bluuebunny/crossref_metadata_2025 huggingface dataset:
Applications of the rep‐PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution
Authors: Ishii Satoshi , Sadowsky Michael J.
Published: February 2009

A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence‐based PCR or rep‐PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or ‘fingerprints’ of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep‐PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep‐PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep‐PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.
Marine biological collections in the 21st century
Authors: Rainbow Philip S.
Published: February 2009

From the time of Linnaeus forward, it has been appreciated that collections, not least marine biological collections, are fundamental to the understanding of the biodiversity of life on earth, especially when they contain type specimens which define individual species. Historical collections are particularly rich in types and also represent a model of the biodiversity of marine life at the time of the collection, often centuries ago. The taxonomic and systematic importance of collections is well appreciated, as is the significance of time series of data in this period of anthropogenic environmental change. The application of new techniques increases the value of collected material even further, for example, molecular biology techniques allowing the recognition of new (often cryptic) taxa and their distributions, and stable isotope analyses releasing information on past and present ontogenies, geographical distributions and diets. Moreover the new era of information technology with associated digitization enables the release of the information stored in the collections to the scientists of the world.
Linnaeus and the invisible world
Authors: Nyman Hans , Nilsson Lennart
Published: February 2009

Linnaeus expressed his fascination for microscopy in his work Mundum Invisibilem 1767 (the invisible world), which was one of the very first attempts to bring light and order to the microscopic discoveries of the time. Linnaeus wrote about his only microscopic experiment in the same publication. He wanted to know where to place the fungi in his grand ‘Systema Naturae’, but misinterpreted the results of the experiment completely. This is perhaps one of Linnaeus’ greatest and least known mistakes, but one that somehow boosted development anyway.

We took the original microscope models used by Linnaeus, took photos, and compared them with images obtained with modern instruments. Our experiments revealed several new findings, and let us understand why Linnaeus made his mistake. One other finding is that Linnaeus must have used the most modern and advanced compound microscope of his time, a large Cuff microscope in his experiment. Only two large microscopes by Cuff were available in Sweden by the time. A large Cuff microscope was found in Sweden lately. This microscope is probably the actual instrument that Linnaeus used.
Can contemporary transrectal prostate biopsy accurately select candidates for hemi‐ablative focal therapy of prostate cancer?
Authors: Tareen Basir , Godoy Guilherme , Sankin Alex , Temkin Steve , Lepor Herbert , Taneja Samir S.
Published: February 2009

OBJECTIVE

To determine if biopsy characteristics can be used to identify men with unilateral prostate cancer on radical prostatectomy (RP) pathological specimens, thereby selecting candidates for hemi‐ablative focal therapy.

PATIENTS AND METHODS

Of 1458 men who had RP from January 2000 to June 2007, we identified 590 of 880 evaluable patients with unilateral disease on their preoperative biopsy. Charts were reviewed to record preoperative prostate‐specific antigen (PSA) level, high‐grade prostatic intraepithelial neoplasia (HGPIN), clinical stage, Gleason score, perineural invasion (PNI), prostate volume, number of positive cores, and percentage of positive cores. Final surgical pathology was evaluated for unilateral cancer. Univariate analysis was used (logistic regression method) to identify independent predictors of unilateral disease on the RP specimen. A subset analysis was done in men with low‐risk disease, defined as clinical stage T1C, Gleason score <7 and a PSA level of <10 ng/mL.

RESULTS

Of 590 men with unilateral disease on biopsy, 163 (27.3%) had unilateral disease on the RP specimen. Pathological features, including HGPIN (P = 0.714), Gleason score (P > 0.608), PNI (P = 0.714), number of positive cores (P = 0.076), percentage of cores positive (P = 0.056), prostate volume (P = 0.285), and PSA level (P = 0.062) did not improve the prediction of unilateral disease. When men with unilateral cancer were further stratified to include only those with low‐risk disease, 28.4% had unilateral disease on the RP specimen. None of the biopsy or clinical features evaluated were predictors of unilateral disease on the RP specimen.

CONCLUSION

Unilateral prostate cancer on biopsy predicts unilateral disease on RP pathology in only 27.6% of cases. The predictive ability is not improved by adding biopsy and clinical characteristics. Additional methods are needed to accurately identify men appropriate for focal therapy.
A tertiary experience of urethral diverticulectomy: diagnosis, imaging and surgical outcomes
Authors: Ockrim Jeremy L. , Allen Daryl J. , Shah P. Julian , Greenwell Tamsin J.
Published: February 2009

OBJECTIVE

To review the outcomes of consecutive patients referred with urethral diverticula to a tertiary centre; to investigate the diagnostic, imaging and surgical factors relevant to success.

PATIENTS AND METHODS

A retrospective case note review of 30 consecutive patients treated between January 1999–2007 was performed and data retrieved on demographics, presenting symptoms, preoperative imaging, surgical technique, outcomes and need for further intervention.

RESULTS

All patients were tertiary referrals, four after failed local repairs. The mean (range) interval between initial presentation and repair was 48 (1–264) months. Only seven patients (23%) had all three symptoms of the classical triad of dysuria, dyspareunia and dribble, whilst 23% did not have any of these symptoms. Transvaginal ultrasonography showed the diverticulum in six of nine patients, voiding cysto‐urethrography (VCUG) in 13 of 18 patients (72%) and magnetic resonance imaging (MRI) in all 11 patients assessed. MRI accurately imaged diverticular configuration, whilst VCUG assessed detrusor and sphincteric function. Twenty‐nine (97%) patients were cured of their diverticulum; all 19 patients with simple diverticula were cured at first attempt, whilst 17 procedures were performed on the 11 patients with complex diverticula. Twenty of 24 (83%) repairs were successful using three‐layered closure, 9 of 11 using Martius interposition, and one using bulbospongiosus muscle interposition. There were three primary repair failures; two circumferential diverticula repaired with Martius interposition and one partial horseshoe diverticulum repaired without interposition had partial recurrences. Both were subsequently repaired successfully. One patient with chronic urethral pain from multiple, infected recurrences was eventually diverted. A pubovaginal sling procedure was required in only one (3.3%) patient with persistent pre‐existing stress urinary incontinence (SUI).

CONCLUSIONS

The presentation of urethral diverticula is diverse and diagnosis frequently delayed. The most useful preoperative imaging is MRI and VCUG to assess diverticular anatomy and detrusor/urethral function, respectively. In simple cases, transvaginal excision with three‐layer closure is curative, whilst more extensive, persistent or SUI‐associated diverticula require Martius fat interposition. Sling procedures can be deferred until the results of primary excision are assessed.
Multiple Imputation for Combining Confidential Data Owned by Two Agencies
Authors: Kohnen Christine N. , Reiter Jerome P.
Published: February 2009

Statistical agencies that own different databases on overlapping subjects can benefit greatly from combining their data. These benefits are passed on to secondary data analysts when the combined data are disseminated to the public. Sometimes combining data across agencies or sharing these data with the public is not possible: one or both of these actions may break promises of confidentiality that have been given to data subjects. We describe an approach that is based on two stages of multiple imputation that facilitates data sharing and dissemination under restrictions of confidentiality. We present new inferential methods that properly account for the uncertainty that is caused by the two stages of imputation. We illustrate the approach by using artificial and genuine data.
A PROPERTY TAXATION MECHANISM WITH SELF‐ASSESSMENT
Authors: Gstach Dieter
Published: February 2009

This paper analyzes a variant of the classic idea for property taxation based on owner's self‐assessment. To induce reporting of market values tax authorities announce to purchase some of the properties randomly at declared values under certain conditions. These conditions are based on properties of the distribution of declared values. It is proven that a unique Nash equilibrium of this taxation game among tax payers exists in which all of them report market values and tax authorities do not purchase any property.
RE‐ASSESSING THE MEANING OF THOUGHT: HANS URS VON BALTHASAR'S RETRIEVAL OF GREGORY OF NYSSA
Authors: CIRELLI ANTHONY
Published: February 2009

[In order to counter the dominance of subjectivity in modern German philosophy since Kant, the young Hans Urs von Balthasar appealed to the theocentric epistemology of Gregory of Nyssa. By means of a study of Balthasar's Présence et Pensée: Essai sur la philosophie religieuse de Grégoire de Nysse, the purpose of this essay will be to elucidate Balthasar's interpretation of the meaning and orientation of thought according to Gregory of Nyssa's epistemology. After an initial presentation of Balthasar's contention that for Gregory of Nyssa God qua Being (to einai) serves as the constitutive source of thought and, therefore, the necessary orientation for any philosophical reckoning of the meaning of thought, the following issues are addressed: 1.) The meaning of thought as erotic and egressive, 2.) the interpretation of imago dei in relation to thought, 3.) the Incarnation and the ultimate horizon of thought.]
Neurodevelopmental outcomes in children with cerebellar malformations: a systematic review
Authors: BOLDUC MARIE‐EVE , LIMPEROPOULOS CATHERINE
Published: February 2009

Cerebellar malformations are increasingly diagnosed in the fetal period. Consequently, their consideration requires stressful and often critical decisions from both clinicians and families. This has resulted in an emergent need to understand better the impact of these early life lesions on child development. We performed a comprehensive literature search of studies describing neurodevelopmental outcomes of cerebellar malformations between January 1997 and December 2007. Overall, the data suggested that children with isolated inferior vermis hypoplasia (IVH) and mega cisterna magna (MCM) have a good developmental outcome, whereas children with molar tooth sign/Joubert syndrome, vermis hypoplasia, pontocerebellar hypoplasia (PCH) type II, and cerebellar agenesis experience moderate to severe global developmental delays. Reports for Dandy−Walker malformation (DWM) were conflicting; however, the presence of a normally lobulated vermis and the absence of associated brain anomalies were associated with a more favourable outcome. Finally, children with isolated cerebellar hypoplasia experienced fewer impairments. Important methodological limitations highlighted include a lack of standardized outcome measure use in 79% of studies and the predominant use of retrospective study designs (85%), with 40% limited to case reports or case‐series. In summary, rigorous outcome studies describing the spectrum of disabilities in survivors are urgently needed to accurately delineate the long‐term neurodevelopmental consequences of cerebellar malformations.
Walking function, pain, and fatigue in adults with cerebral palsy: a 7‐year follow‐up study
Authors: OPHEIM ARVE , JAHNSEN REIDUN , OLSSON ELISABETH , STANGHELLE JOHAN K
Published: February 2009

Aim To compare walking function, pain, and fatigue in adults with cerebral palsy (CP) 7 years after an initial survey.

Method A multidimensional questionnaire was mailed to 226 people with unilateral (hemiplegic) or bilateral (diplegic) spastic CP who had participated in a 1999 survey. People with additional diagnoses were excluded. Special emphasis was placed on participants with deterioration in walking. The questionnaire was the same as in 1999.

Results One hundred and forty‐nine participants (76 males, 73 females; mean age 40y 5mo, SD 10y 7mo, range 24–76y) with a diagnosis of unilateral (n=81) or bilateral (n=68) spastic CP responded. Fifty‐two per cent of all participants reported deterioration in walking function since debut of walking, compared with 39% 7 years previously. In participants with bilateral CP, 71% reported deteriorated walking, compared with 37% of participants with unilateral CP. Participants with deteriorated walking function had greater pain frequency, pain intensity, impact of pain on daily activities, and physical fatigue and reduced balance. The number of people reporting overall mobility problems was almost double compared with 7 years previously.

Interpretation The main finding was an increased prevalence of deteriorated walking, significantly associated with bilateral spastic CP, pain, fatigue, and reduced balance. Rehabilitation programmes addressing these areas are needed.
Reconstructing community relationships: the impact of sampling error, ordination approach, and gradient length
Authors: Hirst Claire N. , Jackson Donald A.
Published: February 2009

Effectively summarizing complex community relationships is an important feature in studies such as biodiversity, global change, and invasion ecology. The reliability of such community summaries depends on the degree of sampling variability that is present in the data, the structure of the data, and the choice of ordination method, but the relative importance of these factors is not understood. We compared the validity of results from different ordination methods by applying five levels of sampling error to a simulated coenoplane model at two gradient lengths using two types of data (abundance and presence–absence). The multivariate methods we compared were correspondence analysis (CA), detrended correspondence analysis (DCA), non‐metric multidimensional scaling (NMDS), principal component analysis (PCA) and principal coordinates analysis (PCoA). Our results showed CA and PCA using presence–absence data were the most successful methods regardless of sampling error and gradient length, closely followed by the other methods using presence–absence data. With abundance data, PCA and CA were the most successful approaches with the short and long gradients, respectively. Approaches based on PCoA and NMDS using abundance data did not perform well regardless of the choice of distance measure used in the analysis. Both of these methods, along with the PCA using abundance data, were strongly affected by the longer gradient, leading to more distorted results.
Rivers in peril inside and outside protected areas: a systematic approach to conservation assessment of river ecosystems
Authors: Nel Jeanne L. , Roux Dirk J. , Maree Gillian , Kleynhans Cornelius J. , Moolman Juanita , Reyers Belinda , Rouget Mathieu , Cowling Richard M.
Published: February 2009

This paper establishes a framework within which a rapid and pragmatic assessment of river ecosystems can be undertaken at a broad, subcontinental scale, highlighting some implications for achieving conservation of river biodiversity in water‐limited countries. The status of river ecosystems associated with main rivers in South Africa was assessed based on the extent to which each ecosystem had been altered from its natural condition. This requires consistent data on river integrity for the entire country, which was only available for main rivers; tributaries were thus excluded from the analyses. The state of main river ecosystems in South Africa is dire: 84% of the ecosystems are threatened, with a disturbing 54% critically endangered, 18% endangered, and 12% vulnerable. Protection levels were measured as the proportion of conservation target achieved within protected areas, where the conservation target was set as 20% of the total length of each river ecosystem. Sixteen of the 112 main river ecosystems are moderately to well represented within protected areas; the majority of the ecosystems have very low levels of representation, or are not represented at all within protected areas. Only 50% of rivers within protected areas are intact, but this is a higher proportion compared to rivers outside (28%), providing some of the first quantitative data on the positive role protected areas can play in conserving river ecosystems. This is also the first assessment of river ecosystems in South Africa to apply a similar approach to parallel assessments of terrestrial, marine, and estuarine ecosystems, and it revealed that main river ecosystems are in a critical state, far worse than terrestrial ecosystems. Ecosystem status is likely to differ with the inclusion of tributaries, since options may well exist for conserving critically endangered ecosystems in intact tributaries, which are generally less regulated than main rivers. This study highlights the importance of healthy tributaries for achieving river conservation targets, and the need for managing main rivers as conduits across the landscape to support ecological processes that depend on connectivity. We also highlight the need for a paradigm shift in the way protected areas are designated, as well as the need for integrated river basin management plans to include explicit conservation visions, targets, and strategies to ensure the conservation of freshwater ecosystems and the services they provide.
A comparative evaluation of presence‐only methods for modelling species distribution
Authors: Tsoar Asaf , Allouche Omri , Steinitz Ofer , Rotem Dotan , Kadmon Ronen
Published: February 2009

In spite of increasing application of presence‐only models in ecology and conservation and the growing number of such models, little is known about the relative performance of different modelling methods, and some of the leading models (e.g. GARP and ENFA) have never been compared with one another. Here we compare the performance of six presence‐only models that have been selected to represent an increasing level of model complexity [BIOCLIM, HABITAT, Mahalanobis distance (MD), DOMAIN, ENFA, and GARP] using data on the distribution of 42 species of land snails, nesting birds, and insectivorous bats in Israel. The models were calibrated using data from museum collections and observation databases, and their predictions were evaluated using Cohen's Kappa based on field data collected in a standardized sampling design covering most parts of Israel. Predictive accuracy varied between modelling methods with GARP and MD showing the highest accuracy, BIOCLIM and ENFA showing the lowest accuracy, and HABITAT and DOMAIN showing intermediate accuracy levels. Yet, differences between the various models were relatively small except for GARP and MD that were significantly more accurate than BIOCLIM and ENFA. In spite of large differences among species in prevalence and niche width, neither prevalence nor niche width interacted with the modelling method in determining predictive accuracy. However, species with relatively narrow niches were modelled more accurately than species with wider niches. Differences among species in predictive accuracy were highly consistent over all modelling methods, indicating the need for a better understanding of the ecological and geographical factors that influence the performance of species distribution models.
Changes of traditional agrarian landscapes and their conservation implications: a case study of butterflies in Romania
Authors: Schmitt Thomas , Rákosy László
Published: February 2009

Global biodiversity is decreasing as a result of human activities. In many parts of the world, this decrease is due to the destruction of natural habitats. The European perspective is different. Here, traditional agricultural landscapes developed into species‐rich habitats. However, the European biodiversity heritage is strongly endangered. One of the countries where this biodiversity is best preserved is Romania. We analyse the possible changes in Romania's land‐use patterns and their possible benefits and hazards with respect to biodiversity. As model group, we used butterflies, whose habitat requirements are well understood. We determined the ecological importance of different land‐use types for the conservation of butterflies, underlining the special importance of Romania's semi‐natural grasslands for nature conservation. We found that increasing modern agriculture and abandonment of less productive sites both affect biodiversity negatively — the former immediately and the latter after a lag phase of several years. These perspectives are discussed in the light of the integration of Romania into the European Union.
Only some like it hot — quantifying the environmental niche of the loggerhead sea turtle
Authors: Hawkes Lucy A. , Broderick Annette C. , Coyne Michael S. , Godfrey Matthew H. , Godley Brendan J.
Published: February 2009

Although the Atlantic waters of North America support hundreds of thousands of loggerhead sea turtles (Caretta caretta), remarkably little is known regarding their migratory ecology and habitat use. We integrate satellite tracking with remotely sensed oceanographic data to uncover two different migratory strategies used by loggerhead turtles at the northern part of their range. Most turtles travelled from the nesting beach to forage at higher latitudes in summer, before migrating south to wintering grounds in the autumn. Others moved south after nesting to forage for up to 514 days and did not make an autumn migration. Both groups utilized warm waters at the very edge of the Gulf Stream during winter: for southerly turtles obviating seasonal migration, and for northerly turtles minimizing the distance, time and energy required to reach northern areas for subsequent foraging seasons, avoiding lethally cold winter temperatures in inshore waters at the same latitude, and reducing energy costs that would be incurred within the fast‐flowing Gulf Stream. Females made long resting dives of up to 7 h 24 min, effectively hibernating during the colder months. Offshore federal waters of the USA constitute a more important habitat for both foraging and wintering turtles than previously appreciated. These areas are potential hotspots for interaction with fisheries and proposed US military training activities and should receive special monitoring efforts to fully assess the extent of overlap.
A simulation approach to determine statistical significance of species turnover peaks in a species‐rich tropical cloud forest
Authors: Bach K. , Kessler M. , Gradstein S. R.
Published: February 2009

Use of β‐diversity indices in the study of spatial distribution of species diversity is hampered by the difficulty of applying significance tests. To overcome this problem we used a simulation approach in a study of species turnover of ferns, aroids, bromeliads, and melastomes along an elevational gradient from 1700 m to 3400 m in a species‐rich tropical cloud forest of Bolivia. Three parameters of species turnover (number of upper/lower elevational species limits per elevational step, Wilson–Shmida similarity index between adjacent steps) were analysed. Significant species turnover limits were detected at 2000 (± 50) m and 3050 m, which roughly coincided with the elevational limits of the main vegetation types recognized in the study area. The taxon specificity of elevational distributions implies that no single plant group can be used as a reliable surrogate for overall plant diversity and that the response to future climate change will be taxon‐specific, potentially leading to the formation of plant communities lacking modern analogues. Mean elevational range size of plant species was 490 m (± 369). Elevational range sizes of terrestrial species were shorter than those of epiphytes. We conclude that our simulation approach provides an alternative approach for assessing the statistical significance of levels of species turnover along ecological gradient without the limitations imposed by traditional statistical approaches.
Marine longitudinal biodiversity: causes and conservation
Authors: Briggs John C.
Published: February 2009

The horizontal temperature zones of the earth tend to restrict the latitudinal ranges of species but allow the possibility of exceedingly broad longitudinal dispersals. In the Tropical Zone, biodiversity on the continental shelves is not homogeneous but is concentrated in two conspicuous peaks, one in the Indo‐Pacific Ocean and the other in the Atlantic. The Indo‐Pacific biodiversity peak is located within a relatively small area called the East Indies Triangle. The Atlantic peak is located in the southern Caribbean Sea. Evidence that has been accumulated over the years indicates that each area functions as a centre of origin and evolutionary radiation. What are the causes of these concentrations and their present functions? A newly published model indicates a positive relationship between environmental temperature and the rate of speciation. While this helps to explain the generally high tropical diversity, and the negative relationship between diversity and latitude, it does not provide a reason for the longitudinal concentrations. But, other new research serves to substantiate previous indications of a positive relationship between speciation rate and species diversity. The existence of this positive feedback, together with some contributory factors, provides the reason why concentrations occur. The evolutionary radiation probably begins when the build‐up of species diversity reaches a critical level. The warm‐temperate biotas are derived from the tropics. Their northern longitudinal relationships tend to be minor but, in the southern hemisphere, the West Wind Drift is an important dispersal mechanism for both warm‐temperate and cold‐temperate species. The cold‐temperate biotas peaked in two areas, the North Pacific and the Antarctic; each has developed into a centre of origin. The continuous dispersal of well‐adapted species from the centres helps peripheral communities maintain diversity.
Dealing with uncertain absences in habitat modelling: a case study of a rare ground‐dwelling parrot
Authors: Gibson Lesley , Barrett Brent , Burbidge Allan
Published: February 2009

In the development of a species distribution model based on regression techniques such as generalized linear or additive modelling (GLM/GAM), a basic assumption is that records of species presence and absence are real. However, a common concern in many studies examining species distributions is that absences cannot be inferred with certainty. This is particularly the case where the species is rare, difficult to detect and/or does not occupy all available habitat considered suitable. The western ground parrot (Pezoporus wallicus flaviventris) of southern Western Australia, Australia, is a case in point, as not only is it rare and difficult to detect, but it is also unlikely to occupy all available suitable habitat. A recent survey of ground parrots provided the opportunity to develop a predictive distribution model. As the data were susceptible to false absences, these were replaced with randomly selected ‘pseudo’ absences and modelled using GLM. As a comparison, presence‐only information was modelled using a relatively new approach, MAXENT, a machine‐learning technique that has been shown to perform comparatively well. The predictive performance of both models, as assessed by the receiver operating characteristic plot (ROC) was high (AUC > 0.8), with MAXENT performing only marginally better than the GLM. These approaches both indicated that the ground parrot prefers areas relatively high in altitude, distant from rivers, gently sloping to level habitat, with an intermediate cover of vegetation and where there is a mosaic of vegetation ages. In this case, the use of presence‐only information resulted in the identification of important environmental attributes defining the occurrence of the ground parrot, but additional factors that account for the inability of the bird to occupy all suitable habitat should be a component of model refinement.
Multiscale modelling of the drivers of rainforest boundary dynamics in Kakadu National Park, northern Australia
Authors: Banfai Daniel S. , Brook Barry W. , Bowman David M. J. S.
Published: February 2009

Understanding the relative importance of factors driving savanna–forest dynamics is vital as changes in the extent of tropical forests can have major impacts on global climate and carbon balance, biodiversity, and human well‐being. Comparison of aerial photographs for 50 rainforest patches in Kakadu National Park had previously revealed a landscape wide expansion of rainforest boundaries between 1964 and 2004. Here, we used generalized linear and mixed effects models to assess the role of fire, buffalo impact, and patch characteristics in determining the rate of boundary change. The analysis was conducted at both the patch scale, and within‐patch (plot) scale, to capture the different processes operating. At the patch scale, the rate of change was best explained by rainforest type and historical buffalo impact. Fire activity, patch size, and fragmentation were not important predictors of the rate of change. At the plot scale, distance from rainforest edge was the most important predictor of the probability of change, while the fragmentation and aspect of the boundary were unimportant. Rainforest expansion has occurred through a process of margin extension rather than eruption of new patches. The rainforest expansion is consistent with having been driven primarily by shifts in global change phenomena, such as increased rainfall and atmospheric CO2, rather than changes in disturbance regime. It appears that the current fire regimes are not sufficiently destructive to limit the overall expansion of the rainforest patches. Rainforest type and historical buffalo impact have mediated the rate of change at the patch scale.
Multiple pathways for invasion of anurans on a Pacific island
Authors: Christy Michelle T. , Savidge Julie A. , Rodda Gordon H.
Published: February 2009

Since 1937, thirteen species of non‐indigenous anurans have made their way to Guam. Of these, at least six have established breeding populations. Various pathways led to the introduction of these species to the island. The only anuran intentionally introduced wasChaunus marinus(formerlyBufo marinus), which was brought to Guam as a biocontrol agent.Kaloula picta, K. pulchra, Polypedates leucomystax, and probablyLitoria fallaxarrived as stowaways via maritime or air‐transport vessels.Eleutherodactylus coquiandEuhyas(formerlyEleutherodactylus)planirostrisappear to have entered Guam through the horticultural trade. Specimens ofPseudacris regillawere found among agricultural products and Christmas trees. Five species have been transported to Guam via the aquacultural trade. The importation of tilapia, milkfish, and white shrimp from China, Hong Kong, Taiwan, and the Philippines was associated with the introduction to Guam ofFejervarya cancrivora, F. limnocharissensu lato,Microhyla pulchra, Polypedates megacephalus, andSylvirana guentheri(formerlyRana guentheri). Presently, no quarantine or containment guidelines have been established for Guam's aquacultural industry.
How well do we know the Antarctic marine fauna? A preliminary study of macroecological and biogeographical patterns in Southern Ocean gastropod and bivalve molluscs
Authors: Clarke Andrew , Griffiths Huw J. , Linse Katrin , Barnes David K. A. , Crame J. Alistair
Published: February 2009

The aim of this study was to use data for gastropod and bivalve molluscs to determine whether the fauna of the Southern Ocean is sufficiently well known to establish robust biogeographical and macroecological patterns. We chose molluscs for this work because they have been collected by almost every biological expedition to Antarctica, and are relatively well known taxonomically. Sampling of the continental shelf fauna is reasonably full and extensive, although new species are still being described and there are significant gaps in sampling off Wilkes Land and in the Bellingshausen and Amundsen Seas. Species richness was highest in those areas that have been subject to the most intense research activity and this pattern remained even after correction for sampling intensity. The low species richness of the Southern Ocean molluscan fauna compared with many tropical sites is confirmed, and is related principally to the absence of the large number of rare taxa that characterize some tropical assemblages. There is as yet no convincing evidence for a latitudinal cline in molluscan diversity within the Southern Ocean. Multivariate analyses defined biogeographical provinces very similar to those established previously, though they also identified a number of finer‐scale sub‐provinces including a small area of high diversity off Enderby Land. Most Southern Ocean gastropods and bivalves are rare, with limited distributions; relatively few taxa have circumpolar distributions.
Where might the western Svalbard tundra be vulnerable to pink‐footed goose (Anser brachyrhynchus) population expansion? Clues from species distribution models
Authors: Wisz Mary S. , Tamstorf Mikkel P. , Madsen Jesper , Jespersen Martin
Published: February 2009

Pink‐footed geese (Anser brachyrhynchus) breed in the Arctic, where their populations have doubled since the 1980s. There is concern that nesting geese disturb the fragile tundra and lead to a trophic cascade with strong top‐down effects on vegetation and soil processes. A better understanding of the distribution of geese and factors that influence nest site selection is needed to highlight potential problem areas and assess the potential for further population expansion. To help infer the importance of environmental variables on nest site selection, we built generalized additive models using nest observations collected in 2003 and 2004 from the Sassendalen valley, Svalbard, along with a suite of geographical information system explanatory predictors. The fit of the models was very high (explaining over 72% of the deviance), and predictive power to independent samples indicated useful predictions that could discriminate between presences and absence of nests very well (area under the receiver operating characteristic curves exceeded 0.88). Significant predictors of nest site selection included elevation, slope, aspect, percentage of snow cover, percentage of foraging habitat cover, and a spatial autocovariate. Spatial predictions were applied to the broader Nordenskiöldsland region of Svalbard and highlighted the importance of previously unsurveyed locations for nesting.
Biodiversity surrogate groups and conservation priority areas: birds of the Brazilian Cerrado
Authors: Pinto Míriam Plaza , Diniz‐Filho José Alexandre Felizola , Bini Luis Mauricio , Blamires Daniel , Rangel Thiago Fernando L. V. B.
Published: February 2009

The choice of surrogates of biodiversity is an important aspect in conservation biology. The quantification of the coincidence in the spatial patterns of species richness and rarity between different groups and the vulnerability of groups are different approaches frequently considered to accomplish this task. However, a more appropriate approach is to verify the efficiency of priority networks selected using information from one group of organisms to capture the biodiversity of other groups. Using a deconstructive approach, the main purposes of this study were to evaluate the performance of some orders and families of birds in the Cerrado biome (a savanna‐like biome) as surrogates of other bird groups, in a pairwise analysis, and to investigate the characteristics of these groups that predict the efficiency in representation of other groups. We used biogeographical data on bird orders or families with more than 10 species that occur in the Brazilian Cerrado. The best surrogate group was the Thamnophilidae. Moreover, this group is not the most specious, favouring further survey efforts that are necessary to verify the conservation value of areas at suitable scales. The majority of the species from this family are dependent on forest habitats, one of the characteristics that most influenced representativeness level, probably due to the spatial distribution of these habitats throughout the Brazilian Cerrado. Beta diversity patterns of the different groups also affected representativeness, and our analyses showed that the networks selected by a surrogate group will be more effective in the representation of other groups of species if their patterns of beta diversity (not richness) are correlated.
Testing predictions of beetle community patterns derived empirically using remote sensing
Authors: Lassau Scott A. , Hochuli Dieter F.
Published: February 2009

Patterns generated from ecological surveys are rarely tested in similar habitats to assess the accuracy of predictions. Testing empirically derived predictions provides a strong tool for establishing the consistency of general patterns in ecology. We test the consistency of beetle community associations with habitat complexity in open canopy forests and make both community and morphospecies‐level comparisons with results from a previous study. We use Normalized Difference Vegetation Indices (NDVIs) from remote sensing as a surrogate for habitat complexity. The positive relationships between NDVIs and site‐based beetle species richness and abundance were consistent in open canopy forests both south and north of Sydney, Australia. NDVIs were also useful for predicting differences in beetle composition in open canopy forests. Taxon‐specific responses to NDVI differences in ‘southern forests’ were very similar to responses in ‘northern forests’, most likely reflecting beetle trophic roles. This study shows that NDVIs can be used as rapid biodiversity indicators, when integrated with identified faunal responses to vegetation structure, provided that the lower vegetation strata may be measured by remote sensing.
How far and how fast do bryophytes travel at the landscape scale?
Authors: Hutsemekers V. , Dopagne C. , Vanderpoorten A.
Published: February 2009

Dispersal ability is a factor of prime importance to explain biotic distributions. Yet, it is extremely difficult to measure directly. In this study, we take advantage of the natural experimental design of slag heap colonization in Belgium to document the timing and range of dispersal of bryophytes at the landscape scale. On the basis of a species atlas with a 4 × 4 km grid, the minimum distance separating species found on 52 slag heaps from potential source populations was determined. Minimum dispersal rates were inferred by coupling the information on minimum distance between slag heap and source populations with time since colonization. The number of species per slag heap is significantly correlated with time since colonization and area size. The frequency distribution of the longest dispersal events is highly skewed, with 44% of the species recruited within the nearest 6 km. In the remaining 56% of the species, recruitments from source populations located within a range of at least 6–86 km occurred within a period of less than 50 years. The majority of the species that are not recruited within the nearest vicinity of the slag heaps, including rare species at the regional scale, occur on slag heaps that have been colonized for 25–50 years. Most recently colonized slag heaps are indeed characterized by ‘fugitive’, weedy species, whereas slag heaps that have been colonized for > 50 years tend to accumulate perennial species with a ‘stayer’ life strategy. These observations suggest that rare species may display the dispersal ability to travel across the landscape, but are subsequently limited by their ability to establish a viable community because of more competitive neighbours. Rare species therefore tend to accumulate at intermediate colonization stages, which represent a trade‐off between an increasing probability of colonization with time and a decreasing probability of establishment due to competition.
Solving the maximum representation problem to prioritize areas for the conservation of terrestrial mammals at risk in Oaxaca
Authors: Illoldi‐Rangel Patricia , Fuller Trevon , Linaje Miguel , Pappas Christopher , Sánchez‐Cordero Víctor , Sarkar Sahotra
Published: February 2009

Oaxaca, located in south‐west México within the Mesoamerican biodiversity hotspot, holds exceptionally high biodiversity for several taxa, including mammals. It has four decreed natural protected areas (NPAs) covering 5% of its total area, but only three of these, covering only 0.2% of the area, are strictly protected as National Parks. The current study develops ecological niche models for 183 terrestrial mammals for use as biodiversity surrogates in a systematic conservation planning exercise. Forty‐five of these species were selected on the basis of their being either endangered or threatened or otherwise listed under the Mexican Red List or because they were endemic to either Oaxaca or to Mexico. The niche models were constructed with a machine‐learning algorithm (GARP, Genetic Algorithm for Rule‐Set Prediction) and refined by restricting each model to sites with suitable vegetation and habitat patches contiguous with known occurrences of the species. If the entire predicted geographical distribution of each of the 45 species listed above is put under protection, the entire state of Oaxaca gets included. Therefore, we imposed different constraints on the maximum area that can be put under protection (5–30% of the area of Oaxaca) and selected nominal conservation area networks based on different percentage representation targets for the species’ modelled distributions based on their conservation status (10–100%). The area selection utilized a rarity‐ and complementarity‐based algorithm (in the ResNet software package). The goal was to have as many as possible of the 45 species at risk meet their specified representation targets in the budgeted area. The methods developed here combine ecological niche modelling and area prioritization algorithms for integrated conservation planning in a protocol that is suitable for other highly biodiverse regions.
Extinction patterns in the avifauna of the Hawaiian islands
Authors: Boyer Alison G.
Published: February 2009

Through the continuing accumulation of fossil evidence, it is clear that the avifauna of the Hawaiian Islands underwent a large‐scale extinction event around the time of Polynesian arrival. A second wave of extinctions since European colonization has further altered this unique avifauna. Here I present the first systematic analysis of the factors characterizing the species that went extinct in each time period and those that survived in order to provide a clearer picture of the possible causal mechanisms. These analyses were based on mean body size, dietary and ecological information and phylogenetic lineage of all known indigenous, non‐migratory land and freshwater bird species of the five largest Hawaiian Islands. Extinct species were divided into ‘prehistoric’ and ‘historic’ extinction categories based on the timing of their last occurrence. A model of fossil preservation bias was also incorporated. I used regression trees to predict probability of prehistoric and historic extinction based on ecological variables. Prehistoric extinctions showed a strong bias toward larger body sizes and flightless, ground‐nesting species, even after accounting for preservation bias. Many small, specialized species, mostly granivores and frugivores, also disappeared, implicating a wide suite of human impacts including destruction of dry forest habitat. In contrast, the highest extinction rates in the historic period were in medium‐sized nectarivorous and insectivorous species. These differences result from different causal mechanisms underlying the two waves of extinction.
Common species have lower taxonomic diversity Evidence from the urban floras of Brussels and Rome
Authors: Ricotta Carlo , Godefroid Sandrine , Celesti‐Grapow Laura
Published: February 2009

The species pool hypothesis claims that the large‐scale regional species pool is the chief parameter in determining small‐scale species richness through filtering of species that can persist within a community on the basis of their tolerance of the abiotic environment. Accordingly, different environmental conditions give rise to different species assemblages. From a taxonomic perspective, under the assumption of trait conservatism, co‐occurring species that experience similar environmental conditions are likely to be more taxonomically similar than ecologically distant species. The next step consists in understanding how commonness and rarity of individual species produce the observed taxonomic diversity. In this paper, the importance of environmental filtering in regulating the taxonomic structure of rare and common plant species in the urban floras of Brussels (Belgium) and Rome (Italy) is tested. First, we computed the taxonomic diversity of the rare and common species of Brussels and Rome based on the branching topology of the Linnaean taxonomic trees. Next, using a randomization procedure, we determined whether the taxonomic diversity of the rare species was significantly higher than the diversity of the common species. Results show that, for both urban floras, common species that shape the community matrix and experience similar environmental conditions have a taxonomic diversity that is significantly lower than that of the rare species that represent a relatively incidental set of species of more ‘disperse’ origin. Finally, from a conservation/management perspective our results imply that, given their high taxonomic heterogeneity, the protection of rare species is a central issue for preserving high levels of diversity in urban areas.