Effort d’échantillonnage et atlas floristiques – exhaustivité des mailles et caractérisation des lacunes dans la connaissance

Floristic atlases have an important input to flora conservation planning even though their data quality varied greatly across countries. This study aimed to assess survey completeness of cells of floristic atlases. Then, a surveying guide is designed to overcome as efficiently as possible sampling biases. A review and analyses on a wide dataset were carried out to select an estimator of the true species richness of surveyed cells. The Jackknife 1, a non-parametric estimator, appeared as the best compromise for regional floristic atlases. The number of records in each cell was used as an estimator of sampling effort. The ratio between the observed species richness and the estimated species richness measures the completeness of inventories in each surveyed cell. Eighteen variables were selected to describe current inventories and design new surveys. These variables highlight locations, periods and species to be given priority in future studies.     

Regional spatial modeling of topsoil geochemistry

Summary .  Geographic information about the levels of toxics in environmental media is commonly used in regional environmental health studies when direct measurements of personal exposure is limited or unavailable. In this article, we propose a statistical framework for analyzing the spatial distribution of topsoil geochemical properties, including the concentrations of various toxicants. Due to the small-scale heterogeneity of most geochemical topsoil processes, direct measurements of the processes themselves only provide highly localized information; it is thus financially prohibitive to study the spatial patterns of these processes across a large region using traditional geostatistical analyses of point-referenced topsoil data. Instead, it is standard practice to assess geochemical patterns at a regional scale using point-referenced measurements collected in stream sediment because, unlike topsoil data, individual stream sediment geochemical measurements are representative of the surrounding area. We propose a novel multiscale soils (MSS) model that formally synthesizes data collected in topsoil and stream sediment and allows the richer stream sediment information to inform about the topsoil process, which in environmental health studies is typically more relevant. Our model accommodates the small-scale heterogeneity of topsoil geochemical processes by modeling spatial dependence at an aggregate resolution corresponding to hydrologically similar regions known as watersheds. We present an analysis of the levels of arsenic, a toxic heavy metal, in topsoil across the midwestern United States using the MSS model and show that this model has better predictive abilities than alternative approaches using more conventional statistical models for point-referenced spatial data.     

Using Manifold Learning for Atlas Selection in Multi-Atlas Segmentation

Multi-atlas segmentation has been widely used to segment various anatomical structures. The success of this technique partly relies on the selection of atlases that are best mapped to a new target image after registration. Recently, manifold learning has been proposed as a method for atlas selection. Each manifold learning technique seeks to optimize a unique objective function. Therefore, different techniques produce different embeddings even when applied to the same data set. Previous studies used a single technique in their method and gave no reason for the choice of the manifold learning technique employed nor the theoretical grounds for the choice of the manifold parameters. In this study, we compare side-by-side the results given by 3 manifold learning techniques (Isomap, Laplacian Eigenmaps and Locally Linear Embedding) on the same data set. We assess the ability of those 3 different techniques to select the best atlases to combine in the framework of multi-atlas segmentation. First, a leave-one-out experiment is used to optimize our method on a set of 110 manually segmented atlases of hippocampi and find the manifold learning technique and associated manifold parameters that give the best segmentation accuracy. Then, the optimal parameters are used to automatically segment 30 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). For our dataset, the selection of atlases with Locally Linear Embedding gives the best results. Our findings show that selection of atlases with manifold learning leads to segmentation accuracy close to or significantly higher than the state-of-the-art method and that accuracy can be increased by fine tuning the manifold learning process.     

More than a decade of developmental gene expression atlases: where are we now?

To unravel regulatory networks of genes functioning during embryonic development, information on in situ gene expression is required. Enormous amounts of such data are available in literature, where each paper reports on a limited number of genes and developmental stages. The best way to make these data accessible is via spatio-temporal gene expression atlases. Eleven atlases, describing developing vertebrates and covering at least 100 genes, were reviewed. This review focuses on: (i) the used anatomical framework, (ii) the handling of input data and (iii) the retrieval of information. Our aim is to provide insights into both the possibilities of the atlases, as well as to describe what more than a decade of developmental gene expression atlases can teach us about the requirements of the design of the ‘ideal atlas’. This review shows that most ingredients needed to develop the ideal atlas are already applied to some extent in at least one of the discussed atlases. A review of these atlases shows that the ideal atlas should be based on a spatial framework, i.e. a series of 3D reference models, which is anatomically annotated using an ontology with sufficient resolution, both for relations as well as for anatomical terms.     

Mapping avian distributions: the evolution of bird atlases

Capsule An increasing proportion of atlases now map patterns of abundance but they are still a minority even though they require no more input of time or fieldworkers.

Aims To examine quantitatively the evolution of bird atlas methods, from their inception to the present day, to document the most frequently used methods and to quantify temporal changes in them, and so identify broad patterns that might be of use in the planning and interpretation of future atlases.

Methods A database of over 400 atlases was compiled, and a number of variables extracted from each. Temporal trends within, and relationships between, these variables were analysed.

Results Atlases have become significantly reduced in scale over time, covering smaller areas in shorter periods of fieldwork, but at higher spatial resolutions and with increasing numbers of observers per unit area. The number of participating fieldworkers and the size of the region being covered together explain over 70% of variation between atlases in spatial resolution. The number of atlases that have mapped abundance or relative abundance, rather than simply occurrence (presence/absence) or breeding status, has increased significantly over time but remains relatively small. However, such atlases were no more expensive in terms of length of the fieldwork or preparation periods or the number of observers deployed per unit area. There is evidence of a sharp decline in the number of new bird atlases being initiated.

Conclusions There have been significant changes in the way atlas surveys are undertaken, but no standardized method has evolved. This leads to flexibility that allows atlas surveys to be undertaken over areas varying by six orders of magnitude using numbers of observers that vary by five orders of magnitude.     

Newt decline in Western Europe: highlights from relative distribution changes within guilds

The recent increase in the number of monitoring schemes has formed the basis for high quality distribution atlases. This provides the opportunity of estimating global and specific decline patterns across regional and national borders. In this framework, this study focused on four sympatric newt species—including the great crested newt (Triturus cristatus), an Annex 2 European Habitats Directive species, over six geographic areas (five countries) in Western Europe. A relative comparison of distribution maps across time is used here and is based on more than twelve thousands occupied grid cells. It benefits from the definition of a guild, as these species are simultaneously detectable in wetlands. T. cristatus and the alpine newt (Mesotriton alpestris) were the most and the least threatened newt species, respectively, whereas the palmate (Lissotriton helveticus) and smooth newt (Lissotriton vulgaris) had an intermediate decline level at both coarse and fine grain resolutions. However, regional variations across Europe and scale effects were also found. On one hand, these results show that T. cristatus is not only regionally threatened but suffers from a global decline in Western Europe. On another hand, the results indicate that patterns of decline are not uniform within Europe and that species often considered as common and not threatened are, in fact, declining more than others. Finally, the proposed methodology, i.e. using guilds to assess relative decline, would be useful as a complement to other standardized methods in correctly advising conservation managers and policy makers, particularly for species with more subtle declines.     

基于物质流分析和数据包络分析的区域生态效率评价——以江苏省为例

区域生态效率(eco-efficiency)评价是考量区域可持发展的重要内容.基于物质流分析(material flow analysis, MFA)构建区域生态效率评价指标体系,并将污染物排放作为一种非期望输入引入到数据包络分析(data envelopment analysis, DEA)模型中,以江苏省(1990～2005年)为例进行生态效率分析评价.结果表明,江苏省的区域生态效率在1990～2005年期间呈现逐步上升的趋势.但是,同期的总物质投入(total material input, TMI)、物质需求总量(total material requirement, TMR)和污染物排放量也呈上升趋势.因此,江苏省社会经济发展和环境影响总体上呈现"弱脱钩(weak de-link)".     

Designing a winter bird atlas field methodology: issues of time and space in sampling and interactions with habitat

Faunal and floral atlases can provide invaluable information on species distributions and relative abundance, and have played a key role in detecting and diagnosing population changes. Most atlases rely on simple but effective field methods that can be employed by large numbers of volunteer surveyors so as to make the best use of their finite effort. For ornithological atlases, such methods have been modified to better quantify relative abundance in the breeding season. Here, we evaluate how effort should be invested in space (number of samples) and time (time per sample) in order to optimise species lists and relative abundance estimation for birds in Britain and Ireland in winter. Species accumulation curves show only slight differences in the ability to derive complete species lists whether effort is invested in time or in space. However, relative abundance precision is markedly improved if effort is invested in space at the expense of time. These results give clear guidance on the general way in which methods should be devised (i.e. more samples, each for less time), but analyses relating the shape of species accumulation curves to habitat diversity suggest the precise trade-off between surveying in space and time varies between landscapes. Designers of atlases must therefore optimise their study design for the landscape of the particular region in question.     

International Commission for Protection against Environmental Mutagens and Carcinogens. ICPEMC working paper 5/1: Perspectives in mutation epidemiology. 1. Incidence and prevalence of genetic disease (excluding chromosomal aberrations) in human populations

Detailed knowledge of the birth frequency or the cumulative incidence over all ages of genetic diseases in human populations is a prerequisite for assessing the magnitude of possible genetic hazards caused by environmental mutagens. However, both theoretical and practical difficulties are involved in precisely measuring the total frequency of these diseases. Two sets of data from large-scale population studies, one from Northern Ireland and the other from British Columbia, are compared with each other and with the results from ad hoc surveys for individual monogenic disorders. With due allowance for differences in approach, examination indicates that the data from the large-scale population studies are inadequate. However, it could provide a crude estimate of the total frequency of genetic diseases and a fairly reliable estimate of the individual frequency of certain genetic disorders with early onset that are familiar and readily diagnosed. In addition to environmental mutagens, there are a number of factors associated with current human activity that may change the incidence of genetic diseases. In order to monitor the human population for environmental mutagens, the change in frequency of sporadic cases of those genetic diseases that arose from fresh mutation and that can be easily detected as early as possible should be followed closely. The mechanism of data collection currently being employed in some countries for childhood cancers, certain congenital malformations, and inborn errors of metabolism could be extended to include the so-called sentinel phenotypes. The rationale and feasibility of using retinoblastoma and Wilms' tumor (nephroblastoma) as examples of such population monitoring are described.     

Who Counts? Demography of Swidden Cultivators in Southeast Asia

Swidden cultivators are often found as a distinct category of farmers in the literature, but rarely appear in population censuses or other national and regional classifications. This has led to a worldwide confusion on how many people are dependent on this form of agriculture. The most often cited number of 200–300 million dates back to the early 1970s, but the source is obscure. We assess available, published data from nine countries in Southeast Asia and conclude that on this basis it is not possible to provide a firm estimate of the number of swidden cultivators in the region. A conservative range of 14–34 million people engaged in swidden cultivation in the region is suggested, however. We argue that along with improved knowledge of swidden livelihoods, there is an urgent need to develop techniques that will allow for better estimates of swidden populations in order to secure appropriate rural development and poverty reduction in swidden areas.     

Nonrigid Registration Regularized by Shape Information: Application to Atlas Construction of Cardiac CT Images

Cardiac atlases play an important role in the computer-aided diagnosis of cardiovascular diseases, in particular they need to deal with large and highly variable image datasets. In this paper, we propose a new nonrigid registration algorithm incorporating shape information, to produce comprehensive atlases. For one thing, the multiscale gradient orientation features of images are combined to form the construction of multifeature mutual information. Additionally, the shape information of multiple-objects in images is incorporated into the cost function for registration. We demonstrate the merits of the new registration algorithm on the 3D data sets of 15 patients. The experimental results show that the new registration algorithm can outperform the conventional intensity-based registration method. The obtained atlas can represent the cardiac structures more accurately.     

Species richness in mammalian herbivores: patterns in the boreal zone

Latitudinal gradients in species diversity are well established for a number of plant and animal taxa. Both historical and present-day environmental factors have been suggested to be responsible for observed patterns. We tested the hypothesis that current environmental features of the environment (primary productivity and regional landscape structure) may explain the longitudinal variation in species richness of mammalian herbivores in the Holarctic boreal zone. Mammalian herbivore species diversity was strongly correlated with a number of environmental variables measured. We reduced the data set by a principal components analysis (PCA), and found that in the Palearctic, species richness is positively related to warm climate (high temperature sum), the number of hardwood species, and the area of boreal forest. In the Nearctic, species richness increases as the length of the growing season and the number of coniferous tree species increase. Thus indirect measures of primary productivity as well as tree species number may accurately predict species richness in mammalian herbivores. In addition, there seems to be a strong species-area effect at the regional level. The larger and more homogeneous in terms of forest coverage a boreal section is, the more species coexist there.     

The consistency and stability of abundance-occupancy relationships in large-scale population dynamics

1. Abundance-occupancy relationships comprise some of the most general and well-explored patterns in macro-ecology. The theory governing these relationships predicts that species will exhibit a positive interspecific and intraspecific relationship between regional occupancy and local abundance. Abundance-occupancy relationships have important implications in using distributional surveys, such as atlases, to understand and document large-scale population dynamics and the consequences of environmental change. A basic need for interpreting such data bases is a better understanding of whether changes in regional occupancy reflect changes in local abundance across species of varying life-history characteristics. 2. Our objective was to test the predictions of the abundance-occupancy rule using two independent data sets, the New York State Breeding Bird Atlas and the North American Breeding Bird Survey. The New York State Breeding Bird Atlas consists of 5332 25-km(2) survey blocks and is one of the first atlases in the USA to be completed for two time periods (1980-85 and 2000-05). The North American Breeding Survey is a large-scale annual survey intended to document the relative abundance and population change of songbirds throughout the USA. 3. We found that regional occupancy was positively correlated with relative abundance across 98 (beta = 0.60 +/- 0.11 SE, P < 0.001, R(2) = 0.60) and 85 species (beta = 0.67 +/- 0.06 SE, P < 0.001, R(2) = 0.57) in two separate time periods. This relationship proved stable over time and was notably consistent between breeding habitat groups and migratory guilds. 4. Between 1980 and 2005, changes in regional occupancy were highly correlated with long-term abundance trend estimates for 75 species (beta = 5.73 +/- 0.24 SE, P < 0.001, R(2) = 0.88). Over a 20-year period, woodland and resident birds showed an increase in occupancy while grassland species showed the greatest decline; these patterns were mirrored by changes in local abundance. 5. Although exceptions existed, we found most changes in occupancy parallel changes in local abundance. These findings support the basic predictions of the abundance-occupancy rule and demonstrate its consistency and stability in species and groups of varying life-history characteristics.     

Ex Situ Conservation of Orchids in a Warming World

Whilst there is overwhelming scientific evidence that dramatic changes in regional climates are likely to occur throughout the 21st century, the scientific community remains uncertain how the effects of global heating will combine with other environmental factors to affect wild orchid populations. It is, however, likely that many populations will be affected adversely and that in situ conservation techniques by themselves will not be sufficient to prevent the extinction of many species. A range of complimentary ex situ strategies are discussed. Amongst these orchid seed banking has been shown to be an invaluable tool for conserving the maximum amount of genetic diversity in the minimum space and has the potential to enable the conservation of valuable material for possible re-introduction and habitat restoration programmes in the future. The Darwin Initiative project, ‘Orchid Seed Stores for Sustainable Use’ (OSSSU), is currently establishing a global network of orchid seed banks focussing initially on countries with high orchid biodiversity in Asia and Latin America. Particular reference is made to ex situ conservation in China, together with the urgent need to gather more data to determine which habitats and species are most at risk of extinction in the wild in the immediate future.     

How should we assess risk behaviour when determining donor deferral? Reflections on the MSM deferral

Concerns are increasingly being raised in a number of countries in relation to the behavioural donor criteria and in particular the on-going permanent exclusion of men who have had sex with other men (MSM). The justification for this is broadly linked to the use of risk models. Generally current exclusion criteria are broadly defined and indirectly it might be argued that this leads to exclusion based on sexual orientation. Available data indicates compliance issues with the exclusion and recent reviews in Europe have recommended that further research in this area is needed before any change in the current permanent exclusion should be made. Lobby groups however promote a more targetted approach to behavioural criteria. Firm data to support this is however currently lacking. There are a number of possible approaches to assessing risk including the period since the activity took place, the number of partners in a given period, the type of sex act or a combination of these factors. Definition of an optimal approach will need to consider both the sensitivity and specificity of the intervention along with an assessment of ease and consistency of application.     

Environmental Impacts of Consumption in the European Union:High-Resolution Input-Output Tables with Detailed Environmental Extensions

For developing product policy, insight into the environmental effects of products is required. But available life-cycle assessment studies (LCAs) are hardly comparable between different products and do not cover total consumption. Input-output analysis with environmental extensions (EEIOA) of full consumption is not available for the European Union. Available country studies have a low sector resolution and a limited number of environmental extensions. This study fills the gap between detailed LCA and low-resolution EEIOA, specifying the environmental effects of household consumption in the European Union, discerning nearly 500 sectors, while specifying a large number of environmental extensions. Added to the production sectors are a number of consumption activities with direct emissions, such as automobile driving, cooking and heating, and a number of postconsumer waste management sectors. The data for Europe have been constructed by using the sparse available and coarse economic and environmental data on European countries and adding technological detail mainly based on data from the United States.
A small number of products score high on environmental impact per Euro and also have a substantial share of overall consumer expenditure. Several meat and dairy products, household heating, and car driving thus have a large share of the total environmental impact. Due to their sales volume, however, products with a medium or low environmental score per Euro may also have a substantial impact. This is the case with bars and restaurants, clothing, residential construction, and even a service such as telecommunications. The limitations in real European data made heroic assumptions necessary to operationalize the model. One conclusion, therefore, is that provision of data in Europe urgently needs to be improved, at least to the level of sector detail currently available for the United States and Japan.     

Predicting species’ tolerance to salinity and alkalinity using distribution data and geochemical modelling: a case study using Australian grasses

Background and Aims Salt tolerance has evolved many times independently in different plant groups. One possible explanation for this pattern is that it builds upon a general suite of stress-tolerance traits. If this is the case, then we might expect a correlation between salt tolerance and other tolerances to different environmental stresses. This association has been hypothesized for salt and alkalinity tolerance. However, a major limitation in investigating large-scale patterns of these tolerances is that lists of known tolerant species are incomplete. This study explores whether species’ salt and alkalinity tolerance can be predicted using geochemical modelling for Australian grasses. The correlation between taxa found in conditions of high predicted salinity and alkalinity is then assessed.Methods Extensive occurrence data for Australian grasses is used together with geochemical modelling to predict values of pH and electrical conductivity to which species are exposed in their natural distributions. Using parametric and phylogeny-corrected tests, the geochemical predictions are evaluated using a list of known halophytes as a control, and it is determined whether taxa that occur in conditions of high predicted salinity are also found in conditions of high predicted alkalinity.Key Results It is shown that genera containing known halophytes have higher predicted salinity conditions than those not containing known halophytes. Additionally, taxa occurring in high predicted salinity tend to also occur in high predicted alkalinity.Conclusions Geochemical modelling using species’ occurrence data is a potentially useful approach to predict species’ relative natural tolerance to challenging environmental conditions. The findings also demonstrate a correlation between salinity tolerance and alkalinity tolerance. Further investigations can consider the phylogenetic distribution of specific traits involved in these ecophysiological strategies, ideally by incorporating more complete, finer-scale geochemical information, as well as laboratory experiments.     

Finding spatial regularity in mosaic landscapes: two methods integrated

Two methods were employed to find spatial regularity in a complicated mountain landscape of Beijing, China on the basis of functional and structural affinities. The first approach applied Affinity Analysis based on species composition to landscape. The mosaic diversity of the landscape was 3.5298>3, which means the study landscape is complex and controlled by multiple environmental gradients. These landscape types were divided into 3 parts according to the mean affinity values of 0.2143 and 0.7857 (0.5±1 SD). Modal sites are the central types of the landscape, which include a zonal broad-leaved forest of the region and a conifer plantation replacing the former. Outliers are found in the highest altitude and the lowest, both have few species in common with the above two modal types. The remaining landscape types are intermediate sites, which are transitional between modals and outliers, broadly distributed throughout mountain environments. Neighbor types have more species in common than those more widely separated, which probably distributed adjacently in space or in similar quality habitat. The other method employed is the new TWINSPAN analysis by substituting spatial neighboring data of landscape types for species composition data. It clearly divided the landscape types into three groups, i.e., subalpine, middle and low mountain groups, which were correlated with altitude, as well as influenced by human disturbance. The new TWINSPAN classification method is more reliable in finding spatial gradient of patchy landscapes than affinity analysis; however, affinity analysis is useful in finding species diversity pattern and the importance of landscape types in a region. Integrating advantages of the two methods could supply complete and reliable information on how landscape types are distributed in space, which environmental gradient dominates the spatial distribution of the landscape types, as well as where important and unusual types are located.