatergic and cholinergic receptors in the brain. Recently, we reported elevated levels of cerebrospinal fluid (CSF) KYNA in male patients with bipolar disorder. Here, we investigate the relationship between symptomatology and the concentration of CSF KYNA in patients with bipolar I disorder.

Methods:  CSF KYNA levels from euthymic male {n = 21; mean age: 41 years [standard deviation (SD) = 14]} and female [n = 34; mean age: 37 years (SD = 14)] patients diagnosed with bipolar I disorder were analyzed using high‐performance liquid chromatography (HPLC).

Results:  Euthymic bipolar I disorder patients with a lifetime occurrence of psychotic features had higher CSF levels of KYNA {2.0 nm [standard error of the mean (SEM) = 0.2]; n = 43} compared to patients without any history of psychotic features [1.3 nm (SEM = 0.2); n = 12] (p = 0.01). Logistic regression, with age as covariate, similarly showed an association between a history of psychotic features and CSF KYNA levels [n = 55; odds ratio (OR) = 4.9, p = 0.03]. Further, having had a recent manic episode (within the previous year) was also associated with CSF KYNA adjusted for age (n = 34; OR = 4.4, p = 0.03), and the association remained significant when adjusting for a lifetime history of psychotic features (OR = 4.1, p = 0.05).

Conclusions:  Although the causality needs to be determined, the ability of KYNA to influence dopamine transmission and behavior, along with previous reports showing increased brain levels of the compound in patients with schizophrenia and bipolar disorder, may indicate a possible pathophysiological role of KYNA in the development of manic or psychotic symptoms.
Perhaps Unidimensional Is Not Unidimensional
Authors: Dodds Pennie , Rae Babette , Brown Scott
Published: October 2012

Miller (1956) identified his famous limit of 7 ± 2 items based in part on absolute identification—the ability to identify stimuli that differ on a single physical dimension, such as lines of different length. An important aspect of this limit is its independence from perceptual effects and its application across all stimulus types. Recent research, however, has identified several exceptions. We investigate an explanation for these results that reconciles them with Miller’s work. We find support for the hypothesis that the exceptional stimulus types have more complex psychological representations, which can therefore support better identification. Our investigation uses data sets with thousands of observations for each participant, which allows the application of a new technique for identifying psychological representations: the structural forms algorithm of Kemp and Tenenbaum (2008). This algorithm supports inferences not possible with previous techniques, such as multidimensional scaling.
Insect‐bite‐like reaction in patients with chronic lymphocytic leukemia: a study from the Israeli Chronic Lymphocytic Leukemia Study Group
Authors: Bairey Osnat , Goldschmidt Neta , Ruchlemer Rosa , Tadmor Tamar , Rahimi‐Levene Neomi , Yuklea Mona , Shvidel Lev , Berrebi Alain , Polliack Aaron , Herishanu Yair ,   the Israeli Chronic Lymphocytic Leukemia Study Group (ICLLSG)
Published: October 2012

An insect‐bite‐like reaction is known to occur in patients with chronic lymphocytic leukemia (CLL). Most of the literature, however, consists of isolated case reports or small case series. The aim of this retrospective study was to review the national experience with insect‐bite‐like reaction in a large group of patients with CLL. The study cohort of patients with these skin reactions consisted of 48 patients (25 males, 23 females) of mean age 64.8 yr (range 33–89) at skin eruption. Data on clinical, histologic, immunophenotypic, and cytogenetic characteristics, treatment, and outcome were collected from the medical files. Mean time between diagnosis of CLL and appearance of the skin lesions was 3.1 yr (range −4 to 14 yr). The eruption was not related to disease activity or the course of the hematological disease. The eruption preceded the diagnosis of CLL in 10 patients (by 0–4 yr); and followed the diagnosis in 36; in 11 patients, it occurred during therapy for CLL and in nine after therapy. Mean duration of the skin findings was 21.5 months (range 0.3–132). The eruption usually presented in summer, although it occurred also at other times of the year, and predominantly affected the upper and lower limbs, although it also appeared on unexposed areas. Treatment included local ointments, antihistaminics, oral steroids, antibiotics, phototherapy, and dapsone with varying responses. Insect‐bite‐like reactions is a relatively common and disturbing skin reaction in CLL patients, it may be related to the immune dysregulation accompanying CLL and further exacerbated by external factors, including actual insect bites, chemoimmunotherapy, and pyogenic infection.
Adipophilin/perilipin‐2 as a lipid droplet‐specific marker for metabolically active cells and diseases associated with metabolic dysregulation
Authors: Straub Beate Katharina , Gyoengyoesi Benedek , Koenig Maria , Hashani Merita , Pawella Lena Maria , Herpel Esther , Mueller Wolf , Macher‐Goeppinger Stephan , Heid Hans , Schirmacher Peter
Published: October 2012

Aims

Lipid droplets (LDs) are dynamic storage compartments for energy‐rich fats that are nearly ubiquitously present in eukaryotic cells, exerting tissue‐specific functions in metabolically active cell types, and are increased in conditions following cellular damage or lipid overload. The LD–cytoplasm interface is stabilized by amphiphilic proteins of the PAT/perilipin family (perilipin/perilipin‐1, adipophilin/perilipin‐2, and TIP47/perilipin‐3). We evaluated the value of adipophilin immunohistochemistry for the diagnosis of diseases associated with LD accumulation.

Methods and results

In human tissues, adipophilin‐positive LDs were especially prominent in steroidogenic cells of the adrenal gland, testis, and ovary, in hepatocytes and hepatic stellate cells, in cardiac, striated and smooth myocytes, in lactating mammary gland epithelial cells, and in plurivacuolar adipocytes. Variable amounts of adipophilin‐positive LDs were also detected almost ubiquitously in epithelial cells of the gastrointestinal tract and skin. In diseases associated with lipid storage, adipophilin was strongly expressed in lipid‐laden macrophages in atherosclerosis, in cardiomyopathies, kidney diseases, hepatocyte steatosis, colon ischaemia, and at the border of organ infarcts.

Conclusions

Adipophilin immunohistochemistry visualizes small LDs in tissues under physiological and disease conditions that are not visible by conventional light microscopy. Immunohistology for adipophilin may facilitate histomorphological diagnosis of diseases and definition of the extent of metabolic dysregulation, such as in organ infarcts, cardiomyopathies, kidney diseases, and microvesicular steatosis.
Comparison of non‐invasive and invasive blood pressure in aeromedical care
Authors: McMahon N. , Hogg L. A. , Corfield A. R. , Exton A. D.
Published: October 2012

Blood pressure measurement is an essential physiological measurement for all critically ill patients. Previous work has shown that non‐invasive blood pressure is not an accurate reflection of invasive blood pressure measurement. In a transport environment, the effects of motion and vibration may make non‐invasive blood pressure less accurate. Consecutive critically ill patients transported by a dedicated aeromedical retrieval and critical care transfer service with simultaneous invasive and non‐invasive blood pressure measurements were analysed. Two sets of measurements were recorded, first in a hospital environment before departure (pre‐flight) and a second during aeromedical transport (in‐flight). A total of 56 complete sets of data were analysed. Bland‐Altman plots showed limits of agreement (precision) for pre‐flight systolic blood pressure were −37.3 mmHg to 30.0 mmHg, and for pre‐flight mean arterial pressure −20.5 mmHg to 25.0 mmHg. The limits of agreement for in‐flight systolic blood pressure were −40.6 mmHg to 33.1 mmHg, while those for in‐flight mean blood pressure in‐flight were −23.6 mmHg to 24.6 mmHg. The bias for the four conditions ranged from 0.5 to −3.8 mmHg. There were no significant differences in values between pre‐flight and in‐flight blood pressure measurements for all categories of blood pressure measurement. Thus, our data show that non‐invasive blood pressure is not a precise reflection of invasive intra‐arterial blood pressure. Mean blood pressure measured non‐invasively may be a better marker of invasive blood pressure than systolic blood pressure. Our data show no evidence of non‐invasive blood pressures being less accurate in an aeromedical transport environment.
A widespread contaminant enhances invasion success of a marine invader
Authors: McKenzie Louise A. , Brooks Robert C. , Johnston Emma L.
Published: October 2012

1. The global transfer of species by human vectors is continuing despite the use of managerial controls such as antifouling biocides and pesticide applications. The process of introduction now exposes species to novel conditions which may select for tolerance to a contaminant. Invader establishment success is influenced by both the supply of invasive propagules and disturbance. Therefore, it is important to understand whether tolerance to an anthropogenic disturbance, such as contamination, can change the parameters of supply in a way that inadvertently augments the invasion process.

2. To test whether the invasion process is influenced by a widespread contaminant, we investigated how recruitment of the invasive hull‐fouling bryozoan Watersipora subtorquata is affected by exposure to copper‐based antifouling paint. We quantified settlement patterns in control and copper environments and then assessed post‐settlement survival and fitness components.

3. Copper significantly increased total recruitment success despite greater post‐settlement mortality. Surviving recruits differed morphologically, with shorter ancestrulae and smaller colonies in high copper treatments. These results show a strong positive affiliation between larval W. subtorquata and high levels of copper although there are associated fitness costs.

4. Syntheses and applications. We found a direct positive effect of contamination on recruitment of a common invasive species. This process is likely to be relevant to other non‐indigenous species (NIS) that exhibit a positive affiliation with metal contamination. Copper can potentially enhance success at multiple stages of the invasion process, including facilitating transport and establishment, by increasing the supply and retention of individuals into anthropogenically disturbed environments. Identification of tolerance to contamination as a species trait may also aid in predicting a species invasiveness and spread. Management of metal pollution through remediation and alternative copper‐free antifouling techniques would help prevent the spread and establishment of many marine NIS.
Making use of harvest information to examine alternative management scenarios: a body weight‐structured model for wild boar
Authors: Gamelon Marlène , Gaillard Jean‐Michel , Servanty Sabrina , Gimenez Olivier , Toïgo Carole , Baubet Eric , Klein François , Lebreton Jean‐Dominique
Published: October 2012

1. Harvest models are often built to explore the sustainability of the dynamics of exploited populations and to help evaluate hunting management scenarios. Age‐structured models are commonly used for ungulate population dynamics. However, the age of hunted individuals is usually not recorded, and hunting data often only include body weight and sex limiting the usefulness of traditional models.

2. We propose a new modelling approach that fits data collected by hunters to develop management rules when age is not available. Using wild boar Sus scrofa scrofa as a case study, we built a matrix model structured according to sex and body weight whose output can be directly compared with the observed distribution of hunted individuals among sex and body weight classes.

3. In the face of the current wide scale increase in populations of wild boar, the best feasible option to stop or slow down population growth involves targeting the hunting effort to specific sex and body weight classes. The optimal harvest proportion in the target body weight classes is estimated using sensitivity analyses.

4. The number of individuals shot in each sex and body weight class predicted by our model was closely associated with those recorded in the hunting bag. Increasing the hunting pressure on medium‐sized females by 14·6% was the best option to limit growth rate to a target of 0·90.

5. Synthesis and applications. We demonstrate that targeting hunting effort to specific body weight classes could reliably control population growth. Our modelling approach can be applied to any game species where group composition, phenotypic traits or coat colour allows hunters to easily identify sex and body weight classes. This offers a promising tool for applying selective hunting to the management of game species.
Managing the long‐term persistence of a rare cockatoo under climate change
Authors: Berton C. Harris J. , Fordham Damien A. , Mooney Patricia A. , Pedler Lynn P. , Araújo Miguel B. , Paton David C. , Stead Michael G. , Watts Michael J. , Reşit Akçakaya H. , Brook Barry W.
Published: October 2012

1. Linked demographic‐bioclimatic models are emerging tools for forecasting climate change impacts on well‐studied species, but these methods have been used in few management applications, and species interactions have not been incorporated. We combined population and bioclimatic envelope models to estimate future risks to the viability of a cockatoo population posed by climate change, increased fire frequency, beak‐and‐feather disease and reduced management.

2. The South Australian glossy black‐cockatooCalyptorhynchus lathami halmaturinusis restricted to Kangaroo Island, Australia, where it numbers 350 birds and is managed intensively. The cockatoo may be at particular risk from climate change because of its insular geographic constraints and specialised diet on a single plant species,Allocasuarina verticillata. The cockatoo population model was parameterised with mark‐resight‐derived estimates of survival and fecundity from 13 years of demographic data. Species interactions were incorporated by using a climate‐change‐driven bioclimatic model ofAllocasuarina verticillataas a dynamic driver of habitat suitability. A novel application of Latin Hypercube sampling was used to assess the model’s sensitivity to input parameters.

3. Results suggest that unmitigated climate change is likely to be a substantial threat for the cockatoo: all high‐CO2‐concentration scenarios had expected minimum abundances of <160 birds. Extinction was virtually certain if management of nest‐predating brush‐tail possumsTrichosurus vulpeculawas stopped, or adult survival reduced by as little as 5%. In contrast, the population is predicted to increase under low‐emissions scenarios.

4. Disease outbreak, increased fire frequency and reductions in revegetation and management of competitive little corellasCacatua sanguinea, were all predicted to exacerbate decline, but these effects were buffered by the cockatoo population’s high fecundity.

5. Spatial correlates of extinction risk, such as range area and total habitat suitability, were nonlinearly related to projected population size in the high‐CO2‐concentration scenario.

6. Synthesis and applications. Mechanistic demographic‐bioclimatic simulations that incorporate species interactions can provide more detailed viability analyses than traditional bioclimatic models and be used to rank the cost‐effectiveness of management interventions. Our results highlight the importance of managing possum predation and maintaining high adult cockatoo survival. In contrast, corella and revegetation management could be experimentally reduced to save resources.
The biodiversity audit approach challenges regional priorities and identifies a mismatch in conservation
Authors: Dolman Paul M. , Panter Christopher J. , Mossman Hannah L.
Published: October 2012

Despite a strong uptake of evidence‐based approaches, conservation often proceeds from a grossly incomplete understanding of species priorities. To optimize conservation impact within a biogeographical region, quantitative knowledge is needed of the species present, which should be prioritized, and the management interventions these require. The next challenge is to avoid a proliferation of competing species plans, or conversely, a lack of detail within generic habitat‐based approaches.

We present a methodology for biodiversity auditing. We quantified regional biodiversity by systematically collating available species records, allowing objective prioritization. We collated autecological information to integrate multiple species into management guilds with shared requirements, providing evidence‐based guidance for regional conservation.

For two regions of Eastern England, Breckland (2300 km2) and The Broads (2000 km2), we collated 0·83 and 1·5‐million records, respectively. Numbers of species (12 845 and 11 067) and priority species (rare, threatened, designated or regionally restricted: 2097 and 1519, respectively) were orders of magnitude greater than previously recognized. Regional specialists, with a UK range largely or entirely restricted to the region, were poorly recognized posing a risk of regional homogenization.

A large body of autecological information existed for priority species and collating this allowed us to define cross‐taxa management guilds. Numbers of priority species requiring different combinations of ecological processes and conditions were not matched by current conservation practice in Breckland. For example, the current agri‐environment agreements for designated grass heaths potentially catered for only 15% of the 542 priority species and 21% of 47 regional specialists that could potentially benefit from evidence‐based management. A focus on vegetation composition rather than the ecological requirements of priority species underpinned this failure.

Synthesis and applications. The biodiversity audit approach provides an objective model for prioritization and cost‐effective conservation, applicable to regions of Europe where biodiversity has been well characterized. By using this approach to collate available information, management guilds with similar requirements can be defined across taxa, providing evidence‐based guidance for regional conservation.
Local‐scale factors structure wild bee communities in protected areas
Authors: Murray Tomás E. , Fitzpatrick Úna , Byrne Andrew , Fealy Réamonn , Brown Mark J. F. , Paxton Robert J.
Published: October 2012

In the current context of global habitat loss, a fundamental challenge is to understand how ecological processes interact to determine community composition. Despite the accumulating evidence base for global declines in bee populations, few studies have addressed the relative importance of local environmental and large‐scale spatial factors in maintaining diverse bee communities outside of agricultural habitats, and particularly in areas protected for nature conservation.

We analysed bee community data that we collected from 40 Special Areas of Conservation representing five distinct European Natura 2000 priority habitats in Ireland, quantifying local habitat features within each site and surrounding land‐use. Species data were collected in a nested sampling design composed of three hierarchical levels such as ‘site’, ‘habitat’ and ‘region’ and analysed using diversity partitioning. The species–environment relationship was also decomposed into regional‐, landscape‐ and local‐scales by variance partitioning using partial canonical correspondence analysis.

Wild bee species richness and abundance were highly dependent on habitat type, but the majority of regional diversity was contained within sites, as opposed to species turnover across sites and regions. Bee communities were primarily structured by local‐scale factors associated with nesting resources and grazing regime, with non‐Bombus taxa being more sensitive to landscape‐scale differences in adjacent habitats than Bombus taxa. Regional‐scale processes, such as species sorting along longitudinal gradients, were of minor importance in structuring bee communities in this system.

Synthesis and applications. Within habitats, local species richness, rather than species turnover at higher spatial scales, accounted for the majority of regional bee diversity. Local environmental factors were powerful determinants of community composition. Therefore, management effort prioritising the maintenance of a diversity of high‐quality habitats within a broad network of protected areas best facilitates bee conservation in this system. At a regional level, schemes for conserving and restoring important bee habitats must be habitat‐ and taxon‐specific, as the impact of individual local‐scale factors and surrounding land‐use on community composition is highly habitat‐ and taxon‐dependent.
Merging connectivity rules and large‐scale condition assessment improves conservation adequacy in river systems
Authors: Linke Simon , Kennard Mark J. , Hermoso Virgilio , Olden Julian D. , Stein Janet , Pusey Bradley J.
Published: October 2012

Conservation adequacy is defined as the ability of conservation measures to sustain biodiversity. Although river network connectivity is important for maintaining key ecological processes and ensuring persistence of biodiversity, it also facilitates the propagation of threats along river networks, which may compromise the sustainability of freshwater biodiversity and therefore conservation adequacy. This study aims to introduce two modifications to river conservation planning related to connectivity and catchment condition that together can improve the adequacy of the priority areas identified. This will establish an operational framework for end‐users, such as policy makers andNGOs.

We operationalize the connectivity framework that has recently emerged in systematic river conservation planning by using aGIScoding system for catchment location in the conservation software packagemarxan. Additionally, we use a landscape measure of catchment disturbance to direct the conservation plan to the least‐disturbed area while still meeting targets for the conservation of fish species used as surrogates for overall biodiversity in our study catchment, theDalyRiver in northernAustralia. This proxy for condition aggregates information on land‐use, extractive industries, point‐source pollution, and water infrastructure.

We successfully modelled the distribution of 39 fish species based onGIS‐derived landscape descriptors (most important descriptors were; discharge, distance to river mouth, geology and conductivity).

Results from the systematic planning analysis identified a portfolio of watersheds that delivered close to optimal upstream protection with around 4700 stream kilometres (30% of the total network). When using upstream disturbance as an extra penalty, most of the network stayed intact; however, a replacement area was found for a major tributary, which only added an extra 1% of the stream network to the total area.

Synthesis and applications. Improving conservation adequacy by accounting for upstream connectivity and condition using this easy‐to‐implement framework and software package has the potential to facilitate further application of systematic methods in river conservation planning. Furthermore, integrating condition as a discounting factor can also improve conservation adequacy in a broad range of environments (including terrestrial and marine), while not necessarily increasing the management costs.
Vehicle traffic shapes grizzly bear behaviour on a multiple‐use landscape
Authors: Northrup Joseph M. , Pitt Justin , Muhly Tyler B. , Stenhouse Gordon B. , Musiani Marco , Boyce Mark S.
Published: October 2012

Roads cause functional habitat loss, alter movement patterns and can become ecological traps for wildlife. Many of the negative effects of roads are likely to be a function of the human use of roads, not the road itself. However, few studies have examined the effect of temporally and spatially varying traffic patterns on large mammals, which could lead to misinterpretations about the impact of roads on wildlife.

We developed models of traffic volume for an entire road network in south‐western Alberta, Canada, and documented for the first time the response of grizzly bears Ursus arctos L to a wide range of traffic levels.

Traffic patterns caused a clear behavioural shift in grizzly bears, with increased use of areas near roads and movement across roads during the night when traffic was low. Bears selected areas near roads travelled by fewer than 20 vehicles per day and were more likely to cross these roads. Bears avoided roads receiving moderate traffic (20–100 vehicles per day) and strongly avoided high‐use roads (>100 vehicles per day) at all times.

Synthesis and applications. Grizzly bear responses to traffic caused a departure from typical behavioural patterns, with bears in our study being largely nocturnal. In addition, bears selected private agricultural land, which had lower traffic levels, but higher road density, over multi‐use public land. These results improve our understanding of bear responses to roads and can be used to refine management practices. Future management plans should employ a multi‐pronged approach aimed at limiting both road density and traffic in core habitats. Access management will be critical in such plans and is an important tool for conserving threatened wildlife populations.
Radar monitoring of migrating pink‐footed geese: behavioural responses to offshore wind farm development
Authors: Plonczkier Pawel , Simms Ian C.
Published: October 2012

In the context of growing demand for offshore wind energy production in recent years, much effort has been made to determine the collision risk that offshore wind turbines pose to birds. Currently, only limited species‐specific data on migrating birds' avoidance rates and associated mortality at offshore wind farms exist.

During a 4‐year study, bird detection radar was used to monitor behavioural responses and flight changes of migrating pink‐footed geese in relation to two offshore wind farms during and after construction.

Radar recorded a total of 979 goose flocks migrating through the whole study area, of which 571 were visually confirmed as 39 957 pink‐footed geese Anser brachyrhynchus. Overall, we calculated that 97·25% of all flocks recorded by radar, in 2009 and 2010 combined, migrated without any risk of additional mortality associated with the constructed wind farms.

We identified a growing tendency of geese to avoid the wind farms and calculated that, for 2009 and 2010 combined, avoidance was exhibited by 94·46% of the original 292 flocks predicted to enter the wind farms.

Synthesis and applications. Migratory geese responded to offshore wind farms by adopting strong horizontal and vertical avoidance behaviour. For the first time, wind farm avoidance rates have been recorded for pink‐footed geese, and these rates will allow more robust impact assessments to be undertaken for both this species and waterfowl in general. Remote sensing techniques should be used to undertake long‐term impact assessments at offshore wind farms to provide an evidence‐base for assessing the mortality risk for migratory birds.
A continental‐scale tool for acoustic identification of European bats
Authors: Walters Charlotte L. , Freeman Robin , Collen Alanna , Dietz Christian , Brock Fenton M. , Jones Gareth , Obrist Martin K. , Puechmaille Sébastien J. , Sattler Thomas , Siemers Björn M. , Parsons Stuart , Jones Kate E.
Published: October 2012

Acoustic methods are used increasingly to survey and monitor bat populations. However, the use of acoustic methods at continental scales can be hampered by the lack of standardized and objective methods to identify all species recorded. This makes comparable continent‐wide monitoring difficult, impeding progress towards developing biodiversity indicators, trans‐boundary conservation programmes and monitoring species distribution changes.

Here we developed a continental‐scale classifier for acoustic identification of bats, which can be used throughout Europe to ensure objective, consistent and comparable species identifications. We selected 1350 full‐spectrum reference calls from a set of 15 858 calls of 34 European species, from EchoBank, a global echolocation call library. We assessed 24 call parameters to evaluate how well they distinguish between species and used the 12 most useful to train a hierarchy of ensembles of artificial neural networks to distinguish the echolocation calls of these bat species.

Calls are first classified to one of five call‐type groups, with a median accuracy of 97·6%. The median species‐level classification accuracy is 83·7%, providing robust classification for most European species, and an estimate of classification error for each species.

These classifiers were packaged into an online tool, iBatsID, which is freely available, enabling anyone to classify European calls in an objective and consistent way, allowing standardized acoustic identification across the continent.

Synthesis and applications. iBatsID is the first freely available and easily accessible continental‐scale bat call classifier, providing the basis for standardized, continental acoustic bat monitoring in Europe. This method can provide key information to managers and conservation planners on distribution changes and changes in bat species activity through time.
Predicting invasions: alternative models of human‐mediated dispersal and interactions between dispersal network structure and Allee effects
Authors: Chivers Corey , Leung Brian
Published: October 2012

Human‐mediated dispersal has been shown to be the most important vector for the spread of invasive species, yet there has been little evaluation of alternative models of dispersal in terms of differences in their predictions of invasion patterns. Moreover, no analyses have been attempted to elucidate the potential interaction between alternative models of human‐mediated dispersal and population dynamical characteristics, such as Allee effects, which are central to the probability of an invasion.

Two prominent models in the literature which have previously been employed to predict human movement patterns are explored: (i) gravity models, which use the attractiveness of and distance to a location to predict travel patterns, and (ii) random utility models, which assume that individuals decide where to travel by maximizing the benefits that they receive according to some partially observable function of individual and site characteristics.

While distinction is often drawn between them in the literature, we demonstrate that these two approaches can be reduced to alternative functional forms describing the trip‐taking decisions of individuals.

Each model was empirically parameterized using a survey of recreational boaters in Ontario, Canada. Within each model, both boater‐ and site‐specific characteristics were important and the functional form provided by the gravity model was significantly better at capturing the behaviour of recreational boaters

Synthesis and applications. The dispersal and establishment of species into novel habitats are central components of the invasion process and of quantitative risk assessments. However, predictions are dependent on the estimated spatial structure of the dispersal network and its potential interactions with species characteristics. This study demonstrates that Allee effects can interact with dispersal network structure to significantly alter predicted spread rates and that the consequences of these interactions manifest differently at the system and site levels. This modelling framework can be used to inform management interventions aimed at modifying human‐mediated dispersal to reduce the spread of invasive species.
Role of domestic shipping in the introduction or secondary spread of nonindigenous species: biological invasions within the Laurentian Great Lakes
Authors: Briski Elizabeta , Wiley Chris J. , Bailey Sarah A.
Published: October 2012

The most effective way to manage invasive species is to prevent their introduction via vector regulation. While progress has been made in the management of transoceanic ballast water, domestic vessels operating within smaller geographic regions such as the Laurentian Great Lakes, Mediterranean Sea, North Sea or Baltic Sea are often exempt from regulations.

We randomly surveyed unmanaged ballast water moved by domestic vessels within the Laurentian Great Lakes and compared the results with that of exchanged ballast water from transoceanic vessels to assess invasion risk of zooplankton transported by these two types of vessels.

Total abundance and species richness were significantly different between the two vessel types with mean abundance being two magnitudes greater, and species richness being threefold higher in domestic vessels compared with transoceanic vessels. Abundance of restricted taxa – cumulatively the Great Lakes' indigenous and nonindigenous species (NIS) which do not occur in all five lakes – was also significantly higher in domestic vessels (mean densities were 24 170 and 3421 individuals per m3 for domestic and transoceanic vessels, respectively), whereas the abundance of NIS did not differ between vessels (median densities of 2015 and 850 individuals per m3, respectively).

We documented 89 species transported by domestic vessels of which 31 had restricted distribution and eight were NIS. While most NIS were already established in all five lakes, Cercopagis pengoi, a NIS of global concern, and Nitokra hibernica have not been identified from Lake Superior, and both were sampled from ballast water destined for discharge in Lake Superior. Beside the risk of spread of NIS between lakes, domestic shipping can act as a vector for homogenization of indigenous taxa, with at least 21 native species (99 events) being moved outside their historical distribution.

Synthesis and applications. Our study indicates that management of invasive species should consider ecological, not geographical or political boundaries. Domestic vessels operating within a limited geographic region have high potential to introduce or spread species with restricted distribution, demonstrating importance of intraregional ballast water management. Results presented here should interest policy makers and environmental managers who seek to reduce invasion risk.
Rigorous gharial population estimation in theChambal: implications for conservation and management of a globally threatened crocodilian
Authors: Nair Tarun , Thorbjarnarson John B. , Aust Patrick , Krishnaswamy Jagdish
Published: October 2012

India'sChambalRiver hosts the largest population of the critically endangered gharial. Boat‐based daylight surveys to date only provide indices of relative abundance, without measures of survey bias or error. No attempt to quantify detection probabilities in these surveys has yet been made, and thus, absolute density estimates of this population remain unknown.

We surveyed 75 km of theRiverChambal and photographed individual gharials for capture–recapture analysis. The total sampling effort yielded 400 captures. Population closure was supported (z = −1·48,P = 0·069), and closed‐population models were used to estimate abundances.

Models were selected using theAkaikeInformationCriterion (AIC) index of model fit. The best model estimated 231 ± 32 adult, 83 ± 23 subadult and 89 ± 19 juvenile gharials (Mean ± SE), respectively, while the model‐averaged estimate was 220 ± 28 adult, 76 ± 16 subadults and 93 ± 16 juvenile gharials, respectively.

The best model estimated absolute densities of 3·08 ± 0·43, 1·11 ± 0·3 and 1·19 ± 0·25 adult, subadult and juvenile gharials km−1, respectively, while the model‐averaged estimate was 2·93 ± 0·37, 1·01 ± 0·21 and 1·24 ± 0·21 adult, subadult and juvenile gharials km−1, respectively, compared with relative densities of 0·94, 0·45 and 0·30 adult, subadult and juvenile gharials km−1, respectively, from boat‐based daylight surveys. On the basis of our best model, we suggest a detection probability based correction factor of 3·27, 2·47 and 3·97 to boat‐based daylight survey estimates of adult, subadult and juvenile gharials, respectively.

Synthesis and applications. Used within the framework of capture–recapture analysis, photoidentification provides a reliable and noninvasive method of estimating population size and structure in crocodilians. We also opine that without determining the current status of gharials, highly intensive strategies, such as the egg‐collection and rear‐and‐release programmes being implemented currently, initiated on the basis of underestimates of population sizes, are unwarranted and divert valuable conservation resources away from field‐based protection measures, which are essential in the face of threats like hydrologic diversions, sand mining, fishing and bankside cultivation.
Using water residency time to enhance spatio‐temporal connectivity for conservation planning in seasonally dynamic freshwater ecosystems
Authors: Hermoso Virgilio , Ward Doug P. , Kennard Mark J.
Published: October 2012

Addressing spatial connectivity in conservation planning is important to ensure the maintenance of patterns and processes needed to support the persistence of biodiversity. In freshwater ecosystems, spatial connectivity is constrained by the presence of water, which exhibits marked temporal changes in regions with wet–dry seasonal climates. Previous studies have focused on spatial connectivity and overlooked the temporal component, which is required for the functionality of spatial connections (because of temporal changes in water availability).

We identify priority areas for the conservation of freshwater fish, waterbirds and turtles in theMitchellRiver catchment in the wet–dry tropics of northernAustralia. We demonstrate how adequacy of freshwater conservation can be enhanced by integrating an estimate of water residency time (WRT) into the prioritization process.WRTreflects refugial potential and connectivity in freshwater ecosystems and was quantified usingModerateResolutionImagingSpectroradiometer (MODIS) flood and post‐floodLandsat satellite imagery. We compare the spatial allocation of priority areas and the spatial and temporal connectivity under two alternative scenarios: (i) accounting only for spatial connectivity and (ii) integrating spatial and temporal connectivity.

Priority areas identified under the spatial and temporal connectivity scenario showed a 40% increase inWRTvalues with respect to the traditional spatial connectivity scenario. This was achieved at no additional cost in terms of total protected area and maintaining the same spatial connectivity.

Despite priority areas identified under the two alternative scenarios showing intermediate spatial overlap (64%), the selection process was more efficiently biased towards planning units with highWRTvalues.WRTin planning units that were only selected under the temporal connectivity scenario was 2·5 times higher than in planning units that only appeared in the traditional connectivity scenario. This reveals the importance of accounting forWRTwhen identifying freshwater priority areas in wet–dry seasonal environments.

Synthesis and applications: Considering the temporal connectivity in conservation prioritization as we propose here helps to assess periods of longest spatial connections, thereby maximizing the refugial role of freshwater priority areas during dry periods. Using publicly available satellite imagery data and software, our approach allows improved management of aquatic resources and biodiversity during periods of water scarcity, which may increase in incidence and duration with climate change.