分子遗传技术与生物遗传多样性研究

各种分子遗传技术为不同生物种类间进行直接比较和分子水平的遗传多样性的度量、研究提供了新的途径。本文讨论了此类分子水平研究所取得的一些新的进展，并指出了有关分子工具应用于生物多样性研究中存在的一些问题。     

Genetic Data and the Listing of Species Under the U.S. Endangered Species Act

Abstract:  Genetic information is becoming an influential factor in determining whether species, subspecies, and distinct population segments qualify for protection under the U.S. Endangered Species Act. Nevertheless, there are currently no standards or guidelines that define how genetic information should be used by the federal agencies that administer the act. I examined listing decisions made over a 10-year period (February 1996–February 2006) that relied on genetic information. There was wide variation in the genetic data used to inform listing decisions in terms of which genomes (mitochondrial vs. nuclear) were sampled and the number of markers (or genetic techniques) and loci evaluated. In general, whether the federal agencies identified genetic distinctions between putative taxonomic units or populations depended on the type and amount of genetic data. Studies that relied on multiple genetic markers were more likely to detect distinctions, and those organisms were more likely to receive protection than studies that relied on a single genetic marker. Although the results may, in part, reflect the corresponding availability of genetic techniques over the given time frame, the variable use of genetic information for listing decisions has the potential to misguide conservation actions. Future management policy would benefit from guidelines for the critical evaluation of genetic information to list or delist organisms under the Endangered Species Act.     

Interacting Effects of Phenotypic Plasticity and Evolution on Population Persistence in a Changing Climate

Abstract: Climate change affects individual organisms by altering development, physiology, behavior, and fitness, and populations by altering genetic and phenotypic composition, vital rates, and dynamics. We sought to clarify how selection, phenotypic plasticity, and demography are linked in the context of climate change. On the basis of theory and results of recent empirical studies of plants and animals, we believe the ecological and evolutionary issues relevant to population persistence as climate changes are the rate, type, magnitude, and spatial pattern of climate‐induced abiotic and biotic change; generation time and life history of the organism; extent and type of phenotypic plasticity; amount and distribution of adaptive genetic variation across space and time; dispersal potential; and size and connectivity of subpopulations. An understanding of limits to plasticity and evolutionary potential across traits, populations, and species and feedbacks between adaptive and demographic responses is lacking. Integrated knowledge of coupled ecological and evolutionary mechanisms will increase understanding of the resilience and probabilities of persistence of populations and species.     

Understanding the Causes of Disease in European Freshwater Crayfish

Abstract:  Native European freshwater crayfish (Astacida, Decapoda) are under severe pressure from habitat alteration, the introduction of nonindigenous species, and epizootic disease. Crayfish plague, an acute disease of freshwater crayfish caused by the fungus-like agent Aphanomyces astaci , was introduced into Europe in the mid-nineteenth century and is responsible for ongoing widespread epizootic mortality in native European populations. We reviewed recent developments and current practices in the field of crayfish pathology. The severity of crayfish plague has resulted in an overemphasis on it. Diagnostic methods for detecting fungi and fungal-like agents, and sometimes culturing them, are frequently the sole techniques used to investigate disease outbreaks in European freshwater crayfish. Consequently, the causes of a significant proportion of outbreaks are undetermined. Pathogen groups well known for causing disease in other crustaceans, such as viruses and rickettsia-like organisms, are poorly understood or unknown in European freshwater crayfish. Moreover, the pathogenic significance of some long-known pathogens of European freshwater crayfish remains obscure. For effective management of this culturally significant and threatened resource, there is an urgent need for researchers, diagnosticians, and resource managers to address the issue of disease in European freshwater crayfish from a broader perspective than has been applied previously.     

嗜酸微生物生态学与矿物生物浸出技术

综述了嗜酸微生物存在的环境、生态结构和微生物多样性,以及温度、氧对嗜酸微生物的影响.总结了嗜酸微生物群落间存在竞争、捕食、共生、合作等相互作用关系,这对理解矿物的生物浸出具有重要意义.目前对嗜酸微生物生态学的理解主要基于传统的纯菌培养分离技术,但是分子生物学技术的发展提供了更科学的研究手段,将纯菌培养分离技术和分子生物学技术相结合是研究嗜酸微生物生态的有效方法.认为理解嗜酸微生物生态学规律,将有利于开发新的微生物矿物加工技术,我国有必要加强浸矿微生物生态学的研究.表1参24     

Bridging the gap between ecophysiological and genetic knowledge to assess the adaptive potential of European beech

In this study we aimed to combine knowledge of the ecophysiology and genetics of European beech to assess the potential of this species to adapt to environmental change. Therefore, we performed field and experimental studies on the genetic and ecophysiological functioning of beech. This information was integrated through a coupled genetic–ecophysiological model for individual trees that was parameterized with information derived from our own studies or from the literature. Using the model, we evaluated the adaptive response of beech stands in two ways: firstly, through sensitivity analyses (of initial genetic diversity, pollen dispersal distance, heritability of selected phenotypic traits, and forest management, representing disturbances) and secondly, through the evaluation of the responses of phenotypic traits and their genetic diversity to four management regimes applied to 10 study plots distributed over Western Europe. The model results indicate that the interval between recruitment events strongly affects the rate of adaptive response, because selection is most severe during the early stages of forest development. Forest management regimes largely determine recruitment intervals and thereby the potential for adaptive responses. Forest management regimes also determine the number of mother trees that contribute to the next generation and thereby the genetic variation that is maintained. Consequently, undisturbed forests maintain the largest amount of genetic variation, as recruitment intervals approach the longevity of trees and many mother trees contribute to the next generation. However, undisturbed forests have the slowest adaptive response, for the same reasons.Gene flow through pollen dispersal may compensate for the loss in genetic diversity brought about by selection. The sensitivity analysis showed that the total genetic diversity of a 2 ha stand is not affected by gene flow if the pollen distance distribution is varied from highly left-skewed to almost flat. However, a stand with a prevailing short-distance gene flow has a more pronounced spatial genetic structure than stands with equal short- and long-distance gene flows. The build-up of a spatial genetic structure is also strongly determined by the recruitment interval. Overall, the modelling results indicate that European beech has high adaptive potential to environmental change if recruitment intervals are short and many mother trees contribute to the next generation.The findings have two implications for modelling studies on the impacts of climate change on forests. Firstly: it cannot be taken for granted that parameter values remain constant over a time horizon of even a few generations – this is particularly important for threshold values subject to strong selection, like budburst, frost hardiness, drought tolerance, as used in species area models. Secondly: forest management should be taken into account in future assessments, as management affects the rate of adaptive response and thereby the response on trees and forests to environmental change, and because few forests are unmanaged. We conclude that a coupled ecophysiological and quantitative genetic tree model is a useful tool for such studies.     

A summer heat wave decreases the immunocompetence of the mesograzer, Idotea baltica

Extreme events associated with global change will impose increasing stress on coastal organisms. How strong biological interactions such as the host–parasite arms-race are modulated by environmental change is largely unknown. The immune system of invertebrates, in particular phagocytosis and phenoloxidase activity response are key defence mechanisms against parasites, yet they may be sensitive to environmental perturbations. We here simulated an extreme event that mimicked the European heat wave in 2003 to investigate the effect of environmental change on the immunocompetence of the mesograzer Idotea baltica. Unlike earlier studies, our experiment aimed at simulation of the natural situation as closely as possible by using long acclimation, a slow increase in temperature and a natural community setting including the animals’ providence with natural food sources (Zostera marina and Fucus vesiculosus). Our results demonstrate that a simulated heat wave results in decreased immunocompetence of the mesograzer Idotea baltica, in particular a drop of phagocytosis by 50%. This suggests that global change has the potential to significantly affect host–parasite interactions.     

How Research‐Prioritization Exercises Affect Conservation Policy

Abstract: Conservation scientists are concerned about the apparent lack of impact their research is having on policy. By better aligning research with policy needs, conservation science might become more relevant to policy and increase its real‐world salience in the conservation of biological diversity. Consequently, some conservation scientists have embarked on a variety of exercises to identify research questions that, if answered, would provide the evidence base with which to develop and implement effective conservation policies. I synthesized two existing approaches to conceptualizing research impacts. One widely used approach classifies the impacts of research as conceptual, instrumental, and symbolic. Conceptual impacts occur when policy makers are sensitized to new issues and change their beliefs or thinking. Instrumental impacts arise when scientific research has a direct effect on policy decisions. The use of scientific research results to support established policy positions are symbolic impacts. The second approach classifies research issues according to whether scientific knowledge is developed fully and whether the policy issue has been articulated clearly. I believe exercises to identify important research questions have objectives of increasing the clarity of policy issues while strengthening science–policy interactions. This may facilitate the transmission of scientific knowledge to policy makers and, potentially, accelerate the development and implementation of effective conservation policy. Other, similar types of exercises might also be useful. For example, identification of visionary science questions independent of current policy needs, prioritization of best practices for transferring scientific knowledge to policy makers, and identification of questions about human values and their role in political processes could all help advance real‐world conservation science. It is crucial for conservation scientists to understand the wide variety of ways in which their research can affect policy and be improved systematically.     

Elephants as agents of habitat creation for small vertebrates at the patch scale

Ecologists increasingly recognize the ability of certain species to influence ecological processes by engineering the physical environment, but efforts to develop a predictive understanding of this phenomenon are in their early stages. While many believe that the landscape-scale effects of ecosystem engineers will be to increase habitat diversity and therefore the abundance and richness of other species, few generalities exist about the effects of engineering at the scale of the engineered patch. According to one hypothesis, activities that increase structural habitat complexity within engineered patches will have positive effects on the abundance or diversity of other organisms. Here I show that, by damaging trees and increasing their structural complexity, browsing elephants create refuges used by a common arboreal lizard. Observational surveys and a lizard transplant experiment revealed that lizards preferentially occupy trees with real or simulated elephant damage. A second experiment showed that lizards vacate trees when elephant-engineered refuges are removed. Furthermore, local lizard densities increased with (and may be constrained by) local densities of elephant-damaged trees. This facilitative effect of elephants upon lizards via patch-scale habitat modification runs contrary to previously documented negative effects of the entire ungulate guild on lizards at the landscape scale, suggesting that net indirect effects of large herbivores comprise opposing trophic and engineering interactions operating at different spatial scales. Such powerful megaherbivore-initiated interactions suggest that anthropogenic changes in large-mammal densities will have important cascading consequences for ecological communities.     

Network position: a key component in the characterization of social personality types

In recent years, animal social interactions have received much attention in terms of personality research (e.g. aggressive or cooperative interactions). However, other components of social behaviour such as those describing the intensity, frequency, directedness and individual repeatability of interactions in animal groups have largely been neglected. Network analysis offers a valuable opportunity to characterize individual consistency of traits in labile social groups and therein provide novel insights to personality research in ways previously not possible using traditional techniques. Should individual network positions be consistently different between individuals under changing conditions, they might reflect expressions of an individual's personality. Here, we discuss a conceptual framework for using network analyses to infer the presence of individual differences and present a statistical test based on randomization techniques for testing the consistency of network positions in individuals. The statistical tools presented are useful because if particular individuals consistently occupy key positions in social networks, then this is also likely to have consequences for their fitness as well as for that of others in the population. These consequences may be particularly significant since individual network position has been shown to be important for the transmission of diseases, socially learnt information and genetic material between individuals and populations.     

A new approach to investigate the interactions between sediment transport and ecotoxicological processes during flood events

Purpose

The 'step-by step' principle was introduced into the European Union legislation on genetically modified organisms as a means to cope with uncertainty about environmental risks from the release of genetically modified organisms into the environment. The approval process is orientated along the stepwise reduction of containment which reflects a precautionary approach towards the risks of genetically modified organism release. Thus, the gradual reduction of containment should keep pace with the gradual generation of risk-related knowledge. This paper strives to clarify the meaning, legal status and practical importance of the principle. It also looks at whether non-European Union countries have adopted the principle as well, and how they practice it.

Methods

The article is based on research of the relevant legal texts, court cases and legal literature. In addition, a number of dossiers of applications for the European Union authorisation of release and placing on the market of genetically modified seed were analysed.

Results and conclusions

Although 'step-by-step' is not a precise legal rule it does have legal meaning as a principle guiding the risk assessment and management of genetically modified organism introduction into the environment. Assuming a process of gradual reduction of containment and scaling up of release ranging from closed systems via experimental release to cultivation the 'step-by-step principle' requires that the knowledge on environmental risks of genetically modified organisms should be generated on stages previous to the ones where the risk can result in damage. The analysis of the legislation of China, the United States of America and Brazil showed a differentiated approach towards the step-by-step principle.     

Application to the Port of Sines of a new tool for risk assessment in port navigation

This paper describes a first approach on the risk assessment in port navigation using GUIOMAR, an integrated system for port and coastal engineering modelling developed at the National Civil Engineering Laboratory (LNEC), Portugal, using a GIS software environment. A set of automatic procedures was designed to include a new methodology based on the amplitude of the wave-induced vertical movement of a ship along its trajectory. In this methodology, the risk in port navigation is assessed on the basis of a combination of the probability of exceedance of a pre-set threshold for the ship??s vertical movements and its consequences. To test the new procedures, a set of sea wave records obtained at the Sines wave-buoy from 1988 to 2002 was transferred into Sines Port using two numerical models of sea wave propagation and deformation (SWAN and DREAMS), included in the GUIOMAR system. The numerical model WAMIT was used for estimating the wave-induced ship??s vertical movements inside the port. By applying the new procedures, automatic generation of risk maps was carried out for navigation in the vicinity of the West breakwater of the Port of Sines. The recent developments contribute towards a more versatile and efficient GUIOMAR system, which results in a more adequate tool to support decision-making processes in port and coastal management.     

Revisiting the evolution of ecological specialization, with emphasis on insect-plant interactions

Ecological specialization is a fundamental and well-studied concept, yet its great reach and complexity limit current understanding in important ways. More than 20 years after the publication of D. J. Futuyma and G. Moreno's oft-cited, major review of the topic, we synthesize new developments in the evolution of ecological specialization. Using insect-plant interactions as a model, we focus on important developments in four critical areas: genetic architecture, behavior, interaction complexity, and macroevolution. We find that theory based on simple genetic trade-offs in host use is being replaced by more subtle and complex pictures of genetic architecture, and multitrophic interactions have risen as a necessary framework for understanding specialization. A wealth of phylogenetic data has made possible a more detailed consideration of the macroevolutionary dimension of specialization, revealing (among other things) bidirectionality in transitions between generalist and specialist lineages. Technological advances, including genomic sequencing and analytical techniques at the community level, raise the possibility that the next decade will see research on specialization spanning multiple levels of biological organization in non-model organisms, from genes to populations to networks of interactions in natural communities. Finally, we offer a set of research questions that we find to be particularly pressing and fruitful for future research on ecological specialization.     

Invasion with stage-structured coupled map lattices: Application to the spread of scentless chamomile

Two fundamental aspects of invasion dynamics are population growth and population spread. These quantities have been subject of study in biological invasions and can be used to study management and control of organisms. In this paper we derive formulae to calculate wave speed and rates of spread for coupled map lattices. Coupled map lattice models are dynamical models where space and time are discrete. We also show how wave speed and rate of spread can be calculated for structured population coupled map lattices in deterministic, stochastic environments and heterogeneous landscapes. Coupled map lattices are simple mathematical models that can be easily linked to landscape data to study invading organisms control strategies.     

典型POPs的生物降解修复技术研究与发展

生物吸附与降解是解决持久性有机污染物（POPs）最有潜力的方法之一,有必要介绍利用微生物把目标污染物转化为易降解的物质甚至矿化的POPs修复原理及其技术。对此,概述了近年来国内外基于微生物通过膜融合、胞质融合和核融合形成能够降解POPs的杂种细胞的细胞融合技术;基于降解性质粒的相容性,把能够降解不同污染物的质粒组合到一个菌种中,形成多质粒的新菌种,使微生物由于代谢途径的改变能够矿化POPs的基因工程菌构建技术;基于通过某些载体把酶固定于其中实现活性稳定、可以回收及可重复利用的酶固定化技术,以及基于降解菌活性酶分子亚基置换、降解菌活性酶的定点突变、降解酶的体外定向进化这几方面的酶构建技术;进一步分析基于分子生物学提高POPs生物修复能力的原理,指出经生物技术改造的工程菌和固定化酶未能进入实际应用的障碍所在。以多溴联苯醚（PBDEs）的微生物细胞吸收和降解机理作为典型POPs生物修复的案例,强调生物降解的过程强化需要建立多尺度上功能方面的适合;提出了分子生物学与基因工程学的结合在解决POPs环境污染方面未来的基础科学问题与研究思路。综合上述,典型POPs的生物修复技术的构建需要考虑宏观污染物协同降解的工艺理论,在基因水平、分子水平、反应器水平及工程水平上追求更高功能方面的适合。     

Population genetic analysis of Ensis directus unveils high genetic variation in the introduced range and reveals a new species from the NW Atlantic

We report current genetic variation of populations of the razor shell Ensis directus (Conrad 1843) (Mollusca: Bivalvia: Pharidae) in native (North American) and introduced (European) ranges using nuclear and mitochondrial sequence-based markers. We expected less variation within the introduced range, especially considering the frequent mass mortality events observed in Europe since the species was recorded for the first time in 1978. However, we found higher variation in Europe. The possible significance of temporal fluctuations of genetic variation, limited effect of random genetic drift, and multiple introductions are discussed. Interestingly, the multiple-introduction hypothesis contrasts with the gradual colonisation of European coastal waters but is supported by trained clustering analysis and by the intensity of transatlantic shipping. Genetic and morphometric evidence strongly supports that examined individuals from a supposed E. directus population from Newfoundland (Canada) belong to a separate species. This new Ensis is formally described here and named E. terranovensis n.sp.     

Microsatellite analysis of plaice (Pleuronectes platessa L.) in the NE Atlantic: weak genetic structuring in a milieu of high gene flow

Many species of marine fish are typified by large population sizes, strong migratory behavior, high fecundity, and pelagic eggs and larvae that are passively transported by ocean currents, all features that tend to increase gene flow, and hence reduce genetic partitioning, among localized populations. The plaice, Pleuronectes platessa, is a commercially important demersal species that exhibits all of these characteristics. We analyzed genetic variation at eight microsatellite loci in samples of spawning adults (N = 348) from the coasts of Ireland, Iceland, and, for the first time, from the Baltic Sea. Significant differentiation was observed between Iceland and Irish and Baltic Sea samples. However, there were no genetic differences between Irish and Baltic Sea samples, which contrast with the significant differentiation reported between Baltic Sea and North Sea/Atlantic populations of other flatfish species. To increase the data set, we carried out a cross-calibration exercise, allowing us to perform a joint analysis of data with an earlier study on adult and juvenile plaice (N = 480) collected over a broad geographic range, using six microsatellite loci in common to the two studies. Significant differentiation was observed between fish collected at the northern (Iceland, Faeroes, Norway) and southern (Bay of Biscay) parts of the species range. In contrast, the results showed little evidence of genetic structuring over much of the continental shelf of Europe. We believe that bathymetric and hydrographic barriers are the major factors shaping genetic structure, while lack of structure over much of the European continental shelf may be explained by a combination of past historical events, population structure, and dynamics of the species.     

Population genetic structure of the stalked barnacle <Emphasis Type="Italic">Pollicipes pollicipes</Emphasis> (Gmelin, 1789) in the northeastern Atlantic: influence of coastal currents and mesoscale hydrographic structures

Within its distribution range in the northeastern Atlantic, the stalked barnacle Pollicipes pollicipes shows a well-defined pattern of genetic variation, comprising (a) a subtropical/temperate northern assemblage, made up of populations distributed between 47°N and 28°N along the French, Iberian, North African and Canary Islands coastlines, and (b) a single isolated and highly divergent tropical population in the Cape Verde Islands (16°N), at the southernmost limit of the species’ distribution. However, within the northern assemblage several populations show a level of genetic differentiation that allows rejection of the hypothesis of genetic homogeneity. The congruence observed between genetic and hydrographic patterns suggests a crucial role of hydrodynamics, and of the dispersal of the planktonic larvae, in the determination of population structure. Along the southern European Atlantic coast, the Iberian Poleward Current and mesoscale hydrographic structures are, respectively, facilitating gene flow at the regional level and genetic differentiation at the local level. On the Atlantic coast of North Africa, the homogenizing equatorward flow of the Canary Current does not extend as far as the Cape Verde Islands. A demographic expansion is dated to the late Pleistocene, preceding the Eemian interglacial, and is oldest in the case of the long-standing Cape Verde population, sustained by a stable tropical habitat. The divergence between the Cape Verde population and the remaining populations is thus ancient, and suggests that oceanic current patterns may constitute a generalized physical barrier to the dispersal of marine organisms between Cape Verde and the rest of Macaronesia.     

Biological impacts of ocean acidification: a postgraduate perspective on research priorities

Research into the effects of ocean acidification (OA) on marine organisms has greatly increased during the past decade, as realization of the potential dramatic impacts has grown. Studies have revealed the multifarious responses of organisms to OA conditions, indicating a high level of intra- and interspecific variation in species’ ability to accommodate these alterations. If we are to provide policy makers with sound, scientific input regarding the expected consequences of OA, we need a broader understanding of these predicted changes. As a group of 20 multi-disciplinary postgraduate students from around the globe, with a study focus on OA, we are a strong representation of ‘next generation’ scientists in this field. In this unique cumulative paper, we review knowledge gaps in terms of assessing the biological impacts of OA, outlining directions for future research.     

Excessive chromium may cause dietary toxicity in parsley (Petroselinum crispum)

A bibliographical review on the possible effects of radiofrequency radiation (RFR) from wireless telecommunications on living organisms and its impact on amphibians is presented. The technical characteristics of this new technology and the scientific discoveries that are of interest in the study of their effects on wild fauna and amphibians are described. Electromagnetic pollution (in the microwave and in the radiofrequency range) is a possible cause for deformations and decline of some amphibian populations. Keeping in mind that amphibians are reliable bio-indicators, it is of great importance to carry out studies on the effects of this new type of contamination. Finally, some methodologies that could be useful to determine the adverse health effects are proposed.