Allele fixation in a dynamic metapopulation: Founder effects vs refuge effects

The fixation of mutant alleles has been studied with models assuming various spatial population structures. In these models, the structure of the metapopulation that we call the “landscape” (number, size and connectivity of subpopulations) is often static. However, natural populations are subject to repetitive population size variations, fragmentation and secondary contacts at different spatiotemporal scales due to geological, climatic and ecological processes. In this paper, we examine how such dynamic landscapes can alter mutant fixation probability and time to fixation. We consider three stochastic landscape dynamics: (i) the population is subject to repetitive bottlenecks, (ii) to the repeated alternation of fragmentation and fusion of demes with a constant population carrying capacity, (iii) idem with a variable carrying capacity. We show by deriving a variance, a coalescent and a harmonic mean population effective size, and with simulations that these landscape dynamics generate repetitive founder effects which counteract selection, thereby decreasing the fixation probability of an advantageous mutant but accelerate fixation when it occurs. For models (ii) and (iii), we also highlight an antagonistic “refuge effect” which can strongly delay mutant fixation. The predominance of either founder effects or refuge effects determines the time to fixation and mainly depends on the characteristic time scales of the landscape dynamics.     

Spatial indicators for nature conservation from European to local scale

The paper presents an overview of the objectives and exemplary results of the FP 5 project “Spatial Indicators for European Nature Conservation” (SPIN). The SPIN project is focused on the development and testing of advanced classification methods and spatial indicators based on multisensor satellite data and GIS to accomplish monitoring and management tasks in the context of Natura 2000 and nature conservation. A representative selection of eight regional test areas covers a pan-European network and allows comparative investigations to provide accepted recommendations for regional and European nature conservation. The selected results of four case studies are presented and discussed. The range of work covers the production of regional and local habitat maps by object-oriented classification, a case-based reasoning method for change detection as a management support tool for planning and regulating local land use, the selection and application of structural indicators for the monitoring of Natura 2000 habitats and the downscaling and disaggregation of soil information. Results and the further implementation of presented methods are discussed in the conclusions.     

Can we measure ecological sustainability? Landscape pattern as an indicator for naturalness and land use intensity at regional,national and European level

European landscapes have been shaped over the centuries by processes related to human land use, which are reflected in regionally distinct landscape patterns. Since landscape pattern has been linked to biodiversity and other ecological values of the landscapes, this paper explores landscape pattern as a tool for ecological sustainability assessments at the regional (Austrian Cultural Landscapes), national (Austria) and European (European Union + Norway, Switzerland) level with focus on agricultural landscapes. A set of landscape metrics served as a basis to assess naturalness and geometrisation of Austrian and European landscapes as a proxy for their sustainability. To achieve an accurate spatially explicit assessment, we applied a spatial reference framework consisting in units that are homogeneous in biophysical and socio-economic contexts, adapted the regional approach for its application at European level, and developed relative sustainability thresholds for the landscape metrics. The analyses revealed that several landscape metrics, particularly the “Number of Shape Characterising Points” showed a high correlation with the degree of naturalness. The sustainability map of Austria based on an ordinal regression model revealed well-known problem regions of ecological sustainability. At the European level, the relative deviation from the average pattern showed clearly the simplification processes in the landscapes. However, a better spatial resolution of land cover data would add to the refinement of pattern analysis in regions and therefore the assessment of sustainability. We recommend the combination of information of different scales for the formulation and implementation of sustainability policies.     

Modelling land-use sustainability using farmland birds as indicators

Biodiversity on farmland is declining due to agricultural intensification and occurs across many taxa such as plants, insects or birds. Here, we modelled population sizes of five farmland birds in central Germany as the German Sustainability Indicator for Species Diversity (SISD) is based on this taxon. We explored options for sustainable farmland management by generating land-use scenarios at the regional scale. For individual bird species, high SISD scores could be reached by changing environmental variables, such as landscape or crop diversity, percent cover of spring cereals or hedge density. However, contrasting species responses to these variables prevented from reaching high scores for all species simultaneously. We were able to improve the total SISD score from 0.77 at present to 0.94 by increasing landscape and crop diversity or to 0.87 by increasing hedge density and reducing spring cereals, respectively. An economic evaluation of the return losses associated with these changes revealed that annual costs of approx. 5.5 €/ha farmland would suffice for this latter increase by optimizing hedges and spring cereals towards high SISD. We conclude that balancing three levels of trade-offs, i.e. contrasting requirements of species, diverging responses in different landscapes, and alternative economic options, is difficult to achieve without systematic modelling. Yet, by accounting for differences in landscape structure and species distributions at a regional spatial scale and by focusing on clearly defined measures such as hedge density or the cover of spring cereals rather than composite indices like landscape or crop diversity it seems possible to develop realisable, affordable and sustainable management strategies.     

Evaluating outcomes in planning: Indicators and reference values for Swiss landscapes

Evaluation of achievement of set targets is a necessary step in landscape planning in order to learn from the past, reassess implemented measures and enhance trust in public managers and institutions. Though it is commonly accepted that indicators play a major role in such evaluations, so far no accepted framework for evaluating planning outcomes exists. Furthermore, the selection of appropriate indicators and reference values to effectively assess conditions of landscapes and determine whether observed developments can be considered positive or negative remains challenging. Our study contributes to much-needed research on this topic with a proposed evaluation framework built on goals, indicators and reference values. We analyzed the landscape section of eight Swiss cantonal comprehensive plans to specifically address (1) whether currently tracked indicators suffice to evaluate landscape-planning goals; (2) what a minimal set of landscape indicators for regional planning might look like; and (3) how the ratified value approach could be operationalized to develop reference values for landscape indicators. All eight plans have a similar hierarchical goal system with six major landscape goals, up to 18 themes and 21–33 subordinate goals. The studied cantons track from 29 to 84 indicators. We found a considerable imbalance in the ratio between subordinate goals and indicators, with comparatively few indicators being tracked to assess visual and recreational landscape quality. Our proposed minimal indicator set is well balanced since it lists 5–7 indicators for each theme. The general procedure for modeling reference values is based on the assumption that the protection status of a landscape is a proxy for high societal appreciation of a place. Consequently, indicator values for these areas would reflect reference values (ratified values). We illustrate the procedure with the exemplary indicator impervious surface. The proposed indicators and maps are powerful tools for outcome evaluation and also facilitate benchmarking, i.e. interregional comparisons of landscape qualities, which could be very useful for landscape planning in Europe.     

Some connections between physiognomic traits and intelligence

A sample of 84 female subjects (students) was taken and split up on the basis of the IST-ratings (“Intelligence Structure Test” by Amthauer) into two extreme groups of “more intelligent” (N = 14) and “less intelligent” (N = 11) subjects with an aim to testing Kozeny's findings. Using his photographic-statistical method, Kozeny had observed that “more intelligent” people have a more open eye, a smaller and straighter mouth, a stronger chin, and—above all in its side dimensions—a better developed forehead. These physiognomic indicators of differences in intelligence were confirmed to a large extent by the measurements taken from the portraits of the subjects.     

Modelling bird habitat suitability based on landscape parameters at different scales

Habitat suitability as characterized by the presence of a species and by reproductive success was modelled in relation to different parameters of landscape diversity at different scales. Parameters characterizing landscape pattern were determined for the UTM 10 km × 10 km cells covering the whole of Estonia and were correlated to the distribution of over 30 forest bird species. The landscape parameters include areas of lakes, mires and built-up areas, length of borders between different land cover units and length of selected line elements, share of different kinds of forest and peatland. The bird species are grouped by correlation into three major groups: (a) independent, (b) wetland preferring (with subgroups of those avoiding built-up areas and roads and those not) and (c) built-up area dependent (with subgroups depending on the importance of line elements). For selected predator species, nesting success was related to landscape parameters on a finer scale, using cells of 10 km². Land pattern was characterized by total length of line elements (streams, roads, borders, ecotones) and certain areal coverage (forest, mires, fields, built-up areas) within the cell. The impact of variations of food availability was linked to the relation. Possibilities for downscaling and upscaling of relations determined at different scales and areal coverage are discussed.     

Glucuronic acid conjugates

The methods of assay in body fluids of 1-β-alkyl, 1-β-phenyl and 1-β-acyl glucuronic acids (“glucuronide conjugates”) have been reviewed. Most of the 78 references cited (from the literature of the period 1990–1997) concern the glucuronide conjugates of drug metabolites, and these have been considered, for reasons of accessibility, within sections of individual drug classes such as analgesics, anti-cancer agents and opioids. Other glucuronide conjugates are considered under “miscellaneous compounds”. A few gas chromatography and capillary electrophoresis methods are described, but the major technique of assay (62 citations) is reversed-phase high-performance liquid chromatography.     

The nature and affinities of the “robust” Australopithecines: a review

The fossil evidence of the “robust” australopithecines is reviewed with an emphasis on the taxonomic divisions and evolutionary relationships among this group of hominids. The hypodigms of A. robustus, A. crassidens and A. boisei are described, and the significance of morphological variation within and between these species is assessed. Phylogenetic relationships among the “robust” australopithecines are examined using maximum parsimony analysis, and evolutionary scenarios are evaluated in the light of recent discoveries in East Africa.     

Depth estimation by proportions of living larger foraminifera

Estimation of environmental gradients by proportions of species using transfer functions is a viable and proven method. Two new methods enabling exact point estimation of the gradients are developed. The “minimum distance function”, like simple transfer equations, results in a single value, whereas the “transformed proportions method” based on logit-transformed density functions allows additional diagnosis of the coenoclines under investigation. Depth estimations in sublittoral coral reefs using larger foraminifers demonstrate the high precision of both methods.     

From Understanding the Development Landscape of the Canonical Fate-Switch Pair to Constructing a Dynamic Landscape for Two-Step Neural Differentiation

Recent progress in stem cell biology, notably cell fate conversion, calls for novel theoretical understanding for cell differentiation. The existing qualitative concept of Waddington’s “epigenetic landscape” has attracted particular attention because it captures subsequent fate decision points, thus manifesting the hierarchical (“tree-like”) nature of cell fate diversification. Here, we generalized a recent work and explored such a developmental landscape for a two-gene fate decision circuit by integrating the underlying probability landscapes with different parameters (corresponding to distinct developmental stages). The change of entropy production rate along the parameter changes indicates which parameter changes can represent a normal developmental process while other parameters’ change can not. The transdifferentiation paths over the landscape under certain conditions reveal the possibility of a direct and reversible phenotypic conversion. As the intensity of noise increases, we found that the landscape becomes flatter and the dominant paths more straight, implying the importance of biological noise processing mechanism in development and reprogramming. We further extended the landscape of the one-step fate decision to that for two-step decisions in central nervous system (CNS) differentiation. A minimal network and dynamic model for CNS differentiation was firstly constructed where two three-gene motifs are coupled. We then implemented the SDEs (Stochastic Differentiation Equations) simulation for the validity of the network and model. By integrating the two landscapes for the two switch gene pairs, we constructed the two-step development landscape for CNS differentiation. Our work provides new insights into cellular differentiation and important clues for better reprogramming strategies.     

Rethinking ‘style’ for historians and philosophers of science: converging lessons from sexuality, translation, and East Asian studies

Historians and philosophers of science have furnished a wide array of theoretical-historiographical terms to emphasize the discontinuities among different systems of knowledge. Some of the most famous include Thomas Kuhn’s “paradigm”, Michel Foucault’s “episteme”, and the notion of “styles of reasoning” more recently developed by Ian Hacking and Arnold Davidson. This paper takes up this theoretical-historiographical thread by assessing the values and limitations of the notion of “style” for the historical and philosophical study of science. Specifically, reflecting on various methodological and theoretical concerns prompted by sexuality, translation, and East Asian studies, this paper argues that the heretofore ways in which historians and philosophers of science have used the notion of “style” are severely restricted in terms of its mere applicability to the intellectual history of Western science. The particular example of the translation of “homosexuality” into Chinese during the May Fourth era reveals that the notion of “style” has the potential of carrying a much more dynamic conceptual weight, as when used in “styles of argumentation”. The paper also engages briefly with the historiography of scientific “national styles” and ends with some concluding remarks on the limitations of “social histories from below” and the under appreciated importance of “epistemological histories of possibilities”.     

Epigenetics: Judge,jury and executioner of stem cell fate

Emerging evidence is shedding light on a large and complex network of epigenetic modifications at play in human stem cells. This “epigenetic landscape” governs the fine-tuning and precision of gene expression programs that define the molecular basis of stem cell pluripotency, differentiation and reprogramming. This review will focus on recent progress in our understanding of the processes that govern this landscape in stem cells, such as histone modification, DNA methylation, alterations of chromatin structure due to chromatin remodeling and non-coding RNA activity. Further investigation into stem cell epigenetics promises to provide novel advances in the diagnosis and treatment of a wide array of human diseases.     

Opportunities and limitations in assessing the multifunctionality of agriculture within the CAPRI model

In recent years the objectives of agricultural policy have shifted from a principal focus on production and income towards agriculture's provision of public goods summarized by the term ‘multifunctionality’. Agricultural sector models, which are important tools for policy advice, need to be adjusted in order to maintain their relevance and reliability in accordance with policy changes. This paper investigates the strengths and limitations of incorporating multifunctionality indicators in the agricultural sector model Common Agricultural Policy Regional Impact Analysis (CAPRI) by reviewing the existing literature and incorporating such indicators in the model. Multifunctionality indicators are developed and implemented for four selected aspects of multifunctionality: food security, landscape, environmental concerns and rural viability. By running different policy reform scenarios, it is shown that indicators closely related to the underlying economic variables of the sector model may provide useful to describe the effects of policy reforms on agriculture's multifunctionality. However, these indicators do not completely cover the selected aspects of multifunctionality. In order to yield a broader coverage, this paper proposes to strengthen interdisciplinary research by linking agricultural sector models with other model systems like farm-based economical–ecological models, regional economic models or landscape information systems.     

Quantitative characteristic of the catalytic properties and microstructure of cross-linked enzyme aggregates of penicillin acylase

The microstructure and the catalytic properties of cross-linked enzyme aggregates (CLEA) of penicillin acylase (PA) obtained under different conditions were investigated. The period of time left between the enzyme precipitation and the cross-linking step was found to influence the structural organization of the resulting enzyme preparation. Confocal fluorescent microscopy of the so-called “fresh” and “mature” CLEAs PA allowed to estimate the “characteristic” diameter of CLEA PA particles, which appeared to be about 1.6 μm, and revealed that the “mature” type was composed of relatively big particles as compared to the “fresh” type. Complementary kinetic studies showed that the “mature” CLEA PA were more effective in both hydrolytic and synthetic reactions. It was suggested that the aggregate size might regulate the extent of covalent modification of PA and thereby influence the catalytic properties of CLEA.     

Praon Haliday (Hymenoptera: Braconidae: Aphidiinae) of Southeastern Europe: key, host range and phylogenetic relationships

A review of species in the genus Praon Haliday, 1833 is presented. Twenty described species are keyed and illustrated with scanning electron micrographs and line drawings. The Praon species presented in this work have been identified from 67 aphid taxa occurring on 120 plant taxa. Furthermore, 87 original parasitoid–aphid–plant associations of the species mentioned in the key are presented. Phylogenetic relationships among Praon species are reconstructed using parsimony and cladistic distance methods. Praon abjectum is the sister taxon to the remaining Praon species. We recognized three species group: “Parapraon”, “dorsale-yomenae” and “rosaecola”. Monophyly is suggested for “Parapraon” species group and paraphyly for “dorsale-yomenae” group. Finally, by phylogenetic reconstruction, a close phylogenetic relationship between “Parapraon” and “dorsale-yomenae” species group was found.     

Restoration principles applied to cultural landscapes

Restoration models and practise to date have been applied mainly to ecosystems. More recently, there has been a focus on the “landscape perspective” of ecosystem restoration in order to improve nature conservation and management effectiveness.

Here, we clarify some of the differences between ecosystem- and landscape-oriented restoration, and propose four components that should be considered in planning and conceptualising: (a) landscape composition and configuration; (b) traditional land management techniques; (c) linear and point features; and (d) other heritage features. We further discuss the concept of reference landscapes, and the contrasts between restoration and rehabilitation. Spatial approaches to restoration are explored, comparing small areas with complete restoration (“museum landscapes”) from large areas with rehabilitation of landscape physiognomy or point and linear features. The linkages with nature conservation and the sustainable use and management of natural resources are examined in the context of a rapidly changing world.     

On the concept of the effective population size

The concept of the effective population size is discussed. It is shown that the “eigenvalue” and the “inbreeding” effective population sizes are in principle different, even though they have been sometimes identified in the literature. On the other hand the “eigenvalue” and “variance” effective sizes are usually both close when the latter exists. Since, however, there are many models for which a variance effective size cannot in principle exist, it seems useful to introduce the eigenvalue effective size and to examine some of its properties.