Road-related landscape elements as a habitat: A main asset for small mammals in an intensive farming landscape

Road construction creates new habitats for a variety of species. In intensive farming landscapes, road verges may be the only suitable habitat for rodents. However, little attention has been paid to other road-related landscape elements (RRLEs), such as excavation slopes or the central islands of roundabouts, and their importance in a rodent territory. This study investigated all types of RRLE in terms of rodent abundances and habitat quality. RRLEs were compared with the semi-natural elements of the studied landscape using a capture-mark-recapture protocol. Four species and 3154 individuals were captured over a period of four months. Relative abundance and habitat quality were higher in RRLEs than in semi-natural elements. Mapping of the landscape showed that 86% of crop fields are accessible to Microtus arvalis (and almost 100% for Apodemus sylvaticus) from road verges. Our results highlight the importance of road verges and all other RRLEs in the conservation of species diversity in intensive farming landscapes.     

生态保护区外斑块对景观连接度的影响评价

快速的城市化过程带来的生境斑块破碎化及损失会影响物种迁移、捕食等生态活动,对生物多样性构成威胁。然而,现有生态保护区可能无法覆盖其内生物的必要活动范围。生态保护区外的生境斑块对于维持生态过程也具有重要作用,因此识别生态保护区外的关键斑块并加以保护非常重要。以北京市延庆区为研究区,划分两种生境斑块,即核心生境斑块和潜在生境斑块,并基于图论构建生境网络。考虑地表覆盖类型、坡度、人类活动等因素构建生境阻力面。结合未来土地利用类型变化的模拟,研究城市化过程对区域生境网络和景观连接度的影响,选用CLUE-S模型模拟土地利用类型变化的格局。结合生境斑块特征和未来城市土地利用变化情况设计了3种未来生境变化情景。利用连接概率指数(PC)和网络连接度变化率(dI)评价不同生境变化情景下生态保护区外潜在生境斑块的景观连接度重要性,判断保护优先顺序,并分析景观格局变化对不同迁移能力物种的影响。结果表明：生态保护区外的全部潜在生境斑块对维持生境整体景观连接度有最大2.15%的影响,单个潜在生境斑块对维持景观连接度有最大0.28%的影响。此外,景观格局及其变化对不同迁移能力物种的影响差异显著,因此需针对保护物种和城市生境特征设计保护方案,研究区需要优先保护大中型斑块和位于关键位置的小型斑块。为了满足对生物多样性保护的需求,建议在区分生境斑块保护优先顺序时考虑生境斑块对景观连接度的贡献和城市化扩展过程的压力。研究为城市生物多样性保护和生境管理提供了方法参考。     

Characterizing the importance of habitat patches in maintaining landscape connectivity for Tibetan antelope in the Altun Mountain National Nature Reserve,China

Connectivity of habitat patches is crucial for wildlife dispersal and survival, and identifying patches with high importance for maintaining connectivity can aid effective wildlife management. Knowledge of the habitat distribution of the Tibetan antelope in the Altun Mountain National Nature Reserve, which is essential for connectivity analysis, remains limited. We analyzed potential habitat distribution and priority patches using GIS-based habitat suitability modeling with three weighting factors and evaluated the connectivity of habitat patches under four dispersal distance scenarios. Patches with high habitat suitability covered 25.39 % of the total area, and these patches were selected for connectivity analysis as resource patches. Connectivity analysis indicated that, although the overall probability of connectivity (PC) showed an upward trend with increasing dispersal distance, the importance of each patch varied considerably under different dispersal distance scenarios. Transfer analysis of patch numbers between different importance levels revealed that the number of patches becoming less important was higher than the number of patches becoming more important when dispersal distance increased. In addition, nine patches covering 38.49 % of the suitable habitat area were identified as priority patches, in particular the patches near the Kardun and the Karchuka inspection stations. We also found that the habitat distribution of the Tibetan antelope obtained from the suitability model matched the population distribution determined by a field survey. Correlation analysis between patch area and the percentage of PC index value loss (dPC) revealed that the larger patches in this region were more likely to be important for maintaining connectivity.     

Systematic review of the scrub typhus treatment landscape: Assessing the feasibility of an individual participant-level data (IPD) platform

BackgroundScrub typhus is an acute febrile illness caused by intracellular bacteria from the genus Orientia. It is estimated that one billion people are at risk, with one million cases annually mainly affecting rural areas in Asia-Oceania. Relative to its burden, scrub typhus is understudied, and treatment recommendations vary with poor evidence base. These knowledge gaps could be addressed by establishing an individual participant-level data (IPD) platform, which would enable pooled, more detailed and statistically powered analyses to be conducted. This study aims to assess the characteristics of scrub typhus treatment studies and explore the feasibility and potential value of developing a scrub typhus IPD platform to address unanswered research questions.Methodology/principal findingsWe conducted a systematic literature review looking for prospective scrub typhus clinical treatment studies published from 1998 to 2020. Six electronic databases (Ovid Embase, Ovid Medline, Ovid Global Health, Cochrane Library, Scopus, Global Index Medicus), ClinicalTrials.gov, and WHO ICTRP were searched. We extracted data on study design, treatment tested, patient characteristics, diagnostic methods, geographical location, outcome measures, and statistical methodology.Among 3,100 articles screened, 127 were included in the analysis. 12,079 participants from 12 countries were enrolled in the identified studies. ELISA, PCR, and eschar presence were the most commonly used diagnostic methods. Doxycycline, azithromycin, and chloramphenicol were the most commonly administered antibiotics. Mortality, complications, adverse events, and clinical response were assessed in most studies. There was substantial heterogeneity in the diagnostic methods used, treatment administered (including dosing and duration), and outcome assessed across studies. There were few interventional studies and limited data collected on specific groups such as children and pregnant women.Conclusions/significanceThere were a limited number of interventional trials, highlighting that scrub typhus remains a neglected disease. The heterogeneous nature of the available data reflects the absence of consensus in treatment and research methodologies and poses a significant barrier to aggregating information across available published data without access to the underlying IPD. There is likely to be a substantial amount of data available to address knowledge gaps. Therefore, there is value for an IPD platform that will facilitate pooling and harmonisation of currently scattered data and enable in-depth investigation of priority research questions that can, ultimately, inform clinical practice and improve health outcomes for scrub typhus patients.     

Getting the biodiversity intactness index right: the importance of habitat degradation data

Given high‐level commitments to reducing the rate of biodiversity loss by 2010, there is a pressing need to develop simple and practical indicators to monitor progress. In this context, a biodiversity intactness index (BII) was recently proposed, which provides an overall indicator suitable for policy makers. The index links data on land use with expert assessments of how this impacts the population densities of well‐understood taxonomic groups to estimate current population sizes relative to premodern times. However, when calculated for southern Africa, the resulting BII of 84% suggests a far more positive picture of the state of wild nature than do other large‐scale estimates. Here, we argue that this discrepancy is in part an artefact of the coarseness of the land degradation data used to calculate the BII, and that the overall BII for southern Africa is probably much lower than 84%. In particular, based on two relatively inexpensive, ground‐truthed studies of areas not generally regarded as exceptional in terms of their degradation status, we demonstrate that Scholes and Biggs might have seriously underestimated the extent of land degradation. These differences have substantial bearing on BII scores. Urgent attention should be given to the further development of cost‐effective ground‐truthing methods for quantifying the extent of land degradation in order to provide reliable estimates of biodiversity loss, both in southern Africa and more widely.     

Relative importance of habitat and landscape scales on butterfly communities of urbanizing areas

Agricultural decline and urbanization entail rapid alterations of the patterns of organization of rural landscapes in Europe. The spread of the urban footprint to the adjacent countryside contributes to the development of new anthropogenic ecosystems in formerly rural hinterlands. In this study, butterflies are considered as biological indicators of these rapid environmental changes. Our purpose is to better understand changes in biodiversity related to the evolution of available habitats in a mutating landscape. In this study, we investigate butterfly communities of four land-use types (fallow lands, gardens, vineyards, woodlands) within different landscape contexts. Our results reveal that variations in structure and functional composition of these communities are related to different levels of human disturbance at both landscape scale and habitat scale.     

Bird based Index of Biotic Integrity: Assessing the ecological condition of Atlantic Forest patches in human-modified landscape

Wooded biomes converted to human-modified landscapes (HML) are common throughout the tropics, yielding small and isolated forest patches surrounded by an agricultural matrix. Diverse anthropogenic interventions in HMLs influence patches in complex ways, altering natural dynamics. Assessing current condition or ecological integrity in these patches is a challenging task for ecologists. Taking the Brazilian Atlantic Forest as a case study, we used the conceptual framework of the Index of Biotic Integrity (IBI), a multimetric approach, to assess the ecological integrity of eight small forest patches in a highly disturbed HML with different configurations and histories. The IBI was developed using bird assemblages found in these patches, and its performance was compared with analytical approaches commonly used in environmental assessment, such as general richness and Shannon’s diversity index. As a first step, the IBI procedure identifies an existing gradient of human disturbance in the study region and checks which biotic characteristics (candidate metrics) vary systematically across the gradient. A metric is considered valid when its’ relationship with the gradient provides an ecological interpretation of the environment. Then, the final IBI is elaborated using each valid metric, obtaining a score for each site. Over one year of sampling, 168 bird species were observed, providing 74 different bird candidate metrics to be tested against the disturbance gradient. Seven of them were considered valid:richness of threatened species; richness of species that use both “forest and non-forest” habitats; abundance of endemics, abundance of small understory-midstory insectivores, abundance of exclusively forest species; abundance of non-forest species, and abundance of species that forage exclusively in the midstory stratum. Each metric provided complementary information about the patch’s ecological integrity. The resulting IBI showed a significant linear relationship with the gradient of human disturbance, while total species richness and Shannońs diversity index did not. Application of numerical approaches, such as total species richness and Shannon’s diversity, did not distinguish ecological traits among species. The IBI proved better for assessing and interpreting ecological and environmental condition of small patches in highly disturbed HML. The IBI framework, its multimetric character, and the ease with which it can be adapted to diverse situations, make it an effective approach for assessing environmental conditions in the Atlantic Forest region, and also for many other small forest patches in the tropics.     

Enhanced analysis of landscape structure: Inclusion of transition zones and small-scale landscape elements

Landscape diversity is an essential component of biodiversity because it determines the diversity of habitats and species. It is necessary to adopt an adaptive and realizable landscape structure monitoring model for ecosystem management. However, the existing methods of landscape structure analysis often do not consider the transitions between different types of patch, which are dynamic and play several functional roles in landscape structure. Another component of information that has often been ignored is “small-scale landscape elements” inside patches, which leads to within-patch heterogeneity being underestimated. This paper presents a method for solving these problems by regular landscape monitoring using RapidEye remote sensing data. We incorporate the third altitude dimension in landscape structure analysis, especially for detecting certain small-scale landscape structures such as groves, tree rows, and transitions at forest boundaries. For these detailed structures a number of landscape metrics are computed under a three-dimensional perspective. The results indicate that a more realistic and more precise representation of landscape structure is obtained on the basis of the detailed spatial scale and the true surface geometries of patches. Taking transitions into account helps smooth “edge effects” between patches and leads to more realistic quantification of fragmentation.     

Benefits of adjacent habitat patches to the distribution of a crayfish population in a hydro-dynamic wetland landscape

Aquatic macrophyte patches are natural features of wetland ecosystems that serve as habitat for aquatic animals. Previous studies suggest animal densities in Everglades, USA, wetlands are generally less numerous in sawgrass ridges than in deeper lily sloughs. We studied the density distribution of a population of Procambarus fallax in ridge and slough habitat types over a 2-year period, spanning two wet–dry cycles and estimated growth and survival rates under flooded conditions to understand comparative value of each to the crayfish population. Procambarus fallax individuals inhabited and recruited in both marsh habitats. During periods of high water, crayfish densities were similar in both habitats; however, densities in both habitats varied seasonally, leading us to postulate some degree of population redistribution in response to fluctuating water depths. Analysis of size distributions over time revealed juveniles in both habitats and two major recruitment periods each year; distinct juvenile cohorts were present in early winter (Nov–Dec) and mid-summer (July–Aug). An in situ experiment of juvenile growth demonstrated that slough habitat type supported faster growth over ridge habitat. To understand habitat-specific mortality risk, a tethering study during flooded conditions indicated that relative predation risk by aquatic predators was greater in sloughs for all sizes and higher for smaller individuals in both habitats. The comparative importance of ridge and slough balances growth potential and survival probability during flooded conditions. This is the first study through time and across both habitat types analyzing the distribution and size structure of P. fallax population in the Everglades.     

Assessing bee species richness in two Mediterranean communities: importance of habitat type and sampling techniques

The decline of bees has raised concerns regarding their conservation and the maintenance of ecosystem services they provide to bee-pollinated wild flowers and crops. Although the Mediterranean region is a hotspot for bee species richness, their status remains poorly studied. There is an urgent need for cost-effective, reliable, and unbiased sampling methods that give good bee species richness estimates. This study aims: (a) to assess bee species richness in two common Mediterranean habitat types: semi-natural scrub (phrygana) and managed olive groves; (b) to compare species richness in those systems to that of other biogeographic regions, and (c) to assess whether six different sampling methods (pan traps, variable and standardized transect walks, observation plots and trap nests), previously tested in other European biogeographic regions, are suitable in Mediterranean communities. Eight study sites, four per habitat type, were selected on the island of Lesvos, Greece. The species richness observed was high compared to other habitat types worldwide for which comparable data exist. Pan traps collected the highest proportion of the total bee species richness across all methods at the scale of a study site. Variable and standardized transect walks detected the highest total richness over all eight study sites. Trap nests and observation plots detected only a limited fraction of the bee species richness. To assess the total bee species richness in bee diversity hotspots, such as the studied habitats, we suggest a combination of transect walks conducted by trained bee collectors and pan trap sampling.     

基于生境斑块的滇金丝猴景观连接度分析

基于生境斑块,结合最小费用距离并运用图论法对滇金丝猴分布区进行栖息地连接度分析,研究利用猴群的现实分布结合Logistic回归模型确定了景观功能连接的最佳距离阈值,对于功能畅通的组分,以景观指数BC定量识别出作为"踏脚石"的优先保护区域;对于功能不连接的组分,绘制出最小费用路径,确定了该路径中优先恢复区域。结果表明:最佳的最小费用距离阈值为1400,该阈值下猴群主要存在于5个组分中,所有组分中猴群间的连接度优劣排序为组分3组分1组分5组分4,龙马山猴群(G15)没有"踏脚石"斑块使其与同一组分内的其他猴群相连接,应考虑优先恢复该区域的植被,研究成果对于该物种的保护和其他濒危物种的类似研究具有较强的参考价值和借鉴意义。     

EcoGenetics: An R package for the management and exploratory analysis of spatial data in landscape genetics

The integration of ecology and genetics has become established in recent decades, in hand with the development of new technologies, whose implementation is allowing an improvement of the tools used for data analysis. In a landscape genetics context, integrative management of population information from different sources can make spatial studies involving phenotypic, genotypic and environmental data simpler, more accessible and faster. Tools for exploratory analysis of autocorrelation can help to uncover the spatial genetic structure of populations and generate appropriate hypotheses in searching for possible causes and consequences of their spatial processes. This study presents EcoGenetics, an R package with tools for multisource management and exploratory analysis in landscape genetics.     

Persistence of species in a fragmented urban landscape: the importance of dispersal ability and habitat availability for grassland butterflies

Some species cope with, and survive in, urban areas better than others.From a conservation viewpoint it is important to understand why some species arerare or are excluded in the urban landscape, in order that we might take actionto conserve and restore species. Two ecological factors that might explain thedistribution and abundance of butterfly species in the urban landscape aredispersal ability and the availability of suitable habitat. The influence ofthese factors was assessed by examining the distribution and genetic structureof four grassland butterfly species in the West Midlands conurbation, UK. Thefour species differ in their distribution and abundance, mobility and habitatspecificity. No significant fit to the isolation-by-distance model was found forany of the study species at this spatial scale. MeanF _ST values revealed a non-significant level ofpopulation structuring for two species, Pieris napi (L.)and Maniola jurtina (L.), but moderate and significantpopulation differentiation for Pyronia tithonus (L.) andCoenonympha pamphilus (L.). Results suggest that thesespecies are limited more by the availability of suitable habitat than by theirability to move among habitat patches. Conservation strategies for thesegrassland species should initially focus on the creation and appropriatemanagement of suitable habitat. More sedentary species that have already beenexcluded from the conurbation may require a more complex strategy for theirsuccessful restoration.     

Impacts of habitat on butterfly dispersal in tropical forests,parks and grassland patches embedded in an urban landscape

Dispersal distances of 17 species of butterflies in tropical Singapore were significantly greater in forest than in urban habitat. Butterflies in urban plots frequently moved within suitable habitat (park/grassland) patches but rarely crossed non-habitat patches suggesting potential isolation and a need for urban corridors.     

Metapopulation dynamics of the bog fritillary butterfly: movements between habitat patches

Recent studies on metapopulation dynamics have emphasized the need for improved methods for quantifying individual movements between local populations and habitat patches. In this paper, we report on a 6-yr study in which a network of 12 habitat patches occupied by the bog fritillary, Proclossiana eunomia , was surveyed, with special focus on quantifying movements between the habitat patches. We applied the Virtual Migration model which has been designed to estimate survival and migration parameters in a metapopulation of several connected local populations. The model was parameterized using mark-release-recapture data collected during 6 yr. Generally, the estimated parameter values indicated a high level of movements, with roughly half of butterfly-days spent outside the natal patch. Mortality within patches was higher in males than in females. Females tended to be more mobile and spent more time outside their natal patch than males. Further analysis of the MRR data shows that in this protandrous species males tend to move very little between habitat patches before substantial numbers of females have emerged.     

Pathway and ontology analysis: emerging approaches connecting transcriptome data and clinical endpoints

The increasing use of gene expression profiling offers great promise in clinical research into disease biology and its treatment. Along with the ability to measure changing expression levels in thousands of genes at once, comes the challenge of analyzing and interpreting the vast sets of data generated. Analysis tools are evolving rapidly to meet such challenges. The next step is to interpret observed changes in terms of the biological properties or relationships underlying them. One powerful approach is to make associations between the genes that are under investigation and well-known biochemical or signaling pathways, and further to assess the significance of such associations. Similarly, genes can be mapped to standardized biological categories via an ontology resource. We discuss these approaches and several web-based resources and tools designed to facilitate such analyses. This information can be used to facilitate understanding and to help design more focused experiments for validating the relevance and importance of these biological pathways and processes in human disease and therapeutics.