Design and analysis of multiple-choice feeding-preference experiments

Summary A serious omission in ecological methodology is the absence of a rigorous statistical procedure to analyse multiple-choice feeding-preference experiments. A sample of 21 studies in the littoral marine context shows that results from such experiments are used to study a variety of conceptual issues, ranging from nutritional biology to ecosystem dynamics. A majority of such studies have been incorrectly analysed. The analytical problem has two facets: (1) lack of independence in the simultaneous offer of food types and (2) the existence of autogenic changes particular to each food type. Problem (2) requires the use of control arenas without the consumer. A recent advance allows the rigorous analysis of experiments with two food types offered simultaneously. Here I propose a method for the multiple-choice case. For the first problem I suggest the use of multivariate statistical analysis, providing both a parametric and a nonparametric procedure. The second problem is solved using basic statistical theory. I analyse data from an experiment with the sea urchin Tetrapygus niger feeding on three species of algae: Ulva nematoidea, Gymnogongrus furcellatus, and Macrocystis pyrifera. The parametric and nonparametric procedures yielded similar results, and showed that when offered the three species of algae T. niger does not feed at random but shows a preference for U. nematoidea. The method requires that the number of replicates in the treatment and control arenas be the same, and greater than the number of food types. The method is useful for other kinds of multiple-choice experiments.     

BioFTF: An R package for biodiversity assessment with the functional data analysis approach

This paper presents the R package BioFTF, which is a tool for statistical biodiversity assessment in the functional data analysis framework. Diversity is a key topic in many research fields; however, in the literature, it is demonstrated that the existing indices do not capture the different aspects of this concept. Thus, a main drawback is that different indicators may lead to different orderings among communities according to their biodiversity. A possible method to evaluate biodiversity consists in using diversity profiles that are curves depending on a specific parameter. In this setting, it is possible to adopt some functional instruments proposed in the literature, such as the first and second derivatives, the curvature, the radius of curvature and the arc length. Specifically, the derivatives and the curvature (or the radius of curvature) highlight any peculiar behaviour of the profiles, whereas the arc length helps in ranking curves, given the richness. Because these instruments do not solve the issue of ranking communities with different numbers of species, we propose an important methodological contribution that introduces the surface area. Indeed, this tool is a scalar measure that reflects the information provided by the biodiversity profile and allows for ordering communities with different richness. However, this approach requires mathematical skills that the average user may not have; thus, our idea is to provide a user-friendly tool for both non-statistician and statistician practitioners to measure biodiversity in a functional context.     

Image analysis, neural networks, and the taxonomic impediment to biodiversity studies

The taxonomic impediment to biodiversity studies may be influenced radically by the application of new technology, in particular, desktop image analysers and neural networks. The former offer an opportunity to automate objective feature measurement processes, and the latter provide powerful pattern recognition and data analysis tools which are able to 'learn' patterns in multivariate data. The coupling of these technologies may provide a realistic opportunity for the automation of routine species identifications. The potential benefits and limitations of these technologies, along with the development of automated identification systems are reviewed.     

A suite of essential biodiversity variables for detecting critical biodiversity change

Key global indicators of biodiversity decline, such as the IUCN Red List Index and the Living Planet Index, have relatively long assessment intervals. This means they, due to their inherent structure, function as late‐warning indicators that are retrospective, rather than prospective. These indicators are unquestionably important in providing information for biodiversity conservation, but the detection of early‐warning signs of critical biodiversity change is also needed so that proactive management responses can be enacted promptly where required. Generally, biodiversity conservation has dealt poorly with the scattered distribution of necessary detailed information, and needs to find a solution to assemble, harmonize and standardize the data. The prospect of monitoring essential biodiversity variables (EBVs) has been suggested in response to this challenge. The concept has generated much attention, but the EBVs themselves are still in development due to the complexity of the task, the limited resources available, and a lack of long‐term commitment to maintain EBV data sets. As a first step, the scientific community and the policy sphere should agree on a set of priority candidate EBVs to be developed within the coming years to advance both large‐scale ecological research as well as global and regional biodiversity conservation. Critical ecological transitions are of high importance from both a scientific as well as from a conservation policy point of view, as they can lead to long‐lasting biodiversity change with a high potential for deleterious effects on whole ecosystems and therefore also on human well‐being. We evaluated candidate EBVs using six criteria: relevance, sensitivity to change, generalizability, scalability, feasibility, and data availability and provide a literature‐based review for eight EBVs with high sensitivity to change. The proposed suite of EBVs comprises abundance, allelic diversity, body mass index, ecosystem heterogeneity, phenology, range dynamics, size at first reproduction, and survival rates. The eight candidate EBVs provide for the early detection of critical and potentially long‐lasting biodiversity change and should be operationalized as a priority. Only with such an approach can science predict the future status of global biodiversity with high certainty and set up the appropriate conservation measures early and efficiently. Importantly, the selected EBVs would address a large range of conservation issues and contribute to a total of 15 of the 20 Aichi targets and are, hence, of high biological relevance.     

Old and new challenges in using species diversity for assessing biodiversity

Although the maintenance of diversity of living systems is critical for ecosystem functioning, the accelerating pace of global change is threatening its preservation. Standardized methods for biodiversity assessment and monitoring are needed. Species diversity is one of the most widely adopted metrics for assessing patterns and processes of biodiversity, at both ecological and biogeographic scales. However, those perspectives differ because of the types of data that can be feasibly collected, resulting in differences in the questions that can be addressed. Despite a theoretical consensus on diversity metrics, standardized methods for its measurement are lacking, especially at the scales needed to monitor biodiversity for conservation and management purposes. We review the conceptual framework for species diversity, examine common metrics, and explore their use for biodiversity conservation and management. Key differences in diversity measures at ecological and biogeographic scales are the completeness of species lists and the ability to include information on species abundances. We analyse the major pitfalls and problems with quantitative measurement of species diversity, look at the use of weighting measures by phylogenetic distance, discuss potential solutions and propose a research agenda to solve the major existing problems.     

Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science

New information technologies have enabled the scientific collections community and its stakeholders to adapt, adopt, and leverage novel approaches for a nearly 300 years old scientific discipline. Now, few can credibly question the transformational impact of technology on efforts to digitize scientific collections, as IT now reaches into almost every nook and cranny of society. Five to ten years ago this was not the case. Digitization is an activity that museums and academic institutions increasingly recognize, though many still do not embrace, as a means to boost the impact of collections to research and society through improved access. The acquisition and use of scientific collections is a global endeavor, and digitization enhances their value by improved access to core biodiversity information, increases use, relevance and potential downstream value, for example, in the management of natural resources, policy development, food security, and planetary and human health. This paper examines new opportunities to design and implement infrastructure that will support not just mass digitization efforts, but also a broad range of research on biological diversity and physical sciences in order to make scientific collections increasingly relevant to societal needs and interest.     

Local biodiversity and multi-habitat use in empidoid flies (Insecta: Diptera, Empidoidea)

The empidid fauna of four small adjacent biotopes bordering a pond was investigated for 2 consecutive years in Brittany (France). Adult activity was studied using yellow water traps, whereas suitable larval habitats were determined using emergence traps. While 24 species emerged from the soils, 45 flew above the four sites. The number of species emerging from each site was nearly identical. However, the highest number of individuals emerged from the heathland and numbers rapidly declined towards the pond banks. On the contrary, the greatest aerial activity occurred in the woodlot and near the pond banks. Fourteen times less flying activity was found above the dry heathland. The latter appeared to be a site of larval growth but mating and feeding of the adults took place in the woodlot. Reproduction sites and space used by the adults differed among the dominant species. The species assemblage could not be fully explained within the spatial limits of the four sites. Considering the species'behaviour, it is suggested that immigration of species and individuals from other sites should explain these differences. The study, which is supported by four other research works, emphasizes the role of key resource played by ecotonal zones between aquatic and terrestrial ecosystems in the persistence of species over a larger set of habitats. Considering the complementarity of habitats is essential to explain diversity patterns in species which need different space units to complete their life-cycle.     

Statistical analysis of functional response experiments

The aim of this paper is to highlight the benefits of a full data analysis of a functional response data set, compared to the usual one‐pass regression analysis. In a biological control setting where the choice of organism is often based on comparative studies of the functional responses, it is imperative to have both reliable estimates and a feeling of the degree of confidence one is willing to put on the figures. We analyzed a data set involving the freshwater predator Notonecta glauca (Hemiptera) preying on Asellus aquaticus during 24 h. The specific aim of the analysis was to test whether the functional response is of type II or type III. The different stages of a complete analysis are (1) a preliminary inspection of the data, (2) model building, (3) a model check and (4) a combination of the results with independent information. We argue that the analysis is best done with the predation rate as response and define a test for the location of its maximum. The existence of a maximum is typical for type III functional response. We explain why the binomial distribution is a natural error distribution, and how to implement the regression analysis within the family of generalized linear models using two competing link functions, the logit and the reciprocal. There is marked overdispersion which increases with increasing prey numbers. We use prior weights to take account of it. Using all available data, a type III functional response is warranted with the reciprocal link, but not with the logit link Model checks using Pearson residuals and regression diagnostics based on point deletions show that three points have a particularly strong influence on the parameter estimates. If these are deleted, the functional response type III is then warranted for both link functions. The complete analysis enables us to determine the various degrees of uncertainty and to draw biological conclusions with corresponding confidence. We are convinced that the data set shows a type III functional response, but we are less sure about which link function to choose. Furthermore, the marked overdispersion at high density, the regression diagnostics, as well as independent information on a change in the behaviour of the prey at high density, indicate that the experimental conditions may have changed as a function of the prey density.     

3S技术与生物多样性研究

生物多样性是地球生物圈和人类发展的基础,是国际社会所共同关注的焦点问题。3S技术是集遥感、全球定位与地理信息系统于一体的高新技术手段,为生物多样性研究提供强有力的技术支持。近年来该领域的研究越来越受到人们的重视,并取得了大量的研究成果。     

The value of biodiversity experiments

Recent biodiversity experiments have investigated the relationship between diversity and ecosystem functioning by synthesizing plant communities from pools of species that have been experimentally manipulated to vary numbers and types of species present while holding abiotic factors constant. Biodiversity experiments therefore focus on a previously under-explored aspect of global change: the feedback from diversity to environment. Consequences of random manipulation of species communities may not correspond well to those of specific extinction sequences observed in the past in response to extinction drivers that cause highly non-random loss. However, random manipulation provides a good starting point given that existing communities could undergo many alternative orders of species loss in the future in response to a variety of different potential extinction drivers. Further, the effects of some extinction drivers are currently poorly understood and therefore difficult to predict (e.g. climate change) and it may be premature to dismiss the predictions of random scenarios as irrelevant to all real examples of species loss. The first generations of biodiversity experiments have provided valuable, and sometimes unexpected, discoveries about the general nature of the relationship between diversity and ecosystem functioning. These discoveries could not have been made using observational studies. We propose that different examples of extinction loss in the real or a potential future world form a continuum from situations where the results of the first-generation biodiversity experiments will be highly relevant to less relevant. At the one extreme are examples where the effects of biodiversity on ecosystem functioning will be overwhelmed by direct effects of the extinction driver on processes (e.g. chronic eutrophication). At the other extreme are situations where ecosystem processes are not strongly affected by direct effects of the extinction driver and where the effects of species loss on functioning may be more important (e.g. habitat fragmentation). Given the unprecedented uncertainty about the future of biodiversity and the functioning of ecosystems, a general approach with randomly varying species pools was the right place to start in order to provide a general foundation. The new challenge is to test for effects of biodiversity on functioning in real-world examples of species loss.

Zusammenfassung

Biodiversitätsversuche zeichnen sich dadurch aus, dass natürliche Artenpools experimentell reduziert werden und anschließend der Zusammenhang zwischen der Artenzahl und Ökosystemfunktionen unter konstanten abiotischen Umweltbedingungen untersucht wird. Dadurch unterscheiden sich Biodiversitätsexperimente grundsätzlich von anderen Versuchen, die die Biodiversität als Zielvariable behandeln und stattdessen die abiotische Umwelt manipulieren. Die Auswahl der Arten für die reduzierten Artenpools in Biodiversitätsexperimenten erfolgte bisher meist zufällig, während natürliche Aussterbefaktoren wie Eutrophierung nicht alle Arten gleichermassen gefährden. Für verschiedene Aussterbefaktoren ist aber so wenig bekannt, dass ein zufälliges Aussterbeszenario die beste gegenwärtig verfügbare Option ist. Dies trifft insbesondere für mögliche zukünftige Aussterbeprozesse zu, die durch globale Umweltveränderungen (Klima, biologische Invasionen) oder Habitatsfragmentierung ausgelöst werden könnten. Die erste Generation von Biodiversitätsexperimenten mit zufälligen Aussterbeszenarien hat wertvolle, teilweise unerwartete, generelle Zusammenhänge zwischen Artenzahl und Ökosystemfunktionen aufgedeckt. Diese Zusammenhänge ließen sich durch vergleichende Studien nicht erkennen. In Zukunft sollten Biodiversitätsexperimente dennoch vermehrt Aussterbeszenarien simulieren, die in der realen Umwelt mit größter Wahrscheinlichkeit auftreten.     

生物分类和多样性保护

生物分类是生物学领域最基础的研究工作,生物多样性是当前生命科学研究热点之一。概述了生物分类思想的历史发展,探讨了基因组多样性研究中的伦理问题。     

空间尺度对地形异质性-物种多样性关系的影响:粒度和幅度

空间尺度是影响我们理解生态学格局和过程的关键因素.目前已有多种关于物种多样性分布格局形成机制的假说且研究者未达成共识,原因之一是空间尺度对物种多样性分布格局的环境影响因子的解释力和相对重要性有重要影响.地形异质性是物种多样性分布格局的重要影响因素.本文综述了在地形异质性-物种多样性关系的研究中,不同空间粒度和幅度对研究...     

Statistical review of the henhouse experiments: the effects of a pulsed magnetic field on chick embryos.

This paper analyzes data from a study conducted by the United States Office of Naval Research on the effects of pulsed magnetic fields on chick embryos. The experiment involved incubation of eggs under carefully controlled conditions in six different laboratories. The original analysis included inappropriate statistical methodology for analyzing the experimental results. Since the conclusions from this study rest so heavily on the results of statistical analyses, choosing the proper methodology is imperative. The major aim of this paper then is to introduce more appropriate analytic tools and illustrate their use in the present context. Qualitatively our results agree with those of the original analysis; our findings about interactions between effects, however, makes interpretation of these effects more subtle. We apply linear logistic modeling to counts of damaged embryos, using as covariates factors corresponding to exposure, laboratory, incubator, run, and measurements of background radiation. This facilitates estimation of the size of the effects. The effects of laboratory, incubator, and run are explored both as fixed and random effects. We find statistically significant exposure and laboratory effects, in accordance with the original study. However, we also find that the inter-laboratory variation in exposure effect is at least as large as the exposure effect itself. The presence of such effects fundamentally alters the interpretation of the fitted model, as is graphically presented.