Extracting viability landscapes from mutagen-response experiments

This paper outlines a novel approach for determining the importance of various genes to the viability of an organism. The basic idea is to treat a population of cells at various concentrations of mutagen, and determine which genes lose functionality due to genetic drift at the various mutagen concentrations. The more strongly a given collection of genes contributes to the fitness of an organism, the higher the mutation rate required to induce loss of functionality in those genes via genetic drift. We argue that mutagen-based methods, if reliably implementable, can elucidate correlations amongst genes, and determine which sets of genes correspond to redundant pathways in the cell. The data obtained from mutagen-based methods could also be used to organize the genes in a genome into hierarchies of increasing importance to the fitness of the cell. Thus, such methods could shed light on the evolutionary history of an organism.     

From twigs to landscapes – methods for studying ecological effects of forest ungulates

In recent decades considerable attention has been focused on plant-ungulate interactions at various spatial and temporal scales. The cascading effects following ungulate actions are also attracting increasing interest. Our knowledge of the effects of ungulates on plants, communities, landscapes and ecosystems is, therefore, growing. At the same time, shifts in ungulate populations (increases and decreases) in various forested parts of the world together with mounting interest in biodiversity issues have heightened management concerns about plant-ungulate interactions. This paper reviews methodologies commonly applied to the study of ungulate-induced effects at various scales. Non-experimental comparisons have long been used, while simulation and exclosure methods were developed decades ago. However, these methods have been progressively refined, the objectives of studies based on them have broadened, and the results obtained have increasingly highlighted the interactive and dynamic nature of plant-ungulate interactions. Recent research has exploited various new techniques, such as remote sensing, to gather and process data over larger spatial scales, while others, such as GIS and powerful modelling and statistical methods are opening up new ways to analyse data and present information. The nature, design and use of the various commonly used methods, as well as their potentials and limitations, are discussed.     

Models for forest ecosystem management: a European perspective

BACKGROUND: Forest management in Europe is committed to sustainability. In the face of climate change and accompanying risks, however, planning in order to achieve this aim becomes increasingly challenging, underlining the need for new and innovative methods. Models potentially integrate a wide range of system knowledge and present scenarios of variables important for any management decision. In the past, however, model development has mainly focused on specific purposes whereas today we are increasingly aware of the need for the whole range of information that can be provided by models. It is therefore assumed helpful to review the various approaches that are available for specific tasks and to discuss how they can be used for future management strategies. SCOPE: Here we develop a concept for the role of models in forest ecosystem management based on historical analyses. Five paradigms of forest management are identified: (1) multiple uses, (2) dominant use, (3) environmentally sensitive multiple uses, (4) full ecosystem approach and (5) eco-regional perspective. An overview of model approaches is given that is dedicated to this purpose and to developments of different kinds of approaches. It is discussed how these models can contribute to goal setting, decision support and development of guidelines for forestry operations. Furthermore, it is shown how scenario analysis, including stand and landscape visualization, can be used to depict alternatives, make long-term consequences of different options transparent, and ease participation of different stakeholder groups and education. CONCLUSIONS: In our opinion, the current challenge of forest ecosystem management in Europe is to integrate system knowledge from different temporal and spatial scales and from various disciplines. For this purpose, using a set of models with different focus that can be selected from a kind of toolbox according to particular needs is more promising than developing one overarching model, covering ecological, production and landscape issues equally well.     

Scaling from optimal behavior to population dynamics and ecosystem function

While behavioral responses of individual organisms can be predicted with optimal foraging theory, the theory of how individual behavior feeds back to population and ecosystem dynamics has not been fully explored. Ecological models of trophic interactions incorporating behavior of entire populations commonly assume either that populations act as one when making decisions, that behavior is slowly varying or that non-linear effects are negligible in behavioral choices at the population scale. Here, we scale from individual optimal behavior to ecosystem structure in a classic tri-trophic chain where both prey and predators adapt their behavior in response to food availability and predation risk. Behavior is modeled as playing the field, with both consumers and predators behaving optimally at every instant basing their choices on the average population behavior. We establish uniqueness of the Nash equilibrium, and find it numerically. By modeling the interactions as playing the field, we can perform instantaneous optimization at the individual level while taking the entire population into account. We find that optimal behavior essentially removes the effect of top-down forcing at the population level, while drastically changing the behavior. Bottom-up forcing is found to increase populations at all trophic levels. These phenomena both appear to be driven by an emerging constant consumption rate, corresponding to a partial satiation. In addition, we find that a Type III functional response arises from a Type II response for both predators and consumers when their behavior follows the Nash equilibrium, showing that this is a general phenomenon. Our approach is general and computationally efficient and can be used to account for behavior in population dynamics with fast behavioral responses.     

Scatchard plot: Common misinterpretation of binding experiments

The widespread misinterpretation in the literature of ligand-protein binding experiments which show upward curvature in Scatchard plots is emphasized. The most commonly encountered errors are discussed and references to the correct methods of resolution of upward-curved Scatchard plots are given.     

Targeting habitat management in fragmented landscapes: a case study with forest vertebrates

Although improving the quality of habitat patches in fragmented landscapes is a main conservation target few studies have examined patch management in relation to the surrounding landscape. Tackling such an issue needs a cross-scale approach that takes the hierarchical nature of landscapes into account. Here I show the results of a cross-scale study focusing on the distribution patterns of ten forest vertebrate species (birds and mammals). The overarching goal of this study was to understand the strength of patch scale determinants of distribution, following the appropriate control for relevant landscape properties (e.g. habitat loss vs. habitat subdivision). I show how, after controlling for uncertainty in the detection of the species and for the role of landscape properties, patch scale variables still played an important role in determining occupancy patterns of forest vertebrates. For some species variation in the values of patch structure variables increased occurrence probability with only moderate levels of habitat loss, highlighting the fact that habitat management should be targeted towards precise landscape conditions. In other cases the effect of patch variables was strong therefore variation in their values always brought substantial increase/decrease of presence probability. Overall these results strongly suggest that habitat management should never be carried out irrespective of the properties of the surrounding landscape, rather, it should be carefully targeted towards specific landscape contexts (e.g. above a certain amount of habitat) where it is more likely to be effective.     

Demonstrating the importance of intangible ecosystem services from peri-urban landscapes

Among ecosystem services, the various categories of intangible services linked to human perception, such as aesthetics, recreational values and cultural heritage, must be rated alongside tangible services linked to physical processes, such as wildlife habitats, clean water and air, and filter- and buffer effects. This is a pre-requisite for a sustainable development with a balance between ecological, social and economic values. We analyse ecosystem services in areas of the urban fringe of Copenhagen, where the services provided are mainly related to human perception. We employ relatively simple methods in selected landscapes to qualify or quantify the aesthetics and recreational value, and the scale of the welfare economic value of these ecosystem services. In the first case area, the Danish state acquired 50 villas covering more than 50 ha in order to recreate open vistas and gain access for the public to the seaside. In the second case area, peri-urban open landscapes were protected by conservation orders, to maintain and enhance the benefits of green space for the growing urban population. We assess the value – in a broad sense – of these ecosystem services using three practical methods: a landscape evaluation in terms of services and qualities, an assessment of actual recreational use, and finally an assessment of the costs – in terms of residential development values lost – of securing the provision of aesthetic qualities and recreational opportunities.Searching the original planning documents we uncovered the original motivation for the land evaluation and decision. The arguments behind the designation and protection of the areas were primarily aesthetic and potentials for recreational use. The two areas receive annually 2–2.5 million and 400.000 visits respectively, proving their strong recreational value. The value of the demolished houses in the first case area exceeds 115 million €, and the value of the lost development opportunities in the second case area exceeds 280 million €.By combination the three methods, we substantiated that the intangible services may dominate the tangible in cases like these, stressing the need for planners to assess the role and value hereof.     

Translational research: from pot to plot

Plant molecular biology has been the key driver to elucidate molecular pathways underlying plant growth, development and stress responses during the past decades. Although this has led to a plethora of available data, the translation to crop improvement is lagging behind. Here, we argue that plant scientists should become more involved in converting basic knowledge into applications in crops to sustainably support food security and agriculture. As the translatability from model species to crops is rather poor, this kind of translational research requires diligence and a thorough knowledge of the investigated trait in the crop. In addition, the robustness of a trait depends on the genotype and environmental conditions, demanding a holistic approach, which cannot always be evaluated under growth chamber and greenhouse conditions. To date, the improved resolution of many genome‐wide technologies and the emerging expertise in canopy imaging, plant phenotyping and field monitoring make it very timely to move from the pathway specifics to important agronomical realizations, thus from pot to plot. Despite the availability of scientific know‐how and expertise, the translation of new traits to applications using a transgene approach is in some regions of the world, such as Europe, seriously hampered by heavy and nontranslucent legislation for biotech crops. Nevertheless, progress in crop improvement will remain highly dependent on our ability to evaluate improved varieties in field conditions. Here, we plead for a network of protected sites for field trials across the different European climates to test improved biotech traits directly in crops.     

面向生态系统服务的森林生态系统经营:现状、挑战与展望

森林生态系统是地球陆地生态系统的主体,它具有很高的生物生产力和生物量以及丰富的生物多样性,对全球生态系统和人类经济社会发展起着至关重要和无可替代的作用。伴随着人口的不断增长和经济社会的迅猛发展,对森林资源和森林生态系统服务的需求不断高涨,而且人类对森林资源价值的认识也发生了很大程度的改变。推进森林资源可持续经营,增加森林总量、提高森林质量、增强生态功能,已成为中国林业可持续发展乃至推进中国生态文明建设和建设美丽中国的战略任务。本文全面综述了森林生态系统经营发展历程,分析了森林生态系统经营的现状和存在问题,在此基础上,提出整合基于生态系统管理与满足现代人类福祉对森林多重需求的新的森林生态系统经营理念,面向生态系统服务的森林生态系统经营理念是未来的发展趋势。森林经营发展战略表现为:1)从单纯的森林面积数量扩张,转变到提高单位面积的森林生产力和森林质量;2)从单一追求木材生产逐步转变为多目标经营,将森林林产品单一的经营目标转变为广泛的生态、经济和社会等多目标经营;3)森林经营重点从林分水平转变为森林景观的经营,强调森林景观的时空异质性和动态变化,权衡和协同多种生态系统的服务功能,倡导森林景观的多样性和连通性,提高森林与其它土地利用模式镶嵌构成的复合景观的可持续性和稳定性,增强森林生态系统对气候变化影响的适应能力;4)森林生态系统经营将从依赖传统经验的主观决策转变为信息化、数字化和智能化的决策,发展森林生态系统经营决策支持系统和森林景观恢复与空间经营规划系统。     

Beyond the tropics: forest structure in a temperate forest mapped plot

Question: How do the diversity, size structure, and spatial pattern of woody species in a temperate (Mediterranean climate) forest compare to temperate and tropical forests? Location: Mixed evergreen coastal forest in the Santa Cruz Mountains, California, USA. Methods: We mapped, tagged, identified, and measured all woody stems (≥1 cm diameter) in a 6‐ha forest plot, following Center for Tropical Forest Science protocols. We compared patterns to those found in 14 tropical and 12 temperate forest plots. Results: The forest is dominated by Douglas‐fir (Pseudotsuga menziesii) and three species of Fagaceae (Quercus agrifolia, Q. parvula var. shrevei, and Lithocarpus densiflorus), and includes 31 woody species and 8180 individuals. Much of the diversity was in small‐diameter shrubs, treelets, and vines that have not been included in most other temperate forest plots because stems <5‐cm diameter had been excluded from study. The density of woody stems (1363 stems ha^?1) was lower than that in all but one tropical plot. The density of large trees (diameter ≥30 cm) and basal area were higher than in any tropical plot. Stem density and basal area were similar to most other temperate plots, but were less than in low‐diversity conifer forests. Rare species were strongly aggregated, with the degree of aggregation decreasing with abundance so that the most common species were significantly more regular than random. Conclusions: The patterns raise questions about differences in structure and dynamics between tropical and temperate forests; these need to be confirmed with additional temperate zone mapped plots that include small‐diameter individuals.     

Wildfires in the western Canadian boreal forest: Landscape patterns and ecosystem management

Abstract. Mimicking of natural disturbance for ecosystem management requires an understanding of the disturbance processes and the resulting landscape patterns. Since fire is the major disturbance in the boreal forest, three widely held beliefs about fire behavior and resulting landscape patterns are examined in light of the empirical evidence available. These beliefs are: (1) that there is a ‘natural’ fire frequency for boreal ecosystems; (2) that the landscape mosaic created by wildfire is generally one of small, younger patches embedded within a matrix of older forest; and (3) that forest flammability is largely controlled by fuel accumulation. Despite the apparently logical basis for such beliefs, they are not well supported by empirical evidence. This discrepancy is explained by problems such as failure to appreciate the relationship between number of fires and area burned and inappropriate extrapolations or generalizations from other regions and vegetation types. The most important implications for management are that the natural disturbance processes producing landscape patterns in the boreal forest generally operate at much larger scales than management units, and that humans may have more indirect (through landuse change) rather than direct (through fire suppression) effects on the frequency of wildfires.     

An ecosystem approach to restoration and sustainable management of dry forest in southern Peru

The dry forest of the Peruvian south coast has undergone an almost total process of deforestation. Populations here have increased exponentially through immigration supplying labour to urban coastal development, and demonstrably unsustainable agro-industrial expansion for export markets. Society has become dislocated from local traditions of environmental and resource management whilst still retaining a wealth of Andean agricultural expertise. Indigenous communities still hold on to vestiges of traditional knowledge. Relicts of natural vegetation, traditional agriculture and agrobiodiversity continue to sustain ecosystem services. Moreover, offer livelihood options and resources for restoration. These aspects reflect a long cultural trajectory, including famous extinct cultures such as Nasca, that evolved within an ever-changing riparian and agricultural landscape influenced by external forces and which incorporated important processes of plant domestication and adaptation to climatic oscillation.     

Abundance estimates to inform butterfly management: double-observer versus distance sampling

Abundance estimates are used to establish baselines, set recovery targets, and assess management actions, all of which are essential aspects of evidence-based natural resource management. For many rare butterflies, these estimates do not exist, and conservation decisions rely instead on expert opinion. Using Bartram’s scrub-hairstreak (Strymon acis bartrami, US Endangered) as a case study, we present a novel comparison of two methods that permit the incorporation of detection probabilities into abundance estimates, distance sampling and double-observer surveys. Additionally we provide a framework for establishing a systematic sampling scheme for monitoring very rare butterflies. We surveyed butterflies monthly in 2013, increasing intensity to weekly when butterflies were detected. We conducted 19 complete, island-wide surveys on Big Pine Key in the Florida Keys, detecting a total of 59 Bartram’s scrub-hairstreaks across all surveys. Peak daily abundances were similar as estimated with distance sampling, 156 butterflies (95 % CI 65–247), and double-observer, 169 butterflies (95 % CI 65–269). Selecting a method for estimating abundance of rare species involves evaluating trade-offs between methods. Distance sampling requires at least 40 detections, but only one observer, while double-observer requires only 10 detections, but two observers. Double-observer abundance estimates agreed with distance sampling estimates, which suggests that double-observer is a reasonable alternative method to use for estimating detection probability and abundance for rare species that cannot be surveyed with other, more commonly used methods.     

Rhachicreagra (Acrididae, Ommatolampinae): forest grasshoppers from Central america with unique aedeagal asymmetry

Abstract. Rhachicreagra species are confined to Central American wet tropical forests, both lowland and montane. The asymmetric aedeagus with the left penis valve suppressed is unique in the Acridoidea. Keys are provided to both sexes of the seventeen recognized species: achrosta sp.n., anchidiphalara sp.n., astytophallus sp.n., brachysphagiocerca sp.n., drymocnemensis sp.n., gracilis Bruner, Haematodes sp.n., Khayachorsa sp.n., himantocerca sp.n. maya sp.n., melanota sp.n., sp.n., mexicana Hebard, nothra Rehn (= pallipes Bruner, = aeruginosa Bruner syn.n), obsidian sp.n., olmeca sp.n., pomatiaphallus sp.n., sphagicerca sp.n.; the small geographical ranges of these species argue for great care in the choice of representative forest blocks for purposes of faunal conservation in Central America.     

Options for enhancing forest biodiversity across New Zealand's managed landscapes based on ecosystem modelling and spatial design

In most regions of the world removal of environmental stress facilitates regeneration of native plants and habitats. However, in many of New Zealands modified landscapes, exotic species are likely to respond first to any reduction in stress because these fast-growing species are prevalent in local vegetation and dominate seed banks. Given the trend in agriculture towards intensive management on larger units, the indigenous character in New Zealand landscapes is being marginalised and there is the risk that further reduction in visibility of native vegetation may be perpetuated by a growing familiarity and identification with ubiquitous exotic species. Alternative landscapes, based on an understanding of ecosystem processes, need to be explored if biodiversity goals set by international convention and national resource management law are to be achieved. This study provides a set of predictions and pathways, backed by field observations, to underpin a restoration strategy at patch to landscape scales. A forest model, LINKNZ, is employed to simulate species succession under New Zealand conditions. The incorporation of disturbance regimes and species dispersal processes in the model permits a wide range of scenarios to be investigated encompassing indigenous forest development, exotic species interactions with indigenous forest ecosystems, management of mixed introduced-indigenous forests, and landscape dynamics. The results illustrate an approach that identifies potential biosecurity threats and provides additional options for integrating nature and production in New Zealands rural and urban landscapes.     

Why monitoring often fails to inform adaptive management: a case study

Monitoring that facilitates adaptive management requires us to link observed changes in resource condition with management actions. Here, we present a case study to discuss how monitoring should be undertaken so it can facilitate adaptive management. Drawing on monitoring data collected by landholders as part of an incentive programme for native vegetation conservation on private land, we examined whether it was possible to determine to what extent changes in native vegetation condition were affected by funded management actions. Using a simple statistical technique (linear regression), we were unable to find strong links between the intended natural resource management (NRM) outcomes and funded management actions because (i) we could only use data from 22% of the 55 monitored sites as most data sheets were incomplete; (ii) sampling was undertaken in different seasons making it difficult to distinguish change due to management from change due to natural variability; and (iii) management actions were recorded in a generic way only, and not monitored through time, thus making it difficult to link observed changes in vegetation condition to on‐ground management. We suggest that monitoring programmes will only inform adaptive management where NRM bodies can prosecute (i) sampling designs that enable change as a result of management to be distinguished from change due to natural variability, and (ii) protocols that provide consistent data capture between sites and through time.     

Folding landscapes of ankyrin repeat proteins: experiments meet theory

Nearly 6% of eukaryotic protein sequences contain ankyrin repeat (AR) domains, which consist of several repeats and often function in binding. AR proteins show highly cooperative folding despite a lack of long-range contacts. Both theory and experiment converge to explain that formation of the interface between elements is more favorable than formation of any individual repeat unit. IkappaBalpha and Notch both undergo partial folding upon binding perhaps influencing the binding free energy. The simple architecture, combined with identification of consensus residues that are important for stability, has enabled systematic perturbation of the energy landscape by single point mutations that affect stability or by addition of consensus repeats. The folding energy landscapes appear highly plastic, with small perturbations re-routing folding pathways.     

Biological screening of rain forest plot trees from Palawan Island (Philippines)

Study plots totaling 0.2 Ha were established in primary forest in the highlands of central Palawan Island, Philippines. Samples of various anatomical parts [typically leaf + twig (If/tw), stem bark (sb), and root (rt)] were collected from all tree species represented within the plots by individuals having a diameter at breast height > or = 10 cm. In all, 211 distinct samples were obtained from 68 tree species, representing 35 families (not including samples from 4 indeterminate species). Methanol extracts of these samples were tested in in vitro antiplasmodial, brine shrimp toxicity, and cytotoxicity assays. The following samples showed an IC50 < or = 10 microg/mL against either chloroquine-sensitive or chloroquine-resistant clones of Plasmodium falciparum: Acronychia laurifolia (sb), Agathis celebica (lf/tw), Aglaia sp. 1 (sb), Aglaia sp. 2 (lf/tw, rt), Bhesa sp. 1 (rt), Cinnamomum griffithii (lf/tw), Croton leiophyllus (rt), Dysoxylum cauliflorum (rt), Garcinia macgregorii (sb), Lithocarpus sp. 1 (rt, sb), Meliosma pinnata ssp. macrophylla (lf/tw, rt), Myristica guatteriifolia (lf/tw), Ochrosia glomerata (rt, sb), Swintonia foxworthyi (lf/tw), Syzygium sp. 1 (rt), Turpinia pomifera (rt), and Xanthophyllum flavescens (sb). Secondly, those samples which displayed > or = 50% immobilization of brine shrimp at 100 microg/mL were: Acronychia laurifolia (lf/tw/fruit, rt, sb), Agathis celebica (lf/tw, sb), Aglaia sp. 1 (lf/tw), Alphonsea sp. 1 (rt), Ardisia iwahigensis (lf/tw), Arthrophyllum ahernianum (lf/tw, rt, sb), Castanopsis cf. evansii (rt), Cinnamomum griffithii (lf/tw, rt), Croton argyratus (lf/tw), C. leiophyllus (lf/tw, rt), Dysoxylum cauliflorum (fruit, lf/tw, rt), Euonymus javanicus (rt), Glochidion sp. 1 (rt), Polyosma sp. 1 (rt), Symplocos polyandra (rt), Timonius gammillii (sb), and Xanthophyllum flavescens (rt). Lastly, samples which exhibited an IC50 < or = 20 microg/mL against one or more of the cancer cell lines employed (LU1, KB, KB-V1, P-388, LNCaP, or ZR-75-1) include: Acronychia laurifolia (lf/tw/fruit, rt, sb), Aglaia sp. 1 (sb), Aglaia sp. 2 (rt), Alphonsea sp. 1 (rt), Ardisia iwahigensis (lf/tw, rt, sb), Astronia cumingiana (sb), Croton argyratus (lf/tw, rt, sb), C. leiophyllus (lf/tw, rt), Dimorphocalyx murina (lf/tw, rt, sb), Lithocarpus caudatifolius (rt, sb), Litsea cf. sibuyanensis (rt), Syzygium cf. attenuatum (rt, sb), S. confertum (sb), Ternstroemia gitingensis (rt), and Ternstroemia sp. 1 (rt, sb).     

Ecological indicators: Imperative to sustainable forest management

Sustainable forest management (SFM) deals with ecologically sound practices that maintain the forest ecosystem integrity, productivity, resilience and biodiversity. Ecological sustainability ensures continuing function of ecosystems which are considered as ecological life support system. Several attempts have been made world over to develop criteria and indicators, which are specific to various forestry conditions and recognized as appropriate tools for assessing and monitoring progress towards sustainable forest management. In India, the process for measuring forest sustainability has started by evolving national level set of Criteria and indicators in the form of Bhopal–India process. The Bhopal–India process specifies 8 criteria and 43 indicators. The first 4 criteria pertain exclusively to ecology with 21 related indicators. Thus, nearly half of the criteria and indicators pertain to ecological dimensions that largely govern sustainability of forests. Rest of the criteria of the base set pertains to economic and social aspects with related indicators. This provides holistic approach of monitoring the forest resources.