Back to the future: natural history and the way forward in modern fungal ecology

The growing power and increasing availability of molecular tools for identifying fungi in environmental samples has revolutionized the way that fungal ecologists work. As a result, more people from around the globe have jumped into the fungal community sequencing endeavor. Paradoxically, as these extensive datasets accumulate we are often at a loss for interpretation due to the lack of basic autecology and natural history information for most fungi. As a result we are in danger of learning less and about more and more. I suggest that one way forward in fungal ecology is through a modern version of fungal natural history, with a focus on holistic understanding of individual species and ecosystems, but driven by modern genomic and molecular tools. By combining the extensive data generated through environmental sequencing with an intensive, molecular-based natural history we can create a synergy that will propel fungal ecology forward.     

Parasite interactions in natural populations: insights from longitudinal data

The physiological and immunological state of an animal can be influenced by current infections and infection history. Consequently, both ongoing and previous infections can affect host susceptibility to another parasite, the biology of the subsequent infection (e.g. infection length) and the impact of infection on host morbidity (pathology). In natural populations, most animals will be infected by a succession of different parasites throughout the course of their lives, with probably frequent concomitant infections. The relative timing of different infections experienced by a host (i.e. the sequence of infection events), and the effects on factors such as host susceptibility and host survival, can only be derived from longitudinal data on individual hosts. Here we review some of the evidence for the impact of co-infection on host susceptibility, infection biology and pathology focusing on insights obtained from both longitudinal studies in humans and experiments that explicitly consider the sequence of infection. We then consider the challenges posed by longitudinal infection data collected from natural populations of animals. We illustrate their usefulness using our data of microparasite infections associated with field vole (Microtus agrestis) populations to examine impacts on susceptibility and infection length. Our primary aim is to describe an analytical approach that can be used on such data to identify interactions among the parasites. The preliminary analyses presented here indicate both synergistic and antagonistic interactions between microparasites within this community and emphasise that such interactions could have significant impacts on host-parasite fitness and dynamics.     

生物多样性信息学研究进展

生物多样性信息学是一门蓬勃发展的新学科。它将现代的信息技术带入生物多样性及其相关学科的研究领域。它在生物多样性基础数据的数字化、模型工具和各种工具软件的开发、数据整合, 以及全球、地区和国家尺度生物多样性信息网络等多个方面的发展, 向我们展示了未来在全球范围内自由、免费共享生物多样性数据和信息, 以及人们行动起来共同关注、调查与监测野外生物多样性的前景。目前, 已有大量数字化的物种编目、标本馆标本、多媒体影像、研究文献等生物多样性基础信息可以通过互联网检索和利用。其中, 最值得关注的是一些成功的国际性研究项目, 如物种2000、全球生物多样性信息网络、生命条形码以及网络生命大百科全书。这些项目的成功不仅体现在对大量基础信息和数据的发布, 而且它们通过与生物多样性信息标准TDWG(Biodiversity Information Standards: TDWG)的合作, 推动了达尔文核心标准(Darwin Core)等一些重要的生物多样性信息标准的应用, 以及地区和国家性生物多样性信息节点的建立, 这些都为将来全球范围生物多样性信息的共享和数据交换奠定了重要基础。在数字化信息的基础上, 研究人员也开发了一些在特定研究领域应用的数据挖掘和模型工具, 例如基于数字化标本的地理分布预测工具MAXENT, 分类学专家知识管理的LifeDesk。公民科学理念的发展则向我们展示了公众和科学爱好者广泛参与以互联网为基础的生物多样性信息学研究活动。因此, 生物多样性信息学的发展前景广阔, 它将为我们实现全球保护战略目标, 应对生物多样性危机, 解决全球气候变化条件下生物多样性资源管理和利用建立坚实的信息基础。     

A community mobilisation intervention to prevent violence against women and reduce HIV/AIDS risk in Kampala, Uganda (the SASA! Study): study protocol for a cluster randomised controlled trial

ABSTRACT: BACKGROUND: Gender based violence, including violence by an intimate partner, is a major global human rights and public health problem, with important connections with HIV risk. Indeed, the elimination of sexual and gender based violence is a core pillar of HIV prevention for UNAIDS. Integrated strategies to address the gender norms, relations and inequities that underlie both violence against women and HIV/AIDS are needed. However there is limited evidence about the potential impact of different intervention models. This protocol describes the SASA! Study: an evaluation of a community mobilisation intervention to prevent violence against women and reduce HIV/AIDS risk in Kampala, Uganda. METHODS: The SASA! Study is a pair-matched cluster randomised controlled trial being conducted in eight communities in Kampala. It is designed to assess the community-level impact of the SASA! intervention on the following six primary outcomes: attitudes towards the acceptability of violence against women and the acceptability of a woman refusing sex (among male and female community members); past year experience of physical intimate partner violence and sexual intimate partner violence (among females); community responses to women experiencing violence (among women reporting past year physical/sexual partner violence); and past year concurrency of sexual partners (among males). 1583 women and men (aged 18-49 years) were surveyed in intervention and control communities prior to intervention implementation in 2007/8. A follow-up cross-sectional survey of community members will take place in 2012. The primary analysis will be an adjusted cluster-level intention to treat analysis, comparing outcomes in intervention and control communities at follow-up. Complementary monitoring and evaluation and qualitative research will be used to explore and describe the process of intervention implementation and the pathways through which change is achieved. DISCUSSION: This is one of few cluster randomised trials globally to assess the impact of a gender-focused community mobilisation intervention. The multi-disciplinary research approach will enable us to address questions of intervention impact and mechanisms of action, as well as its feasibility, acceptability and transferability to other contexts. The results will be of importance to researchers, policy makers and those working on the front line to prevent violence against women and HIV.     

Finding the Needles in the Metagenome Haystack

In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth’s diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments.     

Dynamics of bacterial community development in the reef coral <Emphasis Type="Italic">Acropora muricata</Emphasis> following experimental antibiotic treatment

Development of the bacterial community associated with the coral Acropora muricata (=formosa) was monitored using 16S rRNA gene-based techniques and abundance counts over time following experimental modification of the existing microbial community using the antibiotic ciprofloxacin. Abundance of bacteria was reduced >99% by the treatment, resulting in significant changes in bacterial community structure. Following redeployment to their natural environment, some settlement and re-growth of bacteria took place within a few hours, including ribosomal types that were not present, or in low abundance, in the natural microbiota. However, complete recovery of the bacterial community required longer than 96 h, which indicates a relatively slow settlement and growth of bacteria from the water column and suggests that turnover of the natural community is similarly slow. The early developing community was dominated by antibiotic-resistant bacteria from the natural microbiota that survived the treatment and proliferated in the absence of natural competitors, but also included some non-resident ribotypes colonizing from the water column. Almost, all these opportunists were significantly reduced or eliminated within 96 h after treatment, demonstrating a high resilience in the natural bacterial community. Potential pathogens, including a Clostridium sp., inhabited the coral at low abundances, only becoming prevalent when the natural microbiota was disturbed by the treatment. The healthy coral-associated microbiota appears to be strongly controlled by microbial interactions.     

An individual-based model of chaparral vegetation response to frequent wildfires

The Santa Monica Mountains are home to many species of chaparral shrubs that provide vegetative cover and whose deep roots contribute to the stability of the steep slopes. Recently, native chaparral have been threatened by an unprecedented drought and frequent wildfires in Southern California. Besides the damage from the wildfires themselves, there is the potential for subsequent structural losses due to erosion and landslides. In this paper, we develop a mathematical model that predicts the impact of drought and frequent wildfires on chaparral plant community structure. We begin by classifying chaparral into two life history types based on their response to wildfires. Nonsprouters are completely killed by a fire, but their seeds germinate in response to fire cues. Facultative sprouters survive by resprouting but also rely on seed germination for post-fire recovery. The individual-based model presented here simulates the growth, seed dispersal, and resprouting behavior of individual shrubs across two life history types as they compete for space and resources in a rectangular domain. The model also incorporates varying annual rainfall and fire frequency as well as the competition between plants for scarce resources. The parameters were fit using seedling and resprout survivorship data as well as point quarter sampling data from 1986 to 2014 at a biological preserve within the natural landscape of the Malibu campus of Pepperdine University. The simulations from our model reproduce the change in plant community structure at our study site which includes the local extinction of the nonsprouter Ceanothus megacarpus due to shortened fire return intervals. Our simulations predict that a combination of extreme drought and frequent wildfires will drastically reduce the overall density of chaparral, increasing the likelihood of invasion by highly flammable exotic grasses. The simulations further predict that the majority of surviving shrubs will be facultative sprouting species such as Malosma laurina.     

Joint inference of population assignment and demographic history

A new approach to assigning individuals to populations using genetic data is described. Most existing methods work by maximizing Hardy-Weinberg and linkage equilibrium within populations, neither of which will apply for many demographic histories. By including a demographic model, within a likelihood framework based on coalescent theory, we can jointly study demographic history and population assignment. Genealogies and population assignments are sampled from a posterior distribution using a general isolation-with-migration model for multiple populations. A measure of partition distance between assignments facilitates not only the summary of a posterior sample of assignments, but also the estimation of the posterior density for the demographic history. It is shown that joint estimates of assignment and demographic history are possible, including estimation of population phylogeny for samples from three populations. The new method is compared to results of a widely used assignment method, using simulated and published empirical data sets.     

The Journal of Morphology as window and mirror: reflections and glimpses on the birth of American biology

The centennial of the Journal of Morphology provides a fitting occasion to reflect upon the condition of American biology surrounding the founding years of the Journal. The Journal was started by C.O. Whitman in 1887. At this same time, the American biological community experienced a gradual change from a community of amateurs based within the natural history tradition to a professional community based within universities with specialized research programs. Many of the changes associated with this maturation process are exhibited in the pages of the first ten volumes of the Journal. They show that the Journal played a central role in communicating research methods and questions to the growing community of professional biologists. Moreover, these same volumes provide an accurate record of the character of the morphological sciences at the end of the 19th century.     

Multilocus genomics of outcrossing plant populations

The structure and organization of natural plant populations can be understood by estimating the genetic parameters related to mating behavior, recombination frequency, and gene associations with DNA-based markers typed throughout the genome. We developed a statistical and computational model for estimating and testing these parameters from multilocus data collected in a natural population. This model, constructed by a maximum likelihood approach and implemented within the EM algorithm, is shown to be robust for simultaneously estimating the outcrossing rate, recombination frequencies and linkage disequilibria. The algorithm built with three or more markers allows the characterization of crossover interference in meiosis and high-order disequilibria among different genes, thus providing a powerful tool for illustrating a detailed picture of genetic diversity and organization in natural populations. Computer simulations demonstrate the statistical properties of the proposed model. This multilocus model will be useful for studying the pattern and amount of genetic variation within and among populations to further infer the evolutionary history of a plant species.     

Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets

Metagenomics holds the promise of greatly advancing the study of diversity in natural communities, but novel theoretical and methodological approaches must first be developed and adjusted for these data sets. We evaluated widely used macroecological metrics of taxonomic diversity on a simulated set of metagenomic samples, using phylogenetically meaningful protein-coding genes as ecological proxies. To our knowledge, this is the first approach of this kind to evaluate taxonomic diversity metrics derived from metagenomic data sets. We demonstrate that abundance matrices derived from protein-coding marker genes reproduce more faithfully the structure of the original community than those derived from SSU-rRNA gene. We also found that the most commonly used diversity metrics are biased estimators of community structure and differ significantly from their corresponding real parameters and that these biases are most likely caused by insufficient sampling and differences in community phylogenetic composition. Our results suggest that the ranking of samples using multidimensional metrics makes a good qualitative alternative for contrasting community structure and that these comparisons can be greatly improved with the incorporation of metrics for both community structure and phylogenetic diversity. These findings will help to achieve a standardized framework for community diversity comparisons derived from metagenomic data sets.     

The influence of ecology and genetics on behavioral variation in salamander populations across the Eastern Continental Divide

Understanding the unique contributions of ecology and history to the distribution of species within communities requires an integrative approach. The Eastern Continental Divide in southwestern Virginia separates river drainages that differ in species composition: the more aquatic, predatory Desmognathus quadramaculatus is present only in the New River drainage (which drains to the Gulf of Mexico), while Desmognathus monticola is present in both the New River drainage and the James River drainage (which drains to the Atlantic Ocean). We investigated natural distributions, behavioral variation in experimental mesocosms, population genetic, and phylogenetic implications of community structure. The presence of D. quadramaculatus increased the terrestriality of D. monticola in natural and experimental situations but to different degrees in allopatric and sympatric populations. Our ecological data suggest that the degree of terrestriality in D. monticola is a result of a balance between the optimal aquatic habitat and risks of predation. Our genetic analyses suggest that D. monticola has experienced a recent range expansion and has only a recent history of association with D. quadramaculatus in Virginia. This is surprising given the strong behavioral variation that exists in populations experiencing unique community compositions over a scale of meters. This study demonstrates the need to combine both ecology and genetics toward an understanding of the factors affecting species distributions, behavioral variation between populations, and patterns of genetic variation across a landscape.     

Unlocking avian museum collections to enable and advance environmental change research

The rate and magnitude of contemporary changes in natural systems is unprecedented in the Earth's history. Studies of wild birds have been critically important in helping us understand and address these environmental changes. Avian collections provide a potentially unique perspective on change through time, but their role in environmental change research is limited by the availability of collections data. Here we describe how avian collections might be unlocked to enable environmental change research, and discuss the opportunities and constraints associated with this. We use the concept of the extended specimen to describe the types of data that could be unlocked from basic data for discoverability to enhanced data that might be directly applied to environmental change questions. We illustrate the type of environmental change research these data might support. We argue that data creation and access is currently limited by funding for digitization, a rather patchy understanding of the needs of the research community and less than adequate data-sharing by institutions and researchers. We develop a blueprint for addressing these issues which includes (1) improvements in sharing the data we are already creating and (2) building a better case for digitization at scale. As one of the largest avian collections in the world, the Natural History Museum, UK, is committed to unlocking our collections, but we will need input and support from the avian research community to do so.     

History,rather than contemporary processes,determines variation in macroinvertebrate diversity in artesian springs: the expansion hypothesis

1. The relative importance of contemporary and historical processes is a fundamental question in understanding patterns of biodiversity. We tested the hypothesis that species‐sorting into different habitats (limnocrenes, rheocrenes, helocrenes), rather than history, would account for the greatest variation in macroinvertebrate diversity in desert artesian springs of The Bonneville Basin, U.S.A. These springs were isolated at the valley scale c. 9000 years ago by aridity and high salinity. Thus, the valley scale will account for the greatest variation in community composition if history and dispersal limitation are important, whereas niche‐based sorting processes will be most important if habitat accounts for the greatest variation in community composition. 2. We identified 302 taxa from 280 sites and used a partial redundancy analysis, additive partitioning and classification strength (CS) to partition the variability in diversity among the springs. The valley scale accounted for more variation in community composition in limnocrene habitats (32.5%) than all other spatial and environmental variables combined. Valleys also accounted for 58% (additive partitioning) and 83% (CS) of the regional variation in diversity in analyses that included all three habitat types. That is, the average community similarity was 25% across the region, but increased to 41% within valleys. By contrast, habitat filtering did not account for significant variation in community composition in any of the analyses. Our study is one of the few suggesting the over‐riding importance of neutral processes in determining patterns of diversity (history and dispersal limitation). 3. The ‘expansion’ hypothesis suggests that the youthful age of a region, combined with slow dispersal by a fauna dominated by generalists, will maximise the imprint of history. These communities appear to exist in a pre‐equilibrial state, where the maximum carrying capacity has not been reached and niche space is plentiful. With time, we predict that local richness will increase while β‐diversity decreases as species expand their distribution across the region. Consequently, the importance of niche‐based processes may increase with time as the imprint of history fades.     

Perception,pattern, chance and the structure of reef fish communities

The recent history of attempts to understand the ecology of fish on coral reefs is surveyed as an example of the way in which science progresses. Scientists are trapped, both by their sensory equipment and by their preconceptions, into viewing the world in certain ways. Paradigms fall only slowly. Scientists are trained to seek pattern in their data, yet in some cases the largely stochastic variation of a system around its mean condition is the more important key to understanding its ecology. The reef fish assemblage provides such a case. It is unlikely that our present understanding of the nature of reef fish communities will survive unchanged by future research. And it is also unlikely that reef fish ecologists are the only ecologists who have difficulty discovering truth! Editorial     

Caries-preventive effect of glass ionomer and resin-based fissure sealants on permanent teeth: An update of systematic review evidence

Background

The 1980s marked the occasion when Geographical Information System (GIS) technology was broadly introduced into the geo-spatial community through the establishment of a strong GIS industry. This technology quickly disseminated across many countries, and has now become established as an important research, planning and commercial tool for a wider community that includes organisations in the public and private health sectors. The broad acceptance of GIS technology and the nature of its functionality have meant that numerous datasets have been created over the past three decades. Most of these datasets have been created independently, and without any structured documentation systems in place. However, search and retrieval systems can only work if there is a mechanism for datasets existence to be discovered and this is where proper metadata creation and management can greatly help. This situation must be addressed through support mechanisms such as Web-based portal technologies, metadata editor tools, automation, metadata standards and guidelines and collaborative efforts with relevant individuals and organisations. Engagement with data developers or administrators should also include a strategy of identifying the benefits associated with metadata creation and publication.

Findings

The establishment of numerous Spatial Data Infrastructures (SDIs), and other Internet resources, is a testament to the recognition of the importance of supporting good data management and sharing practices across the geographic information community. These resources extend to health informatics in support of research, public services and teaching and learning. This paper identifies many of these resources available to the UK academic health informatics community. It also reveals the reluctance of many spatial data creators across the wider UK academic community to use these resources to create and publish metadata, or deposit their data in repositories for sharing. The Go-Geo! service is introduced as an SDI developed to provide UK academia with the necessary resources to address the concerns surrounding metadata creation and data sharing. The Go-Geo! portal, Geodoc metadata editor tool, ShareGeo spatial data repository, and a range of other support resources, are described in detail.

Conclusions

This paper describes a variety of resources available for the health research and public health sector to use for managing and sharing their data. The Go-Geo! service is one resource which offers an SDI for the eclectic range of disciplines using GIS in UK academia, including health informatics. The benefits of data management and sharing are immense, and in these times of cost restraints, these resources can be seen as solutions to find cost savings which can be reinvested in more research.     

试论生物对环境的调节作用

在处理人与自然的战略关系时存在着两种相互对立的观点 :第一种观点认为 ,由于地球位于太阳系合适的轨道上 ,其表面具有独特的有益于生命活动的物理条件。生命系统 (天然的动植物区系 )适应其居住的环境。依靠生命系统本身的作用可以改变环境。通过物种的进化 ,生命系统能适应环境的变化。例如 ,在古代生命系统引发了还原性大气向氧化性大气的转变 ,由此产生了需氧生物 ,而那些厌氧的生物或者灭绝 ,或者转向局部厌氧环境。第二种观点则注重地球环境的物理学上的不稳定性 ,认为地球物理环境正在向与金星或火星类似的没有生命的环境转变 ,而地…