Prevalence and Genotypes of Anaplasma Species and Habitat Suitability for Ticks in a Mediterranean Ecosystem

Anaplasma species are tick-transmitted pathogens that impact veterinary and human health. Sicily is one of the locations where these pathogens are endemic. Sicily represents a typical Mediterranean ecosystem to study Anaplasma infection and tick habitat suitability. The aims of this study were (i) to characterize by 16S rRNA and species-specific msp4 gene PCR the prevalence and genotypes of A. marginale, A. phagocytophilum, and A. ovis in the most abundant host species in Sicilian provinces and (ii) to correlate differences between hosts and between western and eastern Sicily with the habitat suitability for ticks in these regions. Differences were found in the prevalence of Anaplasma spp. between different hosts and between western and eastern provinces. The differences in Anaplasma prevalence between different hosts may be explained by pathogen host tropism. The differences between western and eastern provinces correlated with the tick habitat suitability in these regions. The analysis of Anaplasma genotypes suggested a higher host and regional specificity for A. phagocytophilum than for A. marginale and A. ovis strains, a finding probably associated with the broader host range of A. phagocytophilum. The presence of identical A. marginale genotypes in the two regions may reflect cattle movement. The results for A. ovis suggested the possibility of some genotypes being host specific. These results provide information potentially useful for the management of tick-borne diseases caused by Anaplasma spp. in Sicily and other Mediterranean regions and may contribute to the development of models to predict the risks for these tick-borne pathogens.     

Spatial Transferability of Habitat Suitability Models of Nephrops norvegicus among Fished Areas in the Northeast Atlantic: Sufficiently Stable for Marine Resource Conservation?

Knowledge of the spatial distribution and habitat associations of species in relation to the environment is essential for their management and conservation. Habitat suitability models are useful in quantifying species-environment relationships and predicting species distribution patterns. Little is known, however, about the stability and performance of habitat suitability models when projected into new areas (spatial transferability) and how this can inform resource management. The aims of this study were to model habitat suitability of Norway lobster (Nephrops norvegicus) in five fished areas of the Northeast Atlantic (Aran ground, Irish Sea, Celtic Sea, Scotland Inshore and Fladen ground), and to test for spatial transferability of habitat models among multiple regions. Nephrops burrow density was modelled using generalised additive models (GAMs) with predictors selected from four environmental variables (depth, slope, sediment and rugosity). Models were evaluated and tested for spatial transferability among areas. The optimum models (lowest AICc) for different areas always included depth and sediment as predictors. Burrow densities were generally greater at depth and in finer sediments, but relationships for individual areas were sometimes more complex. Aside from an inclusion of depth and sediment, the optimum models differed between fished areas. When it came to tests of spatial transferability, however, most of the models were able to predict Nephrops density in other areas. Furthermore, transferability was not dependent on use of the optimum models since competing models were also able to achieve a similar level of transferability to new areas. A degree of decoupling between model ‘fitting’ performance and spatial transferability supports the use of simpler models when extrapolating habitat suitability maps to different areas. Differences in the form and performance of models from different areas may supply further information on the processes shaping species’ distributions. Spatial transferability of habitat models can be used to support fishery management when the information is scarce but caution needs to be applied when making inference and a multi-area transferability analysis is preferable to bilateral comparisons between areas.     

Predicting Environmental Suitability for a Rare and Threatened Species (Lao Newt,Laotriton laoensis) Using Validated Species Distribution Models

The Lao newt (Laotriton laoensis) is a recently described species currently known only from northern Laos. Little is known about the species, but it is threatened as a result of overharvesting. We integrated field survey results with climate and altitude data to predict the geographic distribution of this species using the niche modeling program Maxent, and we validated these predictions by using interviews with local residents to confirm model predictions of presence and absence. The results of the validated Maxent models were then used to characterize the environmental conditions of areas predicted suitable for L. laoensis. Finally, we overlaid the resulting model with a map of current national protected areas in Laos to determine whether or not any land predicted to be suitable for this species is coincident with a national protected area. We found that both area under the curve (AUC) values and interview data provided strong support for the predictive power of these models, and we suggest that interview data could be used more widely in species distribution niche modeling. Our results further indicated that this species is mostly likely geographically restricted to high altitude regions (i.e., over 1,000 m elevation) in northern Laos and that only a minute fraction of suitable habitat is currently protected. This work thus emphasizes that increased protection efforts, including listing this species as endangered and the establishment of protected areas in the region predicted to be suitable for L. laoensis, are urgently needed.     

太白山几类植物群落灌木及草本层的最小取样面积研究

采用2条非饱和与2条饱和曲线方程对太白山7种类型植物群落(Ⅰ.锐齿栎林、Ⅱ.铁橡树林、Ⅲ.红桦林、Ⅳ.巴山冷杉-牛皮桦林、Ⅴ.巴山冷杉林、Ⅵ.太白红杉林和Ⅶ.头花杜鹃-大毛状薹草灌草丛)灌木及草本层拟合的种-面积曲线,计算研究精度要求分别为60%、70%、80%、90%时各群落各层的最小取样面积,并进行分析比较.结果表明,不同群落灌木及草本层最小取样面积均随研究精度增高而增大,群落Ⅰ~Ⅶ灌木层的取样面积分别为96、35、73、63、75、1701、8 m2时,草本层为91、91、57、59、71、657、m2时,可满足精度80%以下的研究要求;灌木层的取样面积为163、62、122、104、120、296、35 m2时,草本层为150、151、109、110、126、1192、9 m2时,可满足精度90%的研究要求.方差分析表明,不同群落灌木及草本层最小取样面积存在差异,有些差异达显著水平(P<0.05).因此,在野外调查时应根据研究精度要求和群落类型合理设置最小取样面积.     

Silvicolous on a Small Scale: Possibilities and Limitations of Habitat Suitability Models for Small,Elusive Mammals in Conservation Management and Landscape Planning

Species distribution and endangerment can be assessed by habitat-suitability modelling. This study addresses methodical aspects of habitat suitability modelling and includes an application example in actual species conservation and landscape planning. Models using species presence-absence data are preferable to presence-only models. In contrast to species presence data, absences are rarely recorded. Therefore, many studies generate pseudo-absence data for modelling. However, in this study model quality was higher with null samples collected in the field. Next to species data the choice of landscape data is crucial for suitability modelling. Landscape data with high resolution and ecological relevance for the study species improve model reliability and quality for small elusive mammals like Muscardinus avellanarius. For large scale assessment of species distribution, models with low-detailed data are sufficient. For regional site-specific conservation issues like a conflict-free site for new wind turbines, high-detailed regional models are needed. Even though the overlap with optimally suitable habitat for M. avellanarius was low, the installation of wind plants can pose a threat due to habitat loss and fragmentation. To conclude, modellers should clearly state the purpose of their models and choose the according level of detail for species and environmental data.     

Defining Landscape Resistance Values in Least-Cost Connectivity Models for the Invasive Grey Squirrel: A Comparison of Approaches Using Expert-Opinion and Habitat Suitability Modelling

Least-cost models are widely used to study the functional connectivity of habitat within a varied landscape matrix. A critical step in the process is identifying resistance values for each land cover based upon the facilitating or impeding impact on species movement. Ideally resistance values would be parameterised with empirical data, but due to a shortage of such information, expert-opinion is often used. However, the use of expert-opinion is seen as subjective, human-centric and unreliable. This study derived resistance values from grey squirrel habitat suitability models (HSM) in order to compare the utility and validity of this approach with more traditional, expert-led methods. Models were built and tested with MaxEnt, using squirrel presence records and a categorical land cover map for Cumbria, UK. Predictions on the likelihood of squirrel occurrence within each land cover type were inverted, providing resistance values which were used to parameterise a least-cost model. The resulting habitat networks were measured and compared to those derived from a least-cost model built with previously collated information from experts. The expert-derived and HSM-inferred least-cost networks differ in precision. The HSM-informed networks were smaller and more fragmented because of the higher resistance values attributed to most habitats. These results are discussed in relation to the applicability of both approaches for conservation and management objectives, providing guidance to researchers and practitioners attempting to apply and interpret a least-cost approach to mapping ecological networks.     

In Vino Veritas: An Invitation for Ambitious,Collaborative Proteogenomics Campaigns on Plant and Animal Models

Vitis vinifera has been an emblematic plant for humans since the Neolithic period. Human civilization has been shaped by its domestication as both its medicinal and nutritional values were exploited. It is now cultivated on all habitable continents, and more than 5000 varieties have been developed. A global passion for the art of wine fuels innovation and a profound desire for knowledge on this plant. The genome sequence of a homozygotic cultivar and several RNA‐seq datasets on other varieties have been released paving the way to gaining further insight into its biology and tailoring improvements to varieties. However, its genome annotation remains unpolished. In this issue of Proteomics, Chapman and Bellgard (Proteomics 2017, 17, 1700197) discuss how proteogenomics can help improve genome annotation. By mining shotgun proteomics data, they defined new protein‐coding genes, refined gene structures, and corrected numerous mRNA splicing events. This stimulating study shows how large international consortia could work together to improve plant and animal genome annotation on a large scale. To achieve this aim, time should be invested to generate comprehensive, high‐quality experimental datasets for a wide range of well‐defined lineages and exploit them with pipelines capable of handling giant datasets.     

Whole Plant Carbon Gain of an Endangered Herbaceous Species Aster kantoensis and the Influence of Shading by an Alien Grass Eragrostis curvula in its Gravelly Floodplain Habitat

Aster kantoensis, an endangered plant species, is endemic togravelly floodplains of a few large rivers in central Japan.In recent years, competitive exclusion by alien perennial grassesin its natural habitat has been suspected to be one of the majorfactors threatening this species. In the River Kinu, increasedshading by the perennial alien grass Eragrostis curvula reduceslight availability for A. kantoensis. To reveal the influenceof shading on the establishment and growth of A. kantoensisrosettes, the potential carbon gain of A. kantoensis in itsnatural habitat was estimated using microenvironmental dataand whole plant photosynthetic and respiratory responses tolight and temperature. Whole plant CO₂exchange responses weremeasured with a specifically designed ‘double chamber’,which enabled measurement of the CO₂gas exchange rates of thefoliage (F) and the culm (C; stem and roots) separately. Itwas demonstrated that in a plant with average C/F ratio, positivecarbon gain could be maintained only in the microsites wherethe relative PPFD (photosynthetically active photon flux density)was above 15 or 30% of unshaded conditions in early- or mid-summer,respectively. Increasing C/F ratio, caused by an increase inroot biomass as an adaptive response to drought, resulted ina large reduction in the carbon gain irrespective of microsite,weather and season. The high light requirement of A. kantoensisis interpreted as a cost of the morphological responses necessaryto avoid stresses characteristic of this gravelly floodplainhabitat. Copyright 2000 Annals of Botany Company Aster kantoensis Kitam., Eragrostis curvula Nees, biomass distribution, carbon gain, gravelly floodplain, respiration, shading, whole plant photosynthesis     

Identifying Mozambique's most critical areas for plant conservation: An evaluation of protected areas and Important Plant Areas

Successful protected area networks must represent biodiversity across taxonomic groups. However, too often plant species are overlooked in conservation planning, and the resulting protected areas may, as a result, fail to encompass the most important sites for plant diversity. The Mozambique Tropical Important Plant Areas project sought to promote the conservation of Mozambique's flora through the identification of Important Plant Areas (IPAs). Here, we use the Weighted Endemism including Global Endangerment (WEGE) index to identify the richest areas for rare and endemic plants in Mozambique and subsequently evaluate how well represented these hotspots are within the current protected area and IPA networks. We also examine the congruence between IPA and protected areas to identify opportunities for strengthening the conservation of plants in Mozambique. We found that high WEGE scores, representing areas rich in endemic/near-endemic and threatened species, predict the presence of IPAs in Mozambique, but do not predict the presence of protected areas. We also find that there is limited overlap between IPAs and protected areas in Mozambique. We demonstrate how IPAs could be an important tool for ensuring priority sites for plant diversity are included within protected area network expansions, particularly following the adoption of the “30 by 30” target agreed within the post-2020 Convention on Biological Diversity framework, with great potential for this method to be replicated elsewhere in the global tropics.     

Establishment and Growth of Living Fence Species: An Overlooked Tool for the Restoration of Degraded Areas in the Tropics

Numerous tree species can establish by vegetative means in the tropics. Many are used in agriculture as living fences and in alley cropping and could also be used in a restorational setting. However, little is known about their establishment ability. This study evaluated the establishment ability and cover development of multiple species in three separate field trials in northern Honduras. First, 11 species were evaluated for their ability to establish in a common garden experiment. Second, of the former species, Bursera simaruba and Gliricidia sepium were evaluated for 2 years for their ability to establish vegetatively and develop cover at three deforested sites. Lastly, a study examined whether greater initial stake height and diameter at breast height increased the establishment success and crown development of G. sepium stakes. First, five species, Erythrina berteroana, Erythrina fusca, Jatropha curcas, G. sepium, and B. simaruba, had high establishment success. Others showed promise but may have been planted in the wrong season. Second, establishment for G. sepium was nearly 100% at all sites, whereas B. simaruba ranged from 30–50%. Gliricidia sepium stakes developed more rapidly and attained greater cover than B. simaruba. Dry season planting may increase the establishment success of both species. Lastly, greater initial stake height and diameter at breast height each resulted in greater crown development for G. sepium. The use of living fence species as a restorational tool has been overlooked. Aside from the advantages of planting tree species vegetatively, species can act as seed recruitment foci by attracting seed dispersers and provide shade to improve microclimatic conditions for seedling establishment. The technique described is simple and could have broad application throughout tropical regions.     

FRET技术检测植物类caspase-3蛋白酶活性的质粒构建及其瞬时表达

植物细胞程序性死亡（programmed cell death,PCD）是一种由细胞内部程序控制的、主动的细胞死亡过程。在植物发育、逆境胁迫及超敏反应中,PCD都起着重要的作用。为检测植物PCD过程中类似动物细胞凋亡蛋白酶caspase-3的活性,构建了一个能够在活体植物细胞中实时检测类caspase-3蛋白酶激活的质粒PI—ECFP—EYFP。该质粒在植物细胞中可以表达出两端为青色荧光蛋白（ECFP）和黄色荧光蛋白（EYFP）的融合蛋白。这两个荧光蛋白通过含有caspase-3蛋白酶作用靶点DEVD的短肽相连,从而可以根据荧光共振能量转移现象检测类caspase-3凋亡蛋白酶的激活,以为实时检测植物PCD过程中关键蛋白酶的激活及其调控奠定基础。     

Assessing Invasion Impact: Survey Design Considerations and Implications for Management of An Invasive Marine Plant

We use a three-year study of sheltered low shore assemblages colonised by the non-indigenous Asian kelp Undaria pinnatifida to explore survey design issues for assessing the ecological impacts of invasive species. The weight of evidence overall suggested little impact from Undaria on low shore assemblages, with control–impact contrasts that could plausibly be interpreted as impacts probably reflecting natural causes. We demonstrate that the potential for reaching incorrect conclusions regarding the impacts of invasive species using control–impact designs is greater than when such designs are used to assess traditional forms of anthropogenic impact. We suggest that a before–after control–impact framework is essential, but recognise that such an approach has a number of limitations. In particular, there is no assurance that the before–after impact site will be invaded at all, or to the extent that provides worst-case impact information for coastal managers. We discuss possible ways of assessing invasive species impacts, but suggest that the uncertainty inherent in extrapolating impact information to other places and times means that the precautionary principle should be applied, and worst-case impacts assumed, until the level of scientific uncertainty is reduced. Such an approach should only be applied, however, after an evaluation of the feasibility, costs and benefits of managing a particular pest in relation to other priorities for invasive species.     

水生空心莲子草入侵群落数量分类及其物种分布的环境解释

生境异质性在不同生态层次上影响物种分布与扩散,进而可能影响外来植物的入侵态势。该研究通过在中国21°N～31°N范围内设置23个10m×10m的样地,利用双向聚类(TWINSPAN)和除趋势对应分析(DCA)等数量生态学方法,研究水生型空心莲子草(Alternanthera philoxeroides)入侵群落的结构特征并划分其群丛类型,并采用冗余分析法(RDA)分析空心莲子草种群特征、群落物种分布与环境因子(经度、纬度、海拔、氨态氮、硝态氮、电导率、溶解氧)的关系,以期为生物入侵防治及本土生物多样性保护提供参考。结果显示:(1)23个样地共记录植物48种,隶属于21科42属,空心莲子草优势地位显著,主要伴生种为双穗雀稗(Paspalum paspaloides)、李氏禾(Leersia hexandra)和水蓼(Polygonum hydropiper)。(2)23个样地群落可划分为6组群丛类型,其中空心莲子草+双穗雀稗+水芹(Oenanthe javanica)是最主要的类型。(3)48种植物可划分为4类功能群,分别为先锋种型、优势伴生种型、次要伴生种型和逃避型,功能群的DCA分异性高于群丛类型。(4)群落物种分布状况主要由氨态氮和电导率决定,而物种丰富度及空心莲子草种群特征则受到电导率、经度、海拔和溶解氧等多个环境变量的影响;水生空心莲子草的入侵重要值取决于其无性分枝数和种群盖度。研究表明,水生空心莲子草入侵群落的结构相对简单,应加大对其入侵监测力度并维持较高的生境异质性,以延缓水域生态系统的生物入侵进程。     

A Model for Plant and Crop Growth, Allowing for Competition for Light by the use of Potential and Restricted Projected Crown Zone Areas

Relations for competition for light are developed and used ina plant growth model applicable to the isolated plant, to plantsin even-aged monoculture and to plants in mixed-aged monoculture.In an isolated plant, it is assumed that a leaf area, proportionalto the plant mass, is contained within a crown whose projectedzone area is proportional to plant mass to the 2/3 power. Self-shadingprogressively reduces the specific growth rate. If light werethe sole limiting resource and were constant, one can derivea growth equation, dw/dt = rw[1 - exp (-KW^1/3)]KW^1/3, which,integrated, gives w^1/3 = K^-1 ln {1 + [exp (KW^1/3₀)-1] exp (rt/3)}.It approximates, initially, to a particular case of the Richards(1959) empirical growth equation. In even-aged evenly-spaced monocrops competing only for light,it is assumed that the zone areas merge at canopy closure, andgrowth then follows the expolinear equation of Goudriaan andMonteith (1990), giving a continuous function based on groundcover. For mixed-aged monocrops, we assume a phase of canopyclosure that affects the younger plants earlier than the olderones. Under varying environmental conditions in the field, plant growthmay be affected by other factors in addition, e.g. temperature.In the growth conductance model of Aikman and Scaife (1993),the shading expressions are applied to the light-dependence. Data from two sowings of cabbage and carrot in even-aged andmixed-aged monocrops were used to test the model. The parametervalues derived from the even-aged monocultures predict the growthrates in the mixed-aged monocultures better than models whichassume uniform canopies.Copyright 1994, 1999 Academic Press Growth, model, monocrop, even-aged, mixed-aged, PAR, density, competition, light, shading, zone area, ground cover, temperature, carbon dioxide, expolinear, carrot, Daucus carota L., cabbage, Brassica oleracea L     

Conic Sampling: An Efficient Method for Solving Linear and Quadratic Programming by Randomly Linking Constraints within the Interior

Linear programming (LP) problems are commonly used in analysis and resource allocation, frequently surfacing as approximations to more difficult problems. Existing approaches to LP have been dominated by a small group of methods, and randomized algorithms have not enjoyed popularity in practice. This paper introduces a novel randomized method of solving LP problems by moving along the facets and within the interior of the polytope along rays randomly sampled from the polyhedral cones defined by the bounding constraints. This conic sampling method is then applied to randomly sampled LPs, and its runtime performance is shown to compare favorably to the simplex and primal affine-scaling algorithms, especially on polytopes with certain characteristics. The conic sampling method is then adapted and applied to solve a certain quadratic program, which compute a projection onto a polytope; the proposed method is shown to outperform the proprietary software Mathematica on large, sparse QP problems constructed from mass spectometry-based proteomics.     

Putative and Unique Gene Sequence Utilization for the Design of Species Specific Probes as Modeled by Lactobacillus plantarum

The concept of utilizing putative and unique gene sequences for the design of species specific probes was tested. The abundance profile of assigned functions within the Lactobacillus plantarum genome was used for the identification of the putative and unique gene sequence, csh. The targeted gene (csh) was used as the template for PCR amplification and construction of a non-radioactive DIG labeled probe. The csh derived probe aided in the preliminary and rapid identification of L. plantarum from mixed cultures by colony hybridization. The method described here for the rapid identification of L. plantarum can also be applied for the rapid detection of other bacteria if a unique gene sequence can be identified from its complete genome sequence.     

An Improved Method for Analysis of Polyamines in Plant Tissue by Precolumn Derivatization with o-Phthalaldehyde and Separation by High Performance Liquid Chromatography

An improved high-performance liquid-chromatographic method was developed for estimation of polyamines in crude plant extracts. Polyamines were derivatized with o-phthalaldehyde and mercaptoethanol (OPT). The fluorescent derivatives were eluted from a C₁₈ column with the dimethylcyclohexylamine-phosphate buffer derived by T. Skaaden and T. Greibrokk ([1982] J Chromatogr 247: 111-122) after treatment to remove impurities in the buffer. The method had a sensitivity of 1-2 picomoles and completely resolved nine polyamines (agmatine, spermine, nor-spermidine, spermidine, 3,5-homospermidine, 4,4-homospermidine, 1,3-diaminopropane, putrescine, and cadaverine) in 12 to 14 minutes. An optional ion-exchange step was used to remove less basic amines (including amino acids) and to concentrate the crude extracts. This method was compared with benzoyl chloride derivatization. Use of the benzoyl chloride method vastly under-estimated the amount of polyamine in some plant extracts, a problem not encountered with the OPT procedure. Additionally, the OPT procedure resolved two isomers of homospermidine found in Azolla caroliniana. These two isomers were not resolved with the benzoylation method. Overall, the OPT method described here requires preparation and analysis time similar to other current methods but provides greater sensitivity and selectivity.     

An Analysis of Overstory Tree Canopy Cover in Sites Occupied by Native and Introduced Cottontails in the Northeastern United States with Recommendations for Habitat Management for New England Cottontail

The New England cottontail (Sylvilagus transitionalis) is a high conservation priority in the Northeastern United States and has been listed as a candidate species under the Endangered Species Act. Loss of early successional habitat is the most common explanation for the decline of the species, which is considered to require habitat with dense low vegetation and limited overstory tree canopy. Federal and state wildlife agencies actively encourage landowners to create this habitat type by clearcutting blocks of forest. However, there are recent indications that the species also occupies sites with moderate overstory tree canopy cover. This is important because many landowners have negative views about clearcutting and are more willing to adopt silvicultural approaches that retain some overstory trees. Furthermore, it is possible that clearcuts with no overstory canopy cover may attract the eastern cottontail (S. floridanus), an introduced species with an expanding range. The objective of our study was to provide guidance for future efforts to create habitat that would be more favorable for New England cottontail than eastern cottontail in areas where the two species are sympatric. We analyzed canopy cover at 336 cottontail locations in five states using maximum entropy modelling and other statistical methods. We found that New England cottontail occupied sites with a mean overstory tree canopy cover of 58% (SE±1.36), and was less likely than eastern cottontail to occupy sites with lower overstory canopy cover and more likely to occupy sites with higher overstory canopy cover. Our findings suggest that silvicultural approaches that retain some overstory canopy cover may be appropriate for creating habitat for New England cottontail. We believe that our results will help inform critical management decisions for the conservation of New England cottontail, and that our methodology can be applied to analyses of habitat use of other critical wildlife species.