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.     

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.     

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.     

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.     

历史变域在森林生态系统管理中的应用现状与展望

历史变域描述了自然干扰下生态系统条件和过程的变化范围,能够使人们认识现代生态系统如何变化,为生态系统的有效管理提供了重要的参照和目标,使管理者能够制定有效措施最终使生态系统达到可持续状态.近年来,历史变域在森林生态系统管理中发挥着越来越重要的作用,已成功用于揭示生态系统变化的原因、保护生物多样性和濒危物种及恢复生态系统功能等多个领域.本文介绍了历史变域的概念并对其在森林生态系统管理中的应用及所面临的挑战(数据缺乏、环境变化和人类影响等)进行了论述.加大数据解译和分析的研究力度、注重自然环境和人类社会变化的研究及加强对公众的宣传力度可以更好地认识研究区的生态环境及其主要干扰机制,有利于提高历史变域在生态系统管理中的应用效率,使森林生态系统最终达到可持续的状态.     

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.     

Sustainable management of planted landscapes: lessons from Japan

In Japan, 42?% of forests are planted forests, and most of them were established after World War II (1950–1980) to meet increased wood demands. Although Japanese planted forests are now reaching their planned harvest age, they have not been managed, and their restoration is now being discussed. Japanese foresters have not cut their own forests, and the country’s high wood demands have been met by imports during recent decades. The decline of young forests due to the stagnation of forestry activity is suggested to be partly responsible for the nation-wide decline in early-successional species, which is referred to as the “second crisis of biodiversity.” As a timber-importing nation, it is suggested that Japan has underused the nation’s own forests and has overused forests elsewhere. A revival of Japanese plantation forestry may contribute to the restoration of early-successional species because young planted forests are likely to provide suitable habitats. Furthermore, only 30?% of the current planted forests in Japan will be needed to meet the expected future domestic demand for lumber and plywood without imports. The remaining 70?% of the current planted forests may be restored to natural forests with or without harvesting. The history of Japanese planted forests suggests that some natural trees/forests should be retained, even in the landscapes that specialize in wood production, because part of the planted forests may be economically marginalized in the future, and their restoration to natural forests would then be needed.     

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.     

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.     

Application of random forest algorithm for studying habitat selection of colonial herons and egrets in human-influenced landscapes

Understanding the mechanisms of habitat selection is fundamental to the construction of proper conservation and management plans for many avian species. Habitat changes caused by human beings increase the landscape complexity and thus the complexity of data available for explaining species distribution. New techniques that assume no linearity and capable to extrapolate the response variables across landscapes are needed for dealing with difficult relationships between habitat variables and distribution data. We used a random forest algorithm to study breeding-site selection of herons and egrets in a human-influenced landscape by analyzing land use around their colonies. We analyzed the importance of each land-use variable for different scales and its relationship to the probability of colony presence. We found that there exist two main spatial scales on which herons and egrets select their colony sites: medium scale (4 km) and large scale (10–15 km). Colonies were attracted to areas with large amounts of evergreen forests at the medium scale, whereas avoidance of high-density urban areas was important at the large scale. Previous studies used attractive factors, mainly foraging areas, to explain bird-colony distributions, but our study is the first to show the major importance of repellent factors at large scales. We believe that the newest non-linear methods, such as random forests, are needed when modelling complex variable interactions when organisms are distributed in complex landscapes. These methods could help to improve the conservation plans of those species threatened by the advance of highly human-influenced landscapes.     

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.     

Scaling up from shifting-gap mosaic to geographic distribution in the modeling of forest dynamics

Shifting-gap mosaic is incorporated into the dynamic model of size-structured forests along geographic gradients. In the model named SAL (size–age–location), a forest at a geographic location has a patch-age structure, which approximates the shifting-gap mosaic, and a tree-size structure in each patch of the forest. Growth and recruitment occur in each patch and are regulated by patch-scale crowding in terms of upper basal area. Seed production depends on the basal area density of mother trees at the forest scale. Seeds are dispersed to neighboring locations of the geographic landscape. After a century-long warming treatment, a resident forest zone prevented, over several millennia, an invading forest zone from achieving a steady-state range of geographic distribution. Introducing the gap mosaic into the model did not make substantial changes in the response of latitudinal forest zones to the warming treatment, but only moderately accelerated the migration speed of invader species. Temporal fluctuation in seed production without interspecific synchronization, or the lottery effect, did not facilitate the migration of invader species at all.     

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.     

Rodent eradications as ecosystem experiments: a case study from the Mexican tropics

For effective and efficient pest management it is essential to understand the ecology of the target species and recipient ecosystems. The use of rodent eradication as a restoration tool is well established in temperate regions, but less common in the tropics, presenting an opportunity to undertake scientific learning in tandem with rodent eradications. On a dry tropical archipelago, we used a Before-After-Control-Impact framework to document (1) fluctuations in the abundance and demography of invasive Rattus rattus and Mus musculus on three different islands, (2) the trophic niche of all three invasive rodent populations, and (3) changes in the invertebrate community before and after rodent eradication, also comparing with two rodent free islands. While rat density was high and relatively stable throughout the year, the two mouse populations greatly differed in body size and seasonal dynamics, despite their proximity. The rodents in all three populations were generalist and opportunistic feeders, although stable isotope analyses results indicated major differences among them, driven by food availability and rodent species. Seasonal fluctuations in invertebrate communities depended on rodent invasion status, but recovery in the invertebrate communities one year after rodent removal was limited for all islands. Predictions for other tropical ecosystem biomes require long-term research on more tropical islands. Improving our understanding of island and species-specific contexts of rodent eradications can advance island restoration projects and assist the selection of indicator species for ecosystem recovery.     

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.