Samara Federal Research Scientific Center

Abstract The European Vegetation Archive ( EVA ) is a centralized database of European vegetation plots developed by the IAVS Working Group European Vegetation Survey. It has been in development since 2012 and first made available for use in research projects in 2014. It stores copies of national and regional vegetation‐ plot databases on a single software platform. Data storage in EVA does not affect on‐going independent development of the contributing databases, which remain the property of the data contributors. EVA uses a prototype of the database management software TURBOVEG 3 developed for joint management of multiple databases that use different species lists. This is facilitated by the SynBioSys Taxon Database, a system of taxon names and concepts used in the individual European databases and their corresponding names on a unified list of European flora. TURBOVEG 3 also includes procedures for handling data requests, selections and provisions according to the approved EVA Data Property and Governance Rules. By 30 June 2015, 61 databases from all European regions have joined EVA , contributing in total 1 027 376 vegetation plots, 82% of them with geographic coordinates, from 57 countries. EVA provides a unique data source for large‐scale analyses of European vegetation diversity both for fundamental research and nature conservation applications. Updated information on EVA is available online at http://euroveg.org/eva-database .

Abstract Aim The EUNIS Habitat Classification is a widely used reference framework for European habitat types (habitats), but it lacks formal definitions of individual habitats that would enable their unequivocal identification. Our goal was to develop a tool for assigning vegetation‐plot records to the habitats of the EUNIS system, use it to classify a European vegetation‐plot database, and compile statistically‐derived characteristic species combinations and distribution maps for these habitats. Location Europe. Methods We developed the classification expert system EUNIS‐ESy, which contains definitions of individual EUNIS habitats based on their species composition and geographic location. Each habitat was formally defined as a formula in a computer language combining algebraic and set‐theoretic concepts with formal logical operators. We applied this expert system to classify 1,261,373 vegetation plots from the European Vegetation Archive (EVA) and other databases. Then we determined diagnostic, constant and dominant species for each habitat by calculating species‐to‐habitat fidelity and constancy (occurrence frequency) in the classified data set. Finally, we mapped the plot locations for each habitat. Results Formal definitions were developed for 199 habitats at Level 3 of the EUNIS hierarchy, including 25 coastal, 18 wetland, 55 grassland, 43 shrubland, 46 forest and 12 man‐made habitats. The expert system classified 1,125,121 vegetation plots to these habitat groups and 73,188 to other habitats, while 63,064 plots remained unclassified or were classified to more than one habitat. Data on each habitat were summarized in factsheets containing habitat description, distribution map, corresponding syntaxa and characteristic species combination. Conclusions EUNIS habitats were characterized for the first time in terms of their species composition and distribution, based on a classification of a European database of vegetation plots using the newly developed electronic expert system EUNIS‐ESy. The data provided and the expert system have considerable potential for future use in European nature conservation planning, monitoring and assessment.

Migraine and sleep disorders are common and often burdensome chronic conditions with a high prevalence in the general population, and with considerable socio-economic impact and costs.The existence of a relationship between migraine and sleep disorders has been recognized from centuries by clinicians and epidemiological studies. Nevertheless, the exact nature of this association, the underlying mechanisms and interactions are complex and not completely understood. Recent biochemical and functional imaging studies identified central nervous system structures and neurotransmitters involved in the pathophysiology of migraine and also important for the regulation of normal sleep architecture, suggesting a possible causative role, in the pathogenesis of both disorders, of a dysregulation in these common nervous system pathways.This systematic review summarizes the existing data on migraine and sleep disorders with the aim to evaluate the existence of a causal relationship and to assess the presence of influencing factors. The identification of specific sleep disorders associated with migraine should induce clinicians to systematically assess their presence in migraine patients and to adopt combined treatment strategies.

Despite high rates of exposure, only 5-10% of people infected with Mycobacterium tuberculosis will develop active tuberculosis (TB) disease, suggesting a significant role for genetic variation in the human immune response to this infection. Here, we studied TB association and expression of 18 genes involved in the Toll-like receptor (TLR) pathways. Initially, we genotyped 149 sequence polymorphisms in 375 pulmonary TB patients and 387 controls from Indonesia. We found that four polymorphisms in the TLR8 gene on chromosome X showed evidence of association with TB susceptibility in males, including a non-synonymous polymorphism rs3764880 (Met1Val; P = 0.007, odds ratio (OR) = 1.8, 95% c.i. = 1.2-2.7). We genotyped these four TLR8 polymorphisms in an independent collection of 1,837 pulmonary TB patients and 1,779 controls from Russia and again found evidence of association in males (for rs3764880 P = 0.03, OR = 1.2, 95% c.i. = 1.02-1.48). Combined evidence for association is P = 1.2x10(-3)-6x10(-4). In addition, a quantitative PCR analysis indicated that TLR8 transcript levels are significantly up-regulated in patients during the acute phase of disease (P = 9.36x10(-5)), relative to baseline levels following successful chemotherapy. A marked increase in TLR8 protein expression was also observed directly in differentiated macrophages upon infection with M. bovis bacille Calmette-Guérin (BCG). Taken together, our results provide evidence, for the first time, of a role for the TLR8 gene in susceptibility to pulmonary TB across different populations.

Abstract Motivation Assessing biodiversity status and trends in plant communities is critical for understanding, quantifying and predicting the effects of global change on ecosystems. Vegetation plots record the occurrence or abundance of all plant species co‐occurring within delimited local areas. This allows species absences to be inferred, information seldom provided by existing global plant datasets. Although many vegetation plots have been recorded, most are not available to the global research community. A recent initiative, called ‘sPlot’, compiled the first global vegetation plot database, and continues to grow and curate it. The sPlot database, however, is extremely unbalanced spatially and environmentally, and is not open‐access. Here, we address both these issues by (a) resampling the vegetation plots using several environmental variables as sampling strata and (b) securing permission from data holders of 105 local‐to‐regional datasets to openly release data. We thus present sPlotOpen, the largest open‐access dataset of vegetation plots ever released. sPlotOpen can be used to explore global diversity at the plant community level, as ground truth data in remote sensing applications, or as a baseline for biodiversity monitoring. Main types of variable contained Vegetation plots ( n = 95,104) recording cover or abundance of naturally co‐occurring vascular plant species within delimited areas. sPlotOpen contains three partially overlapping resampled datasets ( c . 50,000 plots each), to be used as replicates in global analyses. Besides geographical location, date, plot size, biome, elevation, slope, aspect, vegetation type, naturalness, coverage of various vegetation layers, and source dataset, plot‐level data also include community‐weighted means and variances of 18 plant functional traits from the TRY Plant Trait Database. Spatial location and grain Global, 0.01–40,000 m². Time period and grain 1888–2015, recording dates. Major taxa and level of measurement 42,677 vascular plant taxa, plot‐level records. Software format Three main matrices (.csv), relationally linked.

Understanding drivers of success for alien species can inform on potential future invasions. Recent conceptual advances highlight that species may achieve invasiveness via performance along at least three distinct dimensions: 1) local abundance, 2) geographic range size, and 3) habitat breadth in naturalized distributions. Associations among these dimensions and the factors that determine success in each have yet to be assessed at large geographic scales. Here, we combine data from over one million vegetation plots covering the extent of Europe and its habitat diversity with databases on species' distributions, traits, and historical origins to provide a comprehensive assessment of invasiveness dimensions for the European alien seed plant flora. Invasiveness dimensions are linked in alien distributions, leading to a continuum from overall poor invaders to super invaders-abundant, widespread aliens that invade diverse habitats. This pattern echoes relationships among analogous dimensions measured for native European species. Success along invasiveness dimensions was associated with details of alien species' introduction histories: earlier introduction dates were positively associated with all three dimensions, and consistent with theory-based expectations, species originating from other continents, particularly acquisitive growth strategists, were among the most successful invaders in Europe. Despite general correlations among invasiveness dimensions, we identified habitats and traits associated with atypical patterns of success in only one or two dimensions-for example, the role of disturbed habitats in facilitating widespread specialists. We conclude that considering invasiveness within a multidimensional framework can provide insights into invasion processes while also informing general understanding of the dynamics of species distributions.

We describe a set of databases that bear information on geometrical and topological properties of 1 281 254 metal coordination centers and 204 828 ligands in 593 879 crystal structures of coordination compounds from the Cambridge Structural Database. These databases contain a number of structural descriptors, which are calculated according to rigorous algorithms and can be used to derive correlations of “chemical composition – structure – property” in an automated mode then forming a knowledge database. Many examples of such correlations and possible applications of the databases for investigation and design of coordination compounds are considered.

Abstract Based on more than 1100 samples of Emys orbicularis and E. trinacris, data on mtDNA diversity and distribution of haplotypes are provided, including for the first time data for Armenia, Georgia, Iran, and the Volga, Ural and Turgay River Basins of Russia and Kazakhstan. Eight mitochondrial lineages comprising 51 individual haplotypes occur in E. orbicularis, a ninth lineage with five haplotypes corresponds to E. trinacris. A high diversity of distinct mtDNA lineages and haplotypes occurs in the south, in the regions where putative glacial refuges were located. More northerly parts of Europe and adjacent Asia, which were recolonized by E. orbicularis in the Holocene, display distinctly less variation; most refuges did not contribute to northern recolonizations. Also in certain southern European lineages a decrease of haplotype diversity is observed with increasing latitude, suggestive of Holocene range expansions on a smaller scale.

Methods recently proposed for generating unipolar pulses in nonlinear media in terahertz and optical electromagnetic ranges are reviewed. Such pulses have nonzero “electric area” (time integral of the field strength over the entire duration of a pulse) and, correspondingly, a significant component of the field with zero frequency, thus exhibiting quasistatic properties. Effective generation of unipolar pulses would allow, e.g., transferring mechanical momentum to charged particles and, thereby, controlling the motion of wave packets of matter, which can be useful for compact accelerators of charged particles and for other applications.

Abstract Aim The first comprehensive checklist of European phytosociological alliances, orders and classes (EuroVegChecklist) was published by Mucina et al. (2016, Applied Vegetation Science , 19 (Suppl. 1), 3–264). However, this checklist did not contain detailed information on the distribution of individual vegetation types. Here we provide the first maps of all alliances in Europe. Location Europe, Greenland, Canary Islands, Madeira, Azores, Cyprus and the Caucasus countries. Methods We collected data on the occurrence of phytosociological alliances in European countries and regions from literature and vegetation‐plot databases. We interpreted and complemented these data using the expert knowledge of an international team of vegetation scientists and matched all the previously reported alliance names and concepts with those of the EuroVegChecklist. We then mapped the occurrence of the EuroVegChecklist alliances in 82 territorial units corresponding to countries, large islands, archipelagos and peninsulas. We subdivided the mainland parts of large or biogeographically heterogeneous countries based on the European biogeographical regions. Specialized alliances of coastal habitats were mapped only for the coastal section of each territorial unit. Results Distribution maps were prepared for 1,105 alliances of vascular‐plant dominated vegetation reported in the EuroVegChecklist. For each territorial unit, three levels of occurrence probability were plotted on the maps: (a) verified occurrence; (b) uncertain occurrence; and (c) absence. The maps of individual alliances were complemented by summary maps of the number of alliances and the alliance–area relationship. Distribution data are also provided in a spreadsheet. Conclusions The new map series represents the first attempt to characterize the distribution of all vegetation types at the alliance level across Europe. There are still many knowledge gaps, partly due to a lack of data for some regions and partly due to uncertainties in the definition of some alliances. The maps presented here provide a basis for future research aimed at filling these gaps.

Abstract Aims To create a comprehensive, consistent and unequivocal phytosociological classification of European marsh vegetation of the class Phragmito‐Magnocaricetea . Location Europe. Methods We applied the Cocktail method to a European data set of 249,800 vegetation plots. We identified the main purposes and attributes on which to base the classification, defined assignment rules for vegetation plots, and prepared formal definitions for all the associations, alliances and orders of the class Phragmito‐Magnocaricetea using formal logic. Each formula consists of the combination of “functional species groups”, cover values of individual species, and in the case of high‐rank syntaxa also of “discriminating species groups” created using the Group Improvement (GRIMP) method. Results The European Phragmito‐Magnocaricetea vegetation was classified into 92 associations grouped in 11 alliances and six orders. New syntaxa (previously invalidly published according to the International Code of Phytosociological Nomenclature) were introduced: Bolboschoeno maritimi‐Schoenoplection tabernaemontani, Glycerio maximae‐Sietum latifolii, Glycerio notatae‐Veronicetum beccabungae, Schoenoplectetum corymbosi and Thelypterido palustris‐Caricetum elongatae. Based on a critical revision, some other syntaxa were rejected or excluded from the class Phragmito‐Magnocaricetea . Conclusions This work provides the first consistent classification of the class Phragmito‐Magnocaricetea at the European scale, which is an important tool for nature conservation. Our classification largely respects previously existing concepts of syntaxa, but it also proposes modifications to the recently published EuroVegChecklist. This work also provides a protocol that can be used for extending the current classification to new syntaxa and geographical regions.

Abstract Aim A fundamental question in macroecology centres around understanding the relationship between species’ local abundance and their distribution in geographical and climatic space (i.e. the multi‐dimensional climatic space or climatic niche). Here, we tested three macroecological hypotheses that link local abundance to the following range properties: (a) the abundance–range size relationship, (b) the abundance–range centre relationship and (c) the abundance–suitability relationship. Location Europe. Taxon Vascular plants. Methods Distribution range maps were extracted from the Chorological Database Halle to derive information on the range and niche sizes of 517 European vascular plant species. To estimate local abundance, we assessed samples from 744,513 vegetation plots in the European Vegetation Archive, where local species’ abundance is available as plant cover per plot. We then calculated the ‘centrality’, that is, the distance between the location of the abundance observation and each species’ range centre in geographical and climatic space. The climatic suitability of plot locations was estimated using coarse‐grain species distribution models (SDMs). The relationships between centrality or climatic suitability with abundance was tested using linear models and quantile regression. We summarized the overall trend across species’ regression slopes from linear models and quantile regression using a meta‐analytical approach. Results We did not detect any positive relationships between a species’ mean local abundance and the size of its geographical range or climatic niche. Contrasting yet significant correlations were detected between abundance and centrality or climatic suitability among species. Main conclusions Our results do not provide unequivocal support for any of the relationships tested, demonstrating that determining properties of species’ distributions at large grains and extents might be of limited use for predicting local abundance, including current SDM approaches. We conclude that environmental factors influencing individual performance and local abundance are likely to differ from those factors driving plant species’ distribution at coarse resolution and broad geographical extents.

The European common lizard, Zootoca vivipara, is the most widespread terrestrial reptile in the world. It occupies almost the entire Northern Eurasia and includes four viviparous and two oviparous lineages. We analysed how female snout-vent length (SVL), clutch size (CS), hatchling mass (HM), and relative clutch mass (RCM) is associated with the reproductive mode and climate throughout the species range and across the evolutionary lineages within Z. vivipara. The studied variables were scored for 1,280 females and over 3,000 hatchlings from 44 geographically distinct study samples. Across the species range, SVL of reproductive females tends to decrease in less continental climates, whereas CS corrected for female SVL and RCM tend to decrease in climates with cool summer. Both relationships are likely to indicate direct phenotypic responses to climate. For viviparous lineages, the pattern of co-variation between female SVL, CS and HM among populations is similar to that between individual females within populations. Consistent with the hypothesis that female reproductive output is constrained by her body volume, the oviparous clade with shortest retention of eggs in utero showed highest HM, the oviparous clade with longer egg retention showed lower HM, and clades with the longest egg retention (viviparous forms) had lowest HM. Viviparous populations exhibited distinctly lower HM than the other European lacertids of similar female SVL, many of them also displaying unusually high RCM. This pattern is consistent with Winkler and Wallin’s model predicting a negative evolutionary link between the total reproductive investment and allocation to individual offspring.

Abstract The paper discusses creation of a digital twin (DT) of plant for an intelligent cyber-physical system for managing precision farming. A new approach to formalization of DT knowledge is proposed to form expert knowledge within the subject area based on the ontological specification of stages of plant growth and development and multi-agent technology for creating stage agents and coordinated dynamic recalculation of stage duration and yield forecast based on events in the environment. The paper proposes a method for calculating the forecast for duration of plant development stages and yield based on expert knowledge. A “tube” model of the range of changes in parameters of plant development for each stage has been developed. The paper also introduces a method for calculating the yield forecast, as well as the dates of beginning and end for each plant development stage within the “tube” during their normal development and in case of critical situations, for example, frost or drought. Ontology of plant development is constructed for implementation of the “tube” model of environmental parameters, which is converted into a digital form within the ontology editor, available for use by agents. The paper describes the structure and functions of a smart plant DT, built on the basis of a knowledge base and a module for multi-agent planning of plant development stages (for example, wheat), integrated with external weather forecast and fact services. A brief description of the created prototype of the intelligent plant DT system in Java is given. Using the system, agronomists can create their own knowledge bases and DTs of the cultivated plants for each field or even field section. The system will be useful in modern crop production for precision farming, not only “place-wise” but also “time-wise”, i.e. in terms of the best time for performing agrotechnical operations.

Новые находки -New records С этого номера мы начинаем публиковать в особой рубрике краткие заметки о новых находках мохообразных.Текст в рубрике предполагается кратким, названия статей -стандартные, указывающие на область, край, и т.д.Для каждой находки указываются координаты [если не отмечены в поле, то вычислены приблизительно по карте], коллектор(ы) в двух написаниях (кириллицей и латиницей), коллекторский номер или дата сбора, места хранения образца.Адреса авторов приводятся в конце рубрики

The fecundity-advantage hypothesis (FAH) explains larger female size relative to male size as a correlated response to fecundity selection. We explored FAH by investigating geographic variation in female reproductive output and its relation to sexual size dimorphism (SSD) in Lacerta agilis, an oviparous lizard occupying a major part of temperate Eurasia. We analysed how sex-specific body size and SSD are associated with two putative indicators of fecundity selection intensity (clutch size and the slope of the clutch size-female size relationship) and with two climatic variables throughout the species range and across two widespread evolutionary lineages. Variation within the lineages provides no support for FAH. In contrast, the divergence between the lineages is in line with FAH: the lineage with consistently female-biased SSD (L. a. agilis) exhibits higher clutch size and steeper fecundity slope than the lineage with an inconsistent and variable SSD (L. a. exigua). L. a. agilis shows lower offspring size (egg mass, hatchling mass) and higher clutch mass relative to female mass than L. a. exigua, that is both possible ways to enhance offspring number are exerted. As the SSD difference is due to male size (smaller males in L. a. agilis), fecundity selection favouring larger females, together with viability selection for smaller size in both sexes, would explain the female-biased SSD and reproductive characteristics of L. a. agilis. The pattern of intraspecific life-history divergence in L. agilis is strikingly similar to that between oviparous and viviparous populations of a related species Zootoca vivipara. Evolutionary implications of this parallelism are discussed.

The review of the salinity tolerance of various macrozoobenthos taxa is based on the published data and the results of our studies. Significant differences in the tolerance of hydrobionts to water salinity in rivers of different arid regions are shown. Leeches, bivalved mollusks, larvae of stoneflies, caddis flies, and mayflies are the most stenohaline species. The taxonomical structure of macrozoobenthos in saline rivers of Lake Elton basin in the arid zone of Russian South is presented.

Ecological theory predicts close relationships between macroclimate and functional traits. Yet, global climatic gradients correlate only weakly with the trait composition of local plant communities, suggesting that important factors have been ignored. Here, we investigate the consistency of climate-trait relationships for plant communities in European habitats. Assuming that local factors are better accounted for in more narrowly defined habitats, we assigned > 300,000 vegetation plots to hierarchically classified habitats and modelled the effects of climate on the community-weighted means of four key functional traits using generalized additive models. We found that the predictive power of climate increased from broadly to narrowly defined habitats for specific leaf area and root length, but not for plant height and seed mass. Although macroclimate generally predicted the distribution of all traits, its effects varied, with habitat-specificity increasing toward more narrowly defined habitats. We conclude that macroclimate is an important determinant of terrestrial plant communities, but future predictions of climatic effects must consider how habitats are defined.

Abstract Aim Plant functional traits summarize the main variability in plant form and function across taxa and biomes. We assess whether geographic range size, climatic niche size, and local abundance of plants can be predicted by sets of traits (trait syndromes) or are driven by single traits. Location Eurasia. Methods Species distribution maps were extracted from the Chorological Database Halle to derive information on the geographic range size and climatic niche size for 456 herbaceous, dwarf shrub and shrub species. We estimated local species abundances based on 740,113 vegetation plots from the European Vegetation Archive, where abundances were available as plant species cover per plot. We compiled a complete species‐by‐trait matrix of 20 plant functional traits from trait databases (TRY, BiolFlor and CLO‐PLA). The relationships of species’ geographic range size, climatic niche size and local abundance with single traits and trait syndromes were tested with multiple linear regression models. Results Generally, traits were more strongly related to local abundances than to broad‐scale species distribution patterns in geographic and climatic space (range and niche size), but both were better predicted by trait combinations than by single traits. Local abundance increased with leaf area and specific leaf area (SLA). Geographic range size and climatic niche size both increased with SLA. While range size increased with plant height, niche size decreased with leaf carbon content. Conclusion Functional traits matter for species’ abundance and distribution at both local and broad geographic scale. Local abundances are associated with different combinations of traits as compared to broad‐scale distributions, pointing to filtering by different environmental and ecological factors acting at distinct spatial scales. However, traits related to the leaf economics spectrum were important for species’ abundance and occurrence at both spatial scales. This finding emphasizes the general importance of resource acquisition strategies for the abundance and distribution of herbaceous, dwarf shrub and shrub species.

The paper is devoted to development of a digital twin (DT) of plant. It is built as a smart system based on the knowledge base on macrostages of plant development and multiagent technology that allows for detailed monitoring and control of plant development, recalculation of forecast, namely, assessment of vegetation quality, future yield and timing for onset of next stages. It uses transition rules between stages upon receipt of data from agronomists on the state of plant development, as well as the actual and forecast weather data. The paper proposes a conceptual plant model based on ontologies and multi-agent technology, which is a network of linked states and transition rules that correspond to macrostages of plant development with the possibility of recalculating their parameters. The paper also covers the main principles of agronomist work with the digital twin of plant.