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Open access (OA) publishing, whereby authors, their institutions, or their granting bodies pay or provide a repository through which peer-reviewed work is available online for free, is championed as a model to increase the number of citations per paper and disseminate results widely, especially to researchers in developing countries. We compared the number of citations of OA and non-OA papers in six journals and four books published since 2000 to test whether OA increases number of citations overall and increases citations made by authors in developing countries. After controlling for type of paper (e.g., review or research paper), length of paper, authors’ citation profiles, number of authors per paper, and whether the author or the publisher released the paper in OA, OA had no statistically significant influence on the overall number of citations per journal paper. Journal papers were cited more frequently if the authors had published highly cited papers previously, were members of large teams of authors, or published relatively long papers, but papers were not cited more frequently if they were published in an OA source. Nevertheless, author-archived OA book chapters accrued up to eight times more citations than chapters in the same book that were not available through OA, perhaps because there is no online abstracting service for book chapters. There was also little evidence that journal papers or book chapters published in OA received more citations from authors in developing countries relative to those journal papers or book chapters not published in OA. For scholarly publications in conservation biology, only book chapters had an OA citation advantage, and OA did not increase the number of citations papers or chapters received from authors in developing countries. [ABSTRACT FROM AUTHOR]

Local-regional (LR) species diversity plots were conceived to assess the contribution of regional and local processes in shaping the patterns of biological diversity, but have been used also to explore the scaling of diversity in terms of its alpha, beta, and gamma components. Here we explore the idea that patterns in the geographical ranges of species over a continent can determine the shape of small region to large region (SRLR) plots, which are equivalent to LR plots when comparing the diversity of sites at two regional scales. To test that idea, we analysed the diversity patterns at two regional scales for the mammals of North America, defined as the mainland from Alaska and Canada to Panama. We developed a theoretical model relating average range size of species over a large-scale region with its average regional point species diversity (RPD). Then, we generated a null model of expected SRLR plots based on theoretical predictions. Species diversities at two scales were modelled using linear and saturation functions for Type I and Type II SRLR relationships, respectively. We applied the models to the case of North American mammals by examining the regional diversity and the RPD for 21 large-scale quadrats (with area equal to 160,000 km2), arranged along a latitudinal gradient. Our model showed that continental and large-scale regional patterns of distribution of species can generate both types of SRLR relationship, and that these patterns can be reflected in LR plots without invoking any kind of local processes. We found that North American nonvolant mammals follow a Type I SRLR relationship, whereas bats follow a Type II pattern. This difference was linked to patterns in which species of the two mammalian groups distribute in geographical space. Traditional LR plots and the new SRLR plots are useful tools in exploring the scaling of species diversity and in showing the relationship between distribution and diversity. Their usefulness in comparing the relative role of local and regional processes is, however, very limited. [ABSTRACT FROM AUTHOR]

To quantify the latitudinal gradient in species richness in the New World Triatominae and to explore the species-energy and area hypotheses as possible causes. The gradient was studied for North and South America, between 43° N and 32° S. A database was constructed containing the geographical distribution of the 118 New World Triatominae species based on data extracted from several published sources. Species richness was recorded as the number of species present within 5° latitudinal bands. We used univariate and multivariate models to analyse the relationship between area within each latitudinal belt, land surface temperature, and potential evapotranspiration as explanatory variables, and species richness. All variables were georeferenced and data were extracted using a GIS. Species richness of Triatominae increases significantly from the poles towards the Equator, peaking over the 5°−10 ° S latitudinal band. It increases according to a linear model, both north and south of the Equator, although a quadratic model fits better to southern hemisphere data. Richness correlates with habitable geographical area, when it is analysed through a nonlinear multiple regression factoring out latitude, only in the southern hemisphere. Regarding the species-energy hypothesis, a multiple regression analysis controlling the effect of latitude shows a significant relationship between temperature and species richness. This effect is more pronounced in the southern hemisphere. Species richness shows a strong longitudinal trend south of the Equator (increasing to the east), but not north of the Equator. This differential pattern is reflected in significant interactions between longitude and both latitude and temperature in models of the species richness of the New World Triatominae. To our knowledge, this is the first time that a latitudinal gradient in species richness has been shown and analysed for obligate haematophagous organisms, and it shows that the species–energy hypothesis can account for this phenomenon. This relationship is stronger in the southern hemisphere. [ABSTRACT FROM AUTHOR]

Presents upcoming research papers on biochemistry to be published in "European Journal of Biochemistry." Discussion of the molecular cloning and sequencing of a cDNA encoding the acyl carrier protein; Exploration of the primary structure of human thyroglobulin; Examination of the reversible activation of hydrogenase from Escherichia coli.

Presents a list of forthcoming papers to be published in 1980 issues of the "European Journal of Biochemistry." Subjects; Authors.

First-year majors organismal biology courses are frequently taught as survey courses that promote memorization rather than synthesis of biological concepts. To address the shortcomings of this approach, we redesigned the organismal portion of our introductory biology curriculum to create a "Foundations of Form and Function" course. Foundations of Form and Function introduces different organismal forms and focuses on the relationship between those forms and the execution of key physiological functions. Goals of our new course include the following: developing student recognition of common characteristics that unite living organisms as well as features that distinguish taxonomic groups, facilitating student understanding of how organisms accomplish similar functions through different forms, and reinforcing course themes with independent student research. In this paper, we describe course learning outcomes, organization, content, assessment, and laboratory activities. We also present student perspectives and outcomes of our course design based on data from four years of student evaluations. Finally, we explain how we modified our course to meet remote learning and social-distancing challenges presented by the COVID-19 pandemic in 2020 and 2021. [ABSTRACT FROM AUTHOR]

Presents information on forthcoming papers and review topics, in January 2003 issue of the journal 'Munksgaard International Publishers.' Review topics to be released, starting from February to December 2003; Papers on organelle acidification and disease; Protein structure and import into the peroxisomal matrix.

Lists forthcoming papers to be featured in the "European Journal of Biochemistry."

Presents a list of papers scheduled to be published in the "European Journal of Biochemistry," as of August 15, 1992. Topics; Authors.

Lists the forthcoming papers to be published in the "European Journal of Biochemistry."

Lists research papers scheduled for publication in the "European Journal of Biochemistry," in 1989. Topics; Authors; Data presented.

Lists the forthcoming papers to be published in the "European Journal of Biochemistry."

Presents a list of forthcoming papers scheduled to be pubilshed in the "European Journal of Biochemistry," in 1988. Subjects; Authorship.

Presents a list of forthcoming papers scheduled for publication in the "European Journal of Biochemistry," in 1988. Topics; Authors; Studies and data to be presented.

Lists the forthcoming papers to be published in the "European Journal of Biochemistry."

Some invasion biologists contend their science has reached a consensus on 4 facts: cost estimates of the effects of nonindigenous species provided in papers by Pimentel et al. are credible; invasive species generally, not just predators, pose significant extinction threats; characteristic biological differences distinguish novel from native species, ecosystems, communities, and processes; and ontological dualism, which distinguishes between natural and anthropogenic processes and influences, plays a useful role in biological inquiry. I contend there is no convincing empirical evidence for any of these propositions. Leading invasion biologists cite their agreement about these propositions as evidence for them and impugn the motives of critics who believe consensus should be based on evidence not the other way around. Article impact statement: Contested invasion biology issues are clarified so opposition groups can together achieve shared goals with evidence‐based solutions. [ABSTRACT FROM AUTHOR]

Lists titles of research papers to be published in the "European Journal of Biochemistry."

Summary: There have been substantial strides forward in our understanding of the contribution of regulatory T (Treg) cells to cancer immunosuppression. In this issue, we present a series of papers highlighting emerging themes on this topic relevant not only to our understanding of the fundamental biology of tumour immunosuppression but also to the design of new immunotherapeutic approaches. The substantially shared biology of CD4+ conventional T (Tconv) and Treg cells necessitates a detailed understanding of the potentially opposing functional consequences that immunotherapies will have on Treg and Tconv cells, a prominent example being the potential for Treg‐mediated hyperprogressive disease following anti‐PD‐1 therapy. Such understanding will aid patient stratification and the rational design of combination therapies. It is also becoming clear, however, that Treg cells within tumours exhibit distinct biological features to both Tconv cells and Treg cells in other tissues. These distinct features provide the opportunity for development of targeted immunotherapies with greater efficacy and reduced potential for inducing systemic toxicity. [ABSTRACT FROM AUTHOR]

We have developed a machine learning framework to accurately extract complex genetic interactions from text. Employing type-specific classifiers, this framework processes research articles to extract various biological events. Subsequently, the algorithm identifies regulation events that take other events as arguments, allowing a nested structure of predictions. All predictions are merged into an integrated network, useful for visualization and for deduction of new biological knowledge. In this paper, we discuss several design choices for an event-based extraction framework. These detailed studies help improving on existing systems, which is illustrated by the relative performance gain of 10% of our system compared to the official results in the recent BioNLP'09 Shared Task. Our framework now achieves state-of-the-art performance with 37.43 recall, 54.81 precision and 44.48 F-score. We further present the first study of feature selection for bio-molecular event extraction from text. While producing more cost-effective models, feature selection can also lead to a better insight into the complexity of the challenge. Finally, this paper tries to bridge the gap between theoretical relation extraction from text and experimental work on bio-molecular interactions by discussing interesting opportunities to employ event-based text mining tools for real-life tasks such as hypothesis generation, database curation and knowledge discovery. [ABSTRACT FROM AUTHOR]

The formation of any tissue involves differentiation, cell dynamics and interactions with adjacent tissues. This paper suggests that the complexity of the system as a whole can be represented as a mathematical graph, that is, a set of connected triples of the general form [ term] < relationship> [ term]. Computationally, such graphs are widely used for modeling data; visually, they form hierarchies and networks. For morphogenesis, the triples are of the general structure < noun > < verb > < noun >, where nouns cover tissues, molecules and networks and verbs describe processes such as moves, differentiates, grows and apoptoses. The paper considers the general formalism of graphs, where graphs are already used in biology, and how developmental anatomy may be described using this format. Representing morphogenesis as a visual graph is complicated as the formalism has to incorporate tissue types, molecular signals, networks, dynamic processes and some aspects, at least, of tissue geometry. The formation of a capillary sprout is chosen as an example of how this complexity can be represented graphically, with colour used to distinguish tissues and molecules. There are three key benefits, beyond its compactness, in using the graph formalism of morphogenesis to complement experimentation. First, it emphasizes the distributed nature of causality in morphogenesis. Secondly, producing all the triples for the visual graph requires explicit formalization of each aspect of the process, and this, in turn, often exposes gaps in knowledge and so suggests new experiments. Thirdly, once the graph has been formalized, triples can be annotated with associated information or IDs (e.g. cell types, publications, gene-expression data) that link to external online resources that may be regularly updated. Such annotations allow the graph to be viewed as a self-maintaining review. The graph approach sees dynamic processes as the drivers of developmental momentum and, because the same processes are used many times during development, it seems appropriate to view them as modules and their underlying networks as genomic subroutines. [ABSTRACT FROM AUTHOR]

The first scientific works that describe corporeal and mental qualities as the result of hereditary transmission appeared around 1800. While the Enlightenment had assumed or posited a potentially free self, new findings in medicine and biology indicated an inherited burden which determines the individual. Reading E.T.A. Hoffmann's Elixiere des Teufels in the context of Erasmus Darwin's Zoonomia, this paper suggests the necessity of opening a new dimension of the discourse on the novel by highlighting the significance of the heredity debate in the life sciences for both the novel's definition of the individual and the novel's self-understanding. The paper argues that Hoffmann questions the empirically justified truth claim of the emerging scientific disciplines and rejects attempts to apply biological models to human psychological and moral behavior. E.T.A. Hoffmann's Elixiere are presented as a key moment in the formation of the novel as that area of the modern world which functions as a meta-critical space for the sciences. [ABSTRACT FROM AUTHOR]

Presents a list of forthcoming papers on biochemistry which appeared in the January 1983 issue of the "European Journal of Biochemistry."

The case-only design provides one approach to assess possible interactions between genetic and environmental factors. It has been shown that if these factors are conditionally independent, then a case-only analysis is not only valid but also very efficient. However, a drawback of the case-only approach is that its conclusions may be biased by genotyping errors. In this paper, our main aim is to propose a method for analysis of case-only studies when these errors occur. We show that the bias can be adjusted through the use of internal validation data, which are obtained by genotyping some sampled individuals twice. Our analysis is based on a simple and yet highly efficient conditional likelihood approach. Simulation studies considered in this paper confirm that the new method has acceptable performance under genotyping errors. [ABSTRACT FROM AUTHOR]

This paper offers highlights from the 100 (plus) years of the Botanical Society of America (BSA) and draws extensively on the archives of the BSA. In addition to examining the founding of the society and the attempt to "professionalize" botany in late 19th century America, the paper also explores the complex relations between the BSA and a number of related societies in the United States, the Society's struggle to create a coherent identity for itself, the place of botany as a whole in the context of the burgeoning biological sciences in the 20th century, and the changing role of the BSA in an international context. The paper assesses both the achievements and the challenges facing the BSA. It closes by offering some historical reflections on the status of "botany" as a science and the historical significance of terms like "plant biology" and "plant science." [ABSTRACT FROM AUTHOR]

The aim of this paper is to enable those who have never reconstructed a phylogeny to do so from scratch. The paper does not attempt to be a comprehensive theoretical guide, but describes one rigorous way of obtaining phylogenetic trees. Those who follow the methods outlined should be able to understand the basic ideas behind the steps taken, the meaning of the phylogenetic trees obtained and the scope of questions that can be answered with phylogenetic methods. The protocols have been successfully tested by volunteers with no phylogenetic experience. [ABSTRACT FROM AUTHOR]

In an influential paper, Harte et al. highlighted the scaling or ‘self-similar’ character of the power law species–area relationship (SAR), and used this feature to derive a species abundance distribution (SAD) and an endemics–area relationship. Here I show that their analysis was incorrect and leads to unrealistic results. I develop a different approach and obtain different results, both for SAD and for endemism. In particular, I show that the power law SAR is naturally associated with the power law statistical distribution, which is the only self-similar distribution and closely matches empirical SADs. The results in this paper shed light on some of the main issues that have been discussed with regard to SARs: their relationship with the lognormal and with the neutral theory, the relative importance of sampling effects vs other mechanisms, and the deviations from a power law. The equations that I develop are simple and easy to apply to field studies. [ABSTRACT FROM AUTHOR]

This paper is concerned with forging new links between geography and biology and technology by delivering a set of shocks to the meaning of accepted categories like ‘nature’ and ‘technology’. To achieve these dual aims, the paper will double click on the icon ‘intelligence’. ‘Intelligence’ prioritizes the active shaping of environments. It thereby allows space for the spaces of the world to themselves become a part of intelligibility and intellect as elements of distributed cognition and, as will become clear, pre-cognition. The paper argues that such a conception of sentience can provide a series of new perspectives, as well as a pressing ethical challenge. [ABSTRACT FROM AUTHOR]

Anna Meyer published her first (and apparently last) scientific paper in 1913, in which she reported, in part, on the organization of the renogenital systems in the "Diotocardia" and "Monotocardia," and the evolutionary signal present in this character suite. Meyer's phylogeny broke with conventional wisdom of her time and she reconstructed early gastropod evolution as a sequence of branching events rather than a continuous grade. Her phylogeny was ignored because it did not correspond to the well-ordered grades that came to dominate gastropod systematics for over 75 years, but her schematics of renogenital configurations have been featured in the literature for over 55 years, sometimes without citation and redrawn to show a different set of relationships. We hope that the translation of her paper from German into English (http://www.ucmp.berkeley.edu/collections/archdat.html) will make her contribution more accessible to workers. [ABSTRACT FROM AUTHOR]

State-of-the-art techniques for analysing X-ray absorption spectra are reviewed, with an eye to biological applications. Recent attempts to perform full spectral fitting of the XANES energy region and beyond for the purpose of structural analysis have met with encouraging success. The present paper analyses the theoretical motivations behind this success and indicates routes for future improvements. The theoretical background is not entirely new, although the point of view is, and some sections and appendices present material that the authors believe has never been published before. The aim of this paper is to provide a theoretical analysis that is as self-contained as possible. [ABSTRACT FROM AUTHOR]

This paper reviews the results of several years' study by a multidisciplinary team comprising geneticists, physiologists, ecologists and statisticians of abiotic stress tolerance in barley. The strategy involves genetic fingerprinting of wild barley lines (Hordeum spontaneum C. Koch) from a range of habitats and testing these for responses to abiotic stresses under controlled conditions. Multiple regression analysis is used to identify genetic markers associated with experimentally determined stress responses. These data are related to site-of-origin ecogeographic data and used to identify areas of useful wild variation. Markers associated with traits of interest can be mapped in genetic mapping populations, revealing areas of the barley genome carrying genes controlling stress responses. This paper highlights our work on associations of amplied fragment length polymorphisms with salt tolerance and describes some initial results of the use of SSRs in studying drought tolerance in barley. [ABSTRACT FROM AUTHOR]

An index measuring interaction importance ( Iimp) was proposed in a paper published on 2010 by the Journal of Ecology. This index, now widely used by researchers, has been claimed to symmetrically range in the interval (−1, 1), with negative values for competition and positive values for facilitation., Here, the index properties are carefully analysed, and it is demonstrated that Iimp can never exceed the value of 0.5 in facilitation., Several years have passed since its publication, yet nobody has corrected the inexact index range, and several researchers continue to inaccurately refer to it. Overlooking this lack of symmetry could potentially lead to biased conclusions., Synthesis. Iimp cannot be treated as a symmetric index for negative and positive interactions. This is only the last of several concerns discussed in literature: current approaches to measuring interaction importance still need to be debated and analysed in depth. [ABSTRACT FROM AUTHOR]

The Food and Agriculture Organization (FAO) predicts that food production must rise 70% over the next 40 years to meet the demands of a growing population that is expected to reach nine billion by the year 2050. Many facets of basic plant science promoted by the Botanical Society of America are important for agriculture; however, more explicit connections are needed to bridge the gap between basic and applied plant research. This special issue, Speaking of Food: Connecting Basic and Applied Plant Science, was conceived to showcase productive overlaps of basic and applied research to address the challenges posed by feeding billions of people and to stimulate more research, fresh connections, and new paradigms. Contributions to this special issue thus illustrate some interactive areas of study in plant science--historical and modem plant-human interaction, crop and weed origins and evolution, and the effects of natural and artificial selection on crops and their wild relatives. These papers provide examples of how research integrating the basic and applied aspects of plant science benefits the pursuit of knowledge and the translation of that knowledge into actions toward sustainable production of crops and conservation of diversity in a changing climate. [ABSTRACT FROM AUTHOR]

The article discusses the significance of citing references in research works pertaining to ecology and the environment. According to the author, research works and such other papers about ecology the foundation of ecological science. The credibility of scientific work depends on its verifiable citations which functions to support the arguments presented in the paper. However, the author argues that there is no existing studies which explore the suitability or even fidelity of citations in ecological journals.

Systems biology is a new, fashionable and well-funded discipline, which to quote from a recent review aims to ‘examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism...’ (Kitano, H. (2002) Science 295:1662–1664). Systems biology will do this by profiting from the vast amounts of biological information that are available in the genomics era and make extensive use of computer modelling. But: ‘many breakthroughs in experimental devices, advanced software and analytical methods are required before the achievements of system biology can live up to their much-touted potential’. This edition of Molecular Microbiology contains a paper that is the product of traditional experimental biology but which could serve as a test case for systems biology. The paper shows how bacteria integrate such disparate subsystems as DNA restriction, homologous recombination and regulated proteolysis to protect their chromosomes from degradation. When systems biology can predict this level of choreography, it will be a mature discipline. [ABSTRACT FROM AUTHOR]

This paper describes our bio-event extraction system developed for the BioNLP 2009 Shared Task 2, with focus on its capability of extracting secondary biological event arguments from literature. Shared Task 2 is particularly interesting because when browsing literature, biologists often need to understand conditions surrounding biological events, which are usually expressed by secondary event arguments (e.g., binding sites). To achieve our goal, we take an approach that extracts n-ary relations from text using event extraction constraints automatically generated from a training corpus. Event constraints consist of sequences of trigger words and semantic roles which we automatically identify using Conditional Random Fields (CRFs). Unlike most other systems participating in this shared task, our system is light-weight and relies on neither external resources (e.g., Ontologies and dictionaries) nor natural language processing software (e.g., POS taggers and parsers). The official test results show that our approach performed well on extracting secondary arguments in Task 2, yielding the highest precision at 76.62% and the second highest F-measure at 43.22%. [ABSTRACT FROM AUTHOR]

In this paper, we trace the route by which genetics could ultimately connect to issue attitudes and suggest that central to this connection are chronic dispositional preferences for mass-scale social rules, order, and conduct-what we label political ideology. The need to resolve bedrock social dilemmas concerning such matters as leadership style, protection from outgroups, and the degree to which norms of conduct are malleable, is present in any large-scale social unit at any time. This universality is important in that it leaves open the possibility that genetics could influence stances on issues of the day. Here, we measure orientation to these bedrock principles in two ways-a survey of conscious, self-reported positions and an implicit association test (IAT) of latent orientations toward fixed or flexible rules of social conduct. In an initial test, both measures were predictive of stances on issues of the day as well as of ideological self-labeling, thereby suggesting that the heritability of specific issue attitudes could be the result of the heritability of general orientations toward bedrock principles of mass-scale group life. [ABSTRACT FROM AUTHOR]

Background/purpose: During the recent years, many diagnostic methods have been proposed aiming at early detection of malignant melanoma. The texture of skin lesions is an important feature to differentiate melanoma from other types of lesions, and different techniques have been designed to quantify this feature. In this paper, we discuss a new approach based on independent component analysis (ICA) for extraction of texture features of skin lesions in clinical images. Methods: After preprocessing and segmentation of the images, features that describe the texture of lesions and show high discriminative characteristics are extracted using ICA, and then these features, along with the color features of the lesions, are used to construct a classification module based on support vector machines for the recognition of malignant melanoma vs. benign nevus. Results: Experimental results showed that combining melanoma and nevus color features with proposed ICA-based texture features led to a classification accuracy of 88.7%. Conclusion: ICA can be used as an effective tool for quantifying the texture of lesions. [ABSTRACT FROM AUTHOR]

Data are often collected for a single species within an ecological community, so quantitative tools for drawing inferences about the unobserved portions of the community from single-species data are valuable. In this paper, we present and examine a method for estimating community dimension (the number of strongly interacting species or groups) from time series data on a single species. The dynamics of one species can be strongly affected by environmental stochasticity acting not only on itself, but also on other species with which it interacts. By fully accounting for the effects of stochasticity on populations embedded in a community, our approach gives better estimates of community dimension than commonly used methods. Using a combination of time series data and simulations, we show that failing to properly account for stochasticity when attempting to relate population dynamics to attributes of the community can give misleading information about community dimension. [ABSTRACT FROM AUTHOR]

In this paper we explore variation in the predator-prey interaction between mink Mustela vison and muskrat Ondatra zibethicus across Canada based on 25 years of mink (predator) and muskrat (prey) data from the Hudson's Bay Company. We show that predator–prey interactions have stronger signatures in the west of Canada than in the east. In particular, we show that the observed phase plot trajectories of mink and muskrat rotate significantly clock-wise, consistent with predator–prey theory. We also investigate four phases of the mink muskrat interaction sequence (predator crash phase, prey recovery phase, etc.) and show that they are all consistent with a strong coupling in the west, whereas the presence of generalist predators and alternative preys can explain deviations from this pattern in the east. [ABSTRACT FROM AUTHOR]

This paper concerns several important points when testing for Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) in genetics. First, we challenge the necessity of using exclusively two-sided tests for LD. Next, we show that the exact 2-sided tests based on the most popular measures of LD are not equivalent, and neither are the standard statistical tests even though the 1-sided tests are equivalent. We show how this results in different inference about LD for two data sets consisting of small groups of markers. Finally, we advocate the use of the conditional p-value for both LD and HWE testing. An important advantage of this p-value is that equivalent 1-sided tests are transformed into equivalent 2-sided tests. [ABSTRACT FROM AUTHOR]

Successful conservation plans are not solely achieved by acquiring optimally designed reserves. Ongoing monitoring and management of the biodiversity in those reserves is an equally important, but often neglected or poorly executed, part of the conservation process. In this paper we address one of the first and most important steps in designing a monitoring program – deciding what to monitor. We present a strategy for prioritizing species for monitoring and management in multispecies conservation plans. We use existing assessments of threatened status, and the degree and spatial and temporal extent of known threats to link the prioritization of species to the overarching goals and objectives of the conservation plan. We consider both broad and localized spatial scales to capture the regional conservation context and the practicalities of local management and monitoring constraints. Spatial scales that are commensurate with available data are selected. We demonstrate the utility of this strategy through application to a set of 85 plants and animals in an established multispecies conservation plan in San Diego County, California, USA. We use the prioritization to identify the most prominent risk factors and the habitats associated with the most threats to species. The protocol highlighted priorities that had not previously been identified and were not necessarily intuitive without systematic application of the criteria; many high-priority species have received no monitoring attention to date, and lower-priority species have. We recommend that in the absence of clear focal species, monitoring threats in highly impacted habitats may be a way to circumvent the need to monitor all the targeted species. [ABSTRACT FROM AUTHOR]

In exploring the relationship between multivariate abundance data and environmental variables, a rarely used approach is to graph raw data separately for each different taxon. It is proposed that such raw data graphs become part of the standard toolset for graphing and analysing multivariate abundances. The key advantage of this approach is that axis scales have quantitative interpretations, enabling quantitative interpretation of patterns in abundance. In contrast, ordinations only present qualitative information. Ordinations are useful for inferring overall, qualitative patterns and raw data graphing is a complementary tool of greater use for answering more specific questions, aimed at a deeper understanding the ecology of a community. It is demonstrated using some well-known examples that our understanding of the nature of associations can be considerably improved by using raw data graphs, even when only plotting a subset of variables. One example describes how an often-cited dataset has been misinterpreted in key methodological papers, because data were interpreted from ordinations alone, with no consideration of plots of the raw data. [ABSTRACT FROM AUTHOR]

Power-law frequency distributions characterize a wide array of natural phenomena. In ecology, biology, and many physical and social sciences, the exponents of these power laws are estimated to draw inference about the processes underlying the phenomenon, to test theoretical models, and to scale up from local observations to global patterns. Therefore, it is essential that these exponents be estimated accurately. Unfortunately, the binning-based methods traditionally used in ecology and other disciplines perform quite poorly. Here we discuss more sophisticated methods for fitting these exponents based on cumulative distribution functions and maximum likelihood estimation. We illustrate their superior performance at estimating known exponents and provide details on how and when ecologists should use them. Our results confirm that maximum likelihood estimation outperforms other methods in both accuracy and precision. Because of the use of biased statistical methods for estimating the exponent, the conclusions of several recently published papers should be revisited. [ABSTRACT FROM AUTHOR]

It has been suggested that alien species with close indigenous relatives in the introduced range may have reduced chances of successful establishment and invasion (Darwin's naturalization hypothesis). Studies trying to test this have in fact been addressing four different hypotheses, and the same data can support some while rejecting others. In this paper, we argue that the phylogenetic pattern will change depending on the spatial and phylogenetic scales considered. Expectations and observations from invasion biology and the study of natural communities are that at the spatial scale relevant to competitive interactions, closely related species will be spatially separated, whereas at the regional scale, species in the same genera or families will tend to co-occur more often than by chance. We also argue that patterns in the relatedness of indigenous and naturalized plants are dependent on the continental/island setting, spatial occupancy levels, and on the group of organisms under scrutiny. Understanding how these factors create a phylogenetic pattern in invasions will help us predict which groups are more likely to invade where, and should contribute to general ecological theory. [ABSTRACT FROM AUTHOR]

This paper explores the effect of spatial processes in a heterogeneous environment on the dynamics of a host-parasitoid interaction. The environment consists of a lattice of favourable (habitat) and hostile (matrix) hexagonal cells, whose spatial distribution is measured by habitat proportion and spatial autocorrelation (inverse of fragmentation). At each time step, a fixed fraction of both populations disperses to the adjacent cells where it reproduces following the Nicholson-Bailey model. Aspects of the dynamics analysed include extinction, stability, cycle period and amplitude, and the spatial patterns emerging from the dynamics. We find that, depending primarily on the fraction of the host population that disperses in each generation and on the landscape geometry, five classes of spatio-temporal dynamics can be objectively distinguished: spatial chaos, spirals, metapopulation, mainland-island and spiral fragments. The first two are commonly found in theoretical studies of homogeneous landscapes. The other three are direct consequences of the heterogeneity and have strong similarities to dynamic patterns observed in real systems (e.g. extinction-recolonisation, source-sink, outbreaks, spreading waves). We discuss the processes that generate these patterns and allow the system to persist. The importance of these results is threefold: first, our model merges into a same theoretical framework dynamics commonly observed in the field that are usually modelled independently. Second, these dynamics and patterns are explained by dispersal rate and common landscape statistics, thus linking in a practical way population ecology to landscape ecology. Third, we show that the landscape geometry has a qualitative effect on the length of the cycles and, in particular, we demonstrate how very long periods can be produced by spatial processes. [ABSTRACT FROM AUTHOR]

1. The fungus-gardening ants and their fungi represent a highly co-evolved, vertically transmitted mutualism. Mutualisms such as these are thought to be reciprocal antagonisms, so that the ants and the fungus can be expected to have some conflicting interests. 2. This paper reports the results from a cultivar switch experiment that documented the effects of switching the native cultivar from the basal ‘higher-attine’ Trachymyrmex septentrionalis with a derived cultivar from the leaf-cutting ant, Atta texana. If the cultivars have been modified significantly during the adaptive radiation of this clade, then they should differ in their ability to produce ant and fungal biomass. If the ants can perceive differences in cultivar performance, then their food preference may also change as a result of the switch. Lastly, if conflict is present in this mutualism, then the sex ratio in the switched colonies should be male biased. 3. Our results showed that food preference was not altered by the new cultivar. The A. texana cultivar did not change the performance of T. septentrionalis colonies relative to colonies that were cultivating conspecific fungal cultivars. Foragers preferred insect faeces and oak staminate flowers over fresh leaves or flowers. Most variation in colony performance was attributable to substrate type. Sex ratio of offspring was not affected by fungal cultivar. With respect to fungal growth, the A. texana cultivar appeared to be more of a generalist, while the T. septentrionalis cultivar performed better on substrates preferred by the ants than those unpreferred. 4. The results of this study indicate that cooperation and not conflict has been more important in shaping the evolutionary ecology of this mutualism. Although the cultivars were certainly genetically and physiologically distinct, these differences did not account for variation in the production of ant biomass or ant behaviour. The emerging picture thus indicates that this mutualism should be viewed as a highly integrated superorganism that is more than the sum of its parts. [ABSTRACT FROM AUTHOR]

1. For many species and circumstances, mark–resighting procedures constitute valid alternatives to capture–recapture methods. Indeed, resightings are generally cheaper to acquire than physically recapturing and rehandling the animals, especially when radiotelemetry or other tracking devices are available. 2. In order to estimate population abundance, the joint hypergeometric maximum likelihood estimator, the Minta–Mangel estimator and the Bowden estimator are implemented innoremark, software which has become very popular with biologists in the past decade. 3. In this paper, the basic assumptions regarding these widely applied procedures are delineated and discussed. A simulation study is performed in order to investigate the robustness of the estimators under failure of the assumptions. 4. Theoretical considerations and simulation results motivate the use of the Bowden estimator which, when marks are distributed quite evenly among groups, constitutes the sole reliable method, offering computational simplicity and robustness. On the other hand, if the marks are distributed unevenly, no mark–resighting procedure seems reliable. An application to a case study is considered. [ABSTRACT FROM AUTHOR]

Information about several papers discussed at the British Society for Matrix Biology Meeting in Autumn 2006 are presented. The first session of the meeting entitled "Matrix gene regulation" saw insightful and thought provoking presentations from various researchers. The second session was entitled "Matrix Development and Disease" and it was opened with a presentation entitled "The role of cell-matrix interactions in osteoclast differentiation: you are what you eat."

Attention is drawn to a source citing some 90 000 papers in vegetation science and related fields published before 1995. A subject index is provided. [ABSTRACT FROM AUTHOR]

Abstract: Comparison of the complete human genome sequence to one of its closest relatives, the chimpanzee genome, provides a unique opportunity for exploring recent evolutionary events affecting the microsatellites in these species. A simple assumption on microsatellite distribution is that the total length of perfect repeats is constant compared to that of imperfect ones regardless of the repeat sequence. In this paper, we show that this is valid for most of the chimpanzee genome but not for a number of human chromosomes. Our results suggest accelerated evolution of microsatellites in the human genome relative to the chimpanzee lineage. [Copyright &y& Elsevier]