Measuring Rao's Q diversity index from remote sensing: An open source solution

Measuring biodiversity is a key issue in ecology to guarantee effective indicators of ecosystem health at different spatial and time scales. However, estimating biodiversity from field observations might present difficulties related to costs and time needed. Moreover, a continuous data update for biodiversity monitoring purposes might be prohibitive. From this point of view, remote sensing represents a powerful tool since it allows to cover wide areas in a relatively low amount of time. One of the most common indicators of biodiversity is Shannon's entropy H′, which is strictly related to environmental heterogeneity, and thus to species diversity. However, Shannon's entropy might show drawbacks once applied to remote sensing data, since it considers relative abundances but it does not explicitly account for distances among pixels’ numerical values. In this paper we propose the use of Rao's Q applied to remotely sensed data, providing a straightforward R-package function to calculate it in 2D systems. We will introduce the theoretical rationale behind Rao's index and then provide applied examples based on the proposed R function.     

A vegetation map of The Netherlands,based on the relationship between ecotopes and types of potential natural vegetation

Summary The method of mapping the vegetation on scale 1: 200,000 and the starting points in relation to the potential natural vegetation and ecotopes, are discussed.In view of the planological background of this study, some restrictions have been added to the concept of potential natural vegetation, concerning the period of development and the human influence.The relationship between soil, ground water and vegetation was studied, which resulted in the map of the potential natural vegetation.Each type of potential natural vegetation stands for a series of vegetation types on the same site. Seven main series, with a number of sub-series are distinguished. Within each vegetation series the plant communities have been spread over five groups, according to their structure and naturalness.Ecotopes and ecotope complexes are considered as landscape ecological units. A list of ecotopes was obtained by interpreting topographical maps and by inventory data.The actual vegetation was mapped by estimating the size of the ecotopes within the separate areas. It was expressed in a five figure code for the five groups from the vegetation and ecotopes is combined into the vegetation map of The Netherlands.Interpretation problems, some of them specific for The Netherlands, are discussed and some remarks are made on the necessity of further research.Contribution to the Symposium on Plant Species and Plant Communities, held at Nijmegen, 11–12 November 1976, on the occasion of the 60th birthday of Professor Victor Westhoff.Nomenclature follows Heukels-van Ooststroom, Flora van Nederland, 18e druk, 1975, Wolters-Noordhoff, Groningen; nomenclature of syntaxa follows Westhoff & den Held (1969)     

Composition and diversity of herbaceous patches in woody vegetation: The effects of grazing,soil seed bank,patch spatial properties and scale

Herbaceous plants contribute much to plant diversity in Mediterranean-type ecosystems though mostly occupying relatively small patches within the dense woody vegetation. While studying species diversity in the herbaceous patches, we hypothesized that grazing, soil seed bank, and spatial properties of the patch affect plant diversity and composition at different spatial scales. The study site was in an LTER site located in the Mediterranean region in north Israel. We determined herbaceous species composition in: (1) randomly sampled quadrats in herbaceous patches in grazed and un-grazed plots; (2) soil seed bank samples taken from the same patches and germinated under optimal greenhouse conditions; (3) quadrats in the same patches sown with a homogenous mixture of local soil samples. Using GIS methods, we determined small-scale spatial characteristics of the herbaceous patches. Alpha and beta diversities were calculated at the patch and plot scales using Shannon's entropy H. Grazing increased alpha diversity of local untreated seed bank samples but decreased alpha diversity of the artificial homogenous soil seed bank mixture at both patch and plot scales. Positive relation between alpha diversity and patch area was detected only under grazing. Grazing increased beta diversity in all three treatments at the patch scale. Grazing decreased the similarity in species composition between above-ground vegetation and soil seed bank. The results indicate that moderate cattle-grazing affects species diversity in the herbaceous patches within the dense maquis. This effect is scale-dependent, and interacts with the effects of soil seed bank and patch spatial-properties: without grazing soil seed bank plays a more important role than patch spatial properties, but under grazing the size and the accessibility of the patch are more important in the determination of herbaceous species composition.     

三工河流域荒漠绿洲植被动态及其成因分析

以三工河流域为例,讨论了植被动态及其地貌、水资源利用、河流廊道和排碱渠等景观要素的变化对植被产生的影响.结果表明,随着景观格局的变化,流域内的植丛高度、盖度及生物量均表现出较大变异性.以河流廊道为核心,通常荒漠绿洲景观格局呈带状分布,且由内向外随水热条件的改变,植被类型由乔灌木林依次向灌丛草甸、盐化草甸、荒漠化草甸和荒漠层次结构过渡.人类活动影响强烈的景观要素,其斑块多样性、破碎度、分离度和斑块密度等指数值较高,而人类活动影响较小的,其优势度和均匀度较高.各景观要素的稳定性不同,其大小顺序为:荒漠>沙砾石地>城镇用地>水体>农田>牧草地>菜地>林地>居民点>盐碱地>荒草地>水浇地>果园.梭梭群落的净生长量高峰值出现在8月,而博乐蒿、琵琶柴群落的净生长量高峰值出现时间各年度不同.博乐蒿群落与海拔相关系数最大,而琵琶柴群落则与土壤水含量、地下水位关系密切,梭梭群落与4～9月降雨量相关系数最大.     

Multi-scale analysis of alpine landscapes with different intensities of abandonment reveals similar spatial pattern changes: Implications for habitat conservation

The abandonment of traditional anthropogenic activities is an important driver shaping landscape patterns. Therefore, multi-scale pattern analysis over time is needed to identify appropriate scales for biodiversity conservation and monitoring of abandoned landscapes. We compared spatial and temporal changes in a pair of alpine watersheds in Italy (Cajada and Tovanella), which are similar in size, geo-climatic conditions, and land-use histories; but have had divergent anthropogenic abandonment processes since the 1950s. We hypothesize that this divergence has led to corresponding dissimilarities in multi-scale patterns of landscape change. To examine this hypothesis, we analyzed land cover maps from three years (1954, 1980/83, 2006) and described the changes using transition matrices. For each year and watershed, landscape heterogeneity and a set of class-level metrics (i.e. percentage of the landscape, area-weighted mean patch size, patch density, area-weighted mean shape index, edge density, and aggregation index) were also measured at different scales using random sampling techniques, and the results were summarized by using scalograms. Woodland expansion occurred mainly at the expenses of grasslands, meadows, and shrublands. These changes were greater during the first time-period (1954-80/83) than in the more recent period (1980/83-2006), with a mean annual value that decreased from +5.18 to +1.33 ha/year and from +4.08 to +1.96 ha/year in the abandoned and managed watersheds, respectively. Landscape heterogeneity decreased over time with a similar pattern in both watersheds, which indicates a general process of homogenization. Management regime affected the spatial-scale response of class-level metrics; these metrics showed a variety of multi-scalar responses, which were not always consistent over time and under different management regimes. When considering the response of the indices across spatial-scales for both watersheds, certain historical curves showed a scale break, representing a significant change in the shape and slope of the curve (i.e. scale divergence). The presence of scale breaks in the scalograms can potentially reveal important thresholds for biodiversity. For example, grassland and meadow patch density at small spatial scales (<200 m radius), which was found to be important for protected butterfly species, had a greater reduction over time in the managed watershed when compared to the abandoned watershed. In conclusion, the findings of this study indicate that there is good potential for understanding changes in landscape patterns under different management abandonment regimes by combining spatial and temporal analysis of class-level metrics.     

A simulated map of the potential natural forest vegetation of Switzerland

Using empirical data (ca. 7500 phytosociological releves), a simple, probabilistic ‘vegetation-site’ model was developed, to simulate geographical distribution of 71 forest community types, representing the potential natural vegetation (PNV) of Switzerland. The model was interfaced to a geographic information system (GIS) and used to generate a numerical vegetation map, on the basis of digital maps of 12 environmental variables including climatic conditions (temperature and precipitation), topography (elevation, slope, aspect), and soil parameters (soil pH and physical soil parameters). The predicted distribution of forest communities was compared with several vegetation maps, prepared for some subregions of Switzerland by means of traditional field methods. Similarity ranged from 50 to 80 %, depending on the community type, level of vegetational hierarchy and the geographical region. The current resolution and accuracy of the simulated vegetation map allows us to study the vegetational patterns on the level of the entire country or its major geographical and climatic regions. The simulated vegetation map is potentially an important tool in ecological risk assessment studies concerning the possible impacts of climate change on the ecological potential of forest sites and biological diversity of forest communities.     

三工河流域荒漠绿洲植被动态及其成因分析

以三工河流域为例,讨论了植被动态及其地貌、水资源利用、河流廊道和排碱渠等景观要素的变化对植被产生的影响．结果表明,随着景观格局的变化,流域内的植丛高度、盖度及生物量均表现出较大变异性．以河流廊道为核心,通常荒漠绿洲景观格局呈带状分布,且由内向外随水热条件的改变,植被类型由乔灌木林依次向灌丛草甸、盐化草甸、荒漠化草甸和荒漠层次结构过渡．人类活动影响强烈的景观要素。其斑块多样性、破碎度、分离度和斑块密度等指数值较高,而人类活动影响较小的,其优势度和均匀度较高．各景观要素的稳定性不同,其大小顺序为：荒漠>沙砾石地>城镇用地>水体>农田>牧草地>莱地>林地>居民点>盐碱地>荒草地>水浇地>果园．梭梭群落的净生长量高峰值出现在8月,而博乐蒿、琵琶柴群落的净生长量高峰值出现时间各年度不同．博乐蒿群落与海拔相关系数最大,而琵琶柴群落则与土壤水含量、地下水位关系密切,梭梭群落与4～9月降雨量相关系数最大。     

Quantitative changes of forest landscapes over the last century across Italy

A key topic in landscape ecology and vegetation science is the quantitative analysis of changes in forest cover over time, through the use of geomatics monitoring tools. Ecologists and landscape researchers are pointing out that a full understanding of ecosystems and landscapes should be based on the analysis of their functioning over long time series. Under this perspective, a long-term historical reconstruction of forest cover is essential. This study has aimed at examining the long-term dynamics of forest landscapes in Italy, over the last century, using recent remote-sensing based map (2012) and an accurate historical map (1936). A forest-non forest approach has been followed by the computation of a variety of landscape metrics using two analysis tools, with the final objective of quantifying changes in forest cover patterns and in the composition of specific landscape elements. Results show that forest landscape structure has significantly changed across Italy, resulting in a general trend of decreasing fragmentation and patchiness, mainly through enlargement of existing forest patches, which have also assumed a more geometrically regular shape. In relative terms, the greatest expansion of forest areas has occurred mainly in lowland districts characterised by the highest level of human pressure in the country.     

Long‐term vegetation stability and the concept of potential natural vegetation in the Neotropics

When vegetation trends over time are analysed from an appropriate long‐term perspective using palaeoecological records, the concept of potential natural vegetation (PNV) is unsupported because of continual vegetation changes driven by natural or anthropic forcings. However, some palaeoecological records show long‐lasting (i.e. millennial) vegetation stability at multidecadal to centennial time scales in the absence of natural and human drivers of change, which fits within the definition of PNV. A more detailed palaeoecological analysis of these records shows that they are an exception rather than a rule, and that they cannot be differentiated from other transient ecological states. Therefore, long records of vegetation stability cannot be considered to be valid evidence for PNV. From a palaeoecological perspective, the PNV concept is concluded to be unnecessary, even in cases of multidecadal to centennial vegetation stability in the absence of environmental disturbance.     

On the relationship between Pielou’s evenness and landscape dominance within the context of Hill’s diversity profiles

Entropy-related biodiversity indices deriving their conceptual basis from Shannon’s information theory have a long history of use in ecology for quantifying community structure and diversity. In addition, in the last two decades, numerous information–theoretical indices, such as the landscape dominance index, have been extensively applied to characterize landscape diversity in space and time. In this contribution, we offer a simple analytical relation between Pielou’s evenness J and landscape dominance D within the broader context of Hill’s parametric diversity family. Within this context, we recommend the use of Hill’s diversity number evenness E_1,0 to overcome the shortcomings both of Pielou’s evenness J and the landscape dominance index D.     

A practical approach to the study of spatial structure in simple cases of heterogeneous vegetation

Abstract. Spatial heterogeneity is a characteristic of most natural ecosystems which is difficult to handle analytically, particularly in the absence of knowledge about the exogenous factors responsible for this heterogeneity. While classical methods for analysis of spatial point patterns usually require the hypothesis of homogeneity, we present a practical approach for partitioning heterogeneous vegetation plots into homogeneous subplots in simple cases of heterogeneity without drastically reducing the data. It is based on the detection of endogenous variations of the pattern using local density and second‐order local neighbour density functions that allow delineation of irregularly shaped subplots that could be considered as internally homogeneous. Spatial statistics, such as Ripley's K‐function adapted to analyse plots of irregular shape, can then be computed for each of the homogeneous subplots. Two applications to forest ecological field data demonstrate that the method, addressed to ecologists, can avoid misinterpretations of the spatial structure of heterogeneous vegetation stands.     

Towards a more transparent use of the potential natural vegetation concept – an answer to Chiarucci et al.

In this paper, the concerns of Chiarucci et al. ( 2010 ) regarding use of the potential natural vegetation (PNV) concept are addressed, as voiced in the forum section of the Journal of Vegetation Science. First, we rectify some unfounded expectations concerning PNV, including a relationship with prehuman vegetation and phytosociology. Second, we point out issues that pose considerable challenges in PNV and require common agreement. Here, we address the issue of time and disturbance. We propose to use the static PNV concept as a baseline, a null model for landscape assessment and in comparisons. Instead of changing the PNV concept itself, we introduce a new term, potential future natural vegetation (PFV) to cover estimations of potential successional outcomes. Finally, we offer a new view of PNV with which we intend to make the use of PNV estimates more transparent. We formalize the PNV theory into a partial cause‐effect model of vegetation that clearly states which effects on vegetation are factored out during its estimation. Further, we also propose to assess PNV in a probabilistic setting, rather than providing a single estimate for one location. This multiple PNV would reflect our uncertainty about the vegetation entity that could persist at the locality concerned. Such uncertainty arises from the overlap of environmental preferences of different mature vegetation types. Thus reformulated, we argue that the PNV concept has much to offer as a null model, especially in landscape ecology and in site comparisons in space and time.     

Simulated distribution of vegetation types in response to climate change on the Tibetan Plateau

Abstract. Questions: What is the relationship between alpine vegetation patterns and climate? And how do alpine vegetation patterns respond to climate changes? Location: Tibetan Plateau, southwestern China. The total area is 2500000 km² with an average altitude over 4000 m. Methods: The geographic distribution of vegetation types on the Tibetan Plateau was simulated based on climatology using a small set of plant functional types (PFTs) embedded in the biogeochemistry‐biography model BIOME4. The paleoclimate for the early Holocene was used to explore the possibility of simulating past vegetation patterns. Changes in vegetation patterns were simulated assuming continuous exponential increase in atmospheric CO concentration, based on a transient ocean‐atmosphere simulation including sulfate aerosol effects during the 21st century. Results: Forest, shrub steppe, alpine steppe and alpine meadow extended while no desert vegetation developed under the warmer and humid climate of the early Holocene. In the future climate scenario, the simulated tree line is farther north in most sectors than at present. There are also major northward shifts of alpine meadows and a reduction in shrub‐dominated montane steppe. The boundary between montane desert and alpine desert will be farther to the south than today. The area of alpine desert would decrease, that of montane desert would increase. Conclusions: The outline of changes in vegetation distribution was captured with the simulation. Increased CO2 concentration would potentially lead to big changes in alpine ecosystems.     

Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators

Transposable elements are widely distributed in archaea, bacteria and eukarya domains. Considerable discrepancies of transposable elements in eukaryotes have been reported, however, the studies focusing on the diversity of transposable element systems in prokaryotes were scarce. Understanding the transposable element system in cyanobacteria by the genome-wide analysis will greatly improve the knowledge of cyanobacterial diversity. In this study, the transposable elements of seventeen cyanobacterial genomes were analyzed. The abundance of insertion sequence (IS) elements differs significantly among the cyanobacterial genomes examined. In particular, water bloom forming Microcystis aeruginosa NIES843 was shown to have the highest abundance of IS elements reaching 10.85% of the genome. IS family is a widely acceptable IS classification unit, and IS subfamily, based on probe sequences, was firstly proposed as the basic classification unit for IS element system, therefore both IS family and IS subfamily were suggested as the two hierarchical units for evaluating the IS element system diversity. In total, 1980 predicted IS elements, within 21 IS families and 132 subfamilies, were identified in the examined cyanobacterial genomes. Families IS4, IS5, IS630 and IS200-605 are widely distributed, and therefore supposed to be the ancestral IS families. Analysis on the intactness of IS elements showed that the percentage of the intact IS differs largely among these cyanobacterial strains. Higher percentage of the intact IS detected in the two hot spring cyanobacterial strains implied that the intactness of IS elements may be related to the genomic stabilization of cyanobacteria inhabiting in the extreme environments. The frequencies between IS elements and miniature inverted-repeat transposable elements (MITEs) were shown to have a linear positive correlation. The transposable element system in cyanobacterial genomes is of hypervariability. With characterization of easy definition and stability, IS subfamily is considered as a reliable lower classification unit in IS element system. The abundance of intact IS, the composition of IS families and subfamilies, the sequence diversity of IS element nucleotide and transposase amino acid are informative and suitable as the indicators for studies on cyanobacterial diversity. Practically, the transposable system may provide us a new perspective to realize the diversity and evolution of populations of water bloom forming cyanobacterial species.     

Effects of recent climate trends on the distribution of potential natural vegetation in Central Germany

Introducing climate quotients for the growing season (Q_gs) provides a way to quantify effects of climate trends with respect to Potential Natural Vegetation (PNV), especially beech forests (Fagus sylvatica L.) in Central Germany. What is crucial in this regard is the great influence of the dominant decrease in the amount of precipitation (up to 40% in the last 50 years) during the growing season versus the dormant season. However, precipitation during the dormant season (which is predominantly increasing: up to 40% in the last 50 years) is also important for replenishing the soil water supply. The Q_gs values of the Climatic Normal period of 1971–2000 are generally higher (up to 12% in lowland areas) compared with the Climatic Normal period of 1961–1990, the extent of the difference being in general inversely proportional to elevation above sea level. What this means for the area under investigation is that humidity conditions, which generally improve as the elevation above sea level increases, have a positive effect on the site potential. However, a comparison of the climatologically important period of 1991–2003 with the period of 1961–1990 (area-wide increase between 12% and 16%) could not identify this positive effect of elevation on precipitation for the area under investigation. With regard to the recent climate-based trends of PNV, we have shown that all natural spatial units in Central Germany are affected by progressing continentality (i.e., dryness) during the growing season and the resulting deterioration of the site potential. The area of potential beech forest at lower elevation has decreased in favour of oak forest as PNV, while less change is observed in the montane area.     

Sea‐level rise,habitat loss,and potential extirpation of a salt marsh specialist bird in urbanized landscapes

Sea‐level rise (SLR) impacts on intertidal habitat depend on coastal topology, accretion, and constraints from surrounding development. Such habitat changes might affect species like Belding's savannah sparrows (Passerculus sandwichensis beldingi; BSSP), which live in high‐elevation salt marsh in the Southern California Bight. To predict how BSSP habitat might change under various SLR scenarios, we first constructed a suitability model by matching bird observations with elevation. We then mapped current BSSP breeding and foraging habitat at six estuarine sites by applying the elevation‐suitability model to digital elevation models. To estimate changes in digital elevation models under different SLR scenarios, we used a site‐specific, one‐dimensional elevation model (wetland accretion rate model of ecosystem resilience). We then applied our elevation‐suitability model to the projected digital elevation models. The resulting maps suggest that suitable breeding and foraging habitat could decline as increased inundation converts middle‐ and high‐elevation suitable habitat to mudflat and subtidal zones. As a result, the highest SLR scenario predicted that no suitable breeding or foraging habitat would remain at any site by 2100 and 2110. Removing development constraints to facilitate landward migration of high salt marsh, or redistributing dredge spoils to replace submerged habitat, might create future high salt marsh habitat, thereby reducing extirpation risk for BSSP in southern California.     

A vegetation-ecological approach to the classification and evaluation of potential natural vegetation of the Fagetea crenatae region in Tohoku (northern Honshu), Japan

A new vegetation-ecological approach is proposed for classification and evaluation of vegetation zones by means of phytosociological landscape analysis, based on the potential natural vegetation. The study area is the “Fagetea crenatae region” of the cool-temperate zone of Tohoku (northern Honshu) and the northern parts of Kanto. The area was divided into 953 geographic quadrats on a base map at a scale of 1 ∶ 500000. Based on climax complexes of vegetation in each quadrat, 55 community sub-groups were distinguished as basic units of community complex and vegetation landscapes. The community sub-groups were then grouped into 17 larger community groups by the phytosociological table method. As a result, three phytogeographic vegetation zones (Japan Sea side, inland areas and Pacific side) were classified. For each of these community sub-groups, five geographical and climatic variables (average altitude, mean annual temperature, Kira's warmth index, annual precipitation and mean annual maximum snow depth) were averaged, and the community sub-groups in the same community group, which resembled each other ecologically, were assembled into 28 clusters. The clusters were combined into 11 ecological groups by means of Pearson's similarity ratio of geographical and climatic characteristics. By comparing these ecological groups as a vegetation complex, four phytogeographic vegetation zones (Japan Sea side, inland areas, Pacific side and northern Honshu) corresponding to each potential natural vegetation region with distinct environmental characteristics, were newly classified.     

农田景观格局对南疆枣园传粉昆虫群落多样性的影响

[目的]明确新疆南疆地区农田景观格局对枣园传粉昆虫群落多样性的影响.[方法]2019和2020年在新疆阿克苏地区共选取29个试验站点,通过陷阱诱集法获取中心枣园内传粉昆虫多样性数据,调查中心枣园周围半径2 000 m范围内土地使用信息,建立枣园传粉昆虫群落指数与景观变量之间的线性混合模型,使用基于赤池信息准则的多模型推...