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Abstract Changes in climate and land use are the most often mentioned factors responsible for the current decline in species diversity. To reduce the effect of these factors, we need reliable predictions of future species distributions. This is usually done by utilizing species distribution models (SDMs) based on expected climate. Here we explore the accuracy of such projections: we use orchid (Orchidaceae) recordings and environmental (mainly climatic) data from the years 1901–1950 in SDMs to predict maps of potential species distributions in 1980–2014. This should enable us to compare the predictions of species distributions in 1980–2014, based on records of species distribution in the years 1901–1950, with real data in the 1980–2014 period. We found that the predictions of the SDMs often differ from reality in this experiment. The results clearly indicate that SDM predictions of future species distributions as a reaction to climate change must be treated with caution.

Questions concerning species diversity have attracted ecologists and biogeographers for over a century, mainly because the diversity of life on Earth is in rapid decline, which is expected to continue in the future. One of the most important current database on species distribution data is the Global Biodiversity Information Facility (GBIF), which contains more than 2 billion occurrences for all organisms, and this number is continuously increasing with the addition of new data and by combining with other applications. Such data also exist in several national databases, most of which are unfortunately often not freely available and not included in GBIF. We suspected that the national databases, mostly professionally maintained by governmental organisations, may be more comprehensive than GBIF, which is not centrally organised and therefore the national databases may give more accurate predictions than GBIF. To test our assumptions, we have compared: (i) the amount of data included in the Czech database called Nálezová databáze ochrany přírody (NDOP, Discovery database of nature protection) with the amount of data in GBIF after its restriction to the Czech Republic, and (ii) the overlap of the predictions of species distributions for the Czech Republic, based on these two databases. We have used the family Orchidaceae as a model group. We found that: (i) there is a significantly larger number of records per studied region (Czech Republic) in NDOP, compared with GBIF, and (ii) the predictions of Maxent based on orchid records in NDOP are overlapping to a great degree with the predictions based on data based on orchid records in GBIF. Bearing in mind these results, we suggest that if only one database is available for the region studied, we must use this one. If more databases are available for the region studied, we should use the database containing most locations (usually some of the local ones, like NDOP), because using more locations implies larger significance of predictions of species distributions.

When examining the probability of extinction of a given orchid species, the species must be viewed as a metapopulation composed of many individual populations connected by migration. In biology, much attention has been paid to the dynamics of metapopulations, especially in the situation where metapopulation dynamics are affected by active migration of individuals between populations. However, this is not the case with orchids. Their seeds are passively spread by wind, and therefore are unable to actively choose the point where they land (passive migrants, unlike, e.g., butterflies, which can actively look for a suitable site that hosts, hosted or can potentially host a population of their species (active migrants). Thus, while active migrants can often find a suitable destination for their migration, passive migrants often die after landing at an unsuitable site. One would therefore expect that, other things being equal, the proportion of suitable sites inhabited by active migrants is larger than that inhabited by passive migrants. In passive migrants (orchids) we may therefore meet metapopulation dynamics of a different, yet unexplored type, in which some existing localities die out and new localities appear, in the vast majority where no orchids have ever grown before. This type of dynamics has not yet been studied anywhere and this paper is intended to be the first step in this direction. The main goal here is therefore empirical determination of actual distributions of population sizes in different metapopulations. We do it in four regions of the Czech Republic and for four species of orchids, considering the factors that influence it.

Orchids can be classified in terms of their pollination into rewarding species, which produce nectar in their flowers that serves as a reward for pollinators and deceptive species, whose flowers do not contain nectar and save energy for other purposes. This paper concentrates on the latter. Deceptive orchids attempt to deceive their pollinators by being similar to some non-orchid rewarding species, but not providing a reward. Each of these strategies has its advantages and disadvantages in terms of their effect on future fitness of a plant and/or population and subsequently its survival as a species. In summary, the literature indicates that deceptive strategies may lower reproductive success, but may be compensated for in that they cost less in terms of energy. This should be taken into consideration when developing management strategies for these species, which is often done by non-orchid specialists. This article is intended for such non-specialist audience and includes a description of the main types of deceptive strategies used by orchids, as well as examples of the most typical species.

Clinical imaging modalities are a mainstay of modern disease management, but the full utilization of imaging-based data remains elusive. Aortic disease is defined by anatomic scalars quantifying aortic size, even though aortic disease progression initiates complex shape changes. We present an imaging-based geometric descriptor, inspired by fundamental ideas from topology and soft-matter physics that captures dynamic shape evolution. The aorta is reduced to a two-dimensional mathematical surface in space whose geometry is fully characterized by the local principal curvatures. Disease causes deviation from the smooth bent cylindrical shape of normal aortas, leading to a family of highly heterogeneous surfaces of varying shapes and sizes. To deconvolute changes in shape from size, the shape is characterized using integrated Gaussian curvature or total curvature. The fluctuation in total curvature (δK) across aortic surfaces captures heterogeneous morphologic evolution by characterizing local shape changes. We discover that aortic morphology evolves with a power-law defined behavior with rapidly increasing δK forming the hallmark of aortic disease. Divergent δK is seen for highly diseased aortas indicative of impending topologic catastrophe or aortic rupture. We also show that aortic size (surface area or enclosed aortic volume) scales as a generalized cylinder for all shapes. Classification accuracy for predicting aortic disease state (normal, diseased with successful surgery, and diseased with failed surgical outcomes) is 92.8±1.7%. The analysis of δK can be applied on any three-dimensional geometric structure and thus may be extended to other clinical problems of characterizing disease through captured anatomic changes.

Epiphytic species are ecologically important and a significant component of biodiversity. To ensure their efficient conservation, we need to understand their ecology and host plant associations. It is also important to investigate how the predicted temperature change will affect their future distribution. Here, we use data collected in Nepal to investigate how epiphytic orchids are associated with host species, their distribution patterns, and how they may be threatened by the predicted increase in temperature towards the end of the 21st century. We used the phi coefficient (Φ) of association to calculate the associations of epiphytic orchid species with plants and rarefaction to describe the diversity of orchids associated with a particular host species. We used interpolation to estimate the distribution of epiphytic orchids and their host species along altitudinal gradients. The phi (Φ) coefficient of association revealed that 30 species of host plants showed more association with different orchid species than expected. The number of epiphytic orchids increased with the number of host individuals. We predict that an increase in temperature by ~3 °C, which is a more moderate value of temperature increase by the end of the 21st century, will affect at least 52 narrow-ranged species of orchids and 58 narrow-ranged species of host plants. Therefore, we should make efforts to prevent many plant species from becoming extinct, as an increase in temperature is likely to affect their existence.

Abstract Soil invertebrates (i.e., soil fauna) are important drivers of many key processes in soils including soil aggregate formation, water retention, and soil organic matter transformation. Many soil fauna groups directly or indirectly participate in litter consumption. However, the quantity of litter consumed by major faunal groups across biomes remains unknown. To estimate this quantity, we reviewed > 1000 observations from 70 studies that determined the biomass of soil fauna across various biomes and 200 observations from 44 studies on litter consumption by soil fauna. To compare litter consumption with annual litterfall, we analyzed 692 observations from 24 litterfall studies and 183 observations from 28 litter stock studies. The biomass of faunal groups was highest in temperate grasslands and then decreased in the following order: boreal forest > temperate forest > tropical grassland > tundra > tropical forest > Mediterranean ecosystems > desert and semidesert. Tropical grasslands, desert biomes, and Mediterranean ecosystems were dominated by termites. Temperate grasslands were dominated by omnivores, while temperate forests were dominated by earthworms. On average, estimated litter consumption (relative to total litter input) ranged from a low of 14.9% in deserts to a high of 100.4% in temperate grassland. Litter consumption by soil fauna was greater in grasslands than in forests. This is the first study to estimate the effect of different soil fauna groups on litter consumption and related processes at global scale.

The Chinese pangolin (Manis pentadactyla) has experienced a rapid population decline throughout its distribution. In Nepal, it mostly occurs outside protected areas; therefore, habitat degradation due to anthropogenic activities is one of the major threats to its survival. However, the scarcity of information on the ecology and distribution of pangolins impedes evidence-based conservation of this species in Nepal. Its habitat preferences and distribution and the factors influencing people’s attitude to its conservation were studied in Gorkha District in central Nepal. Thirteen transects, each 0.5 km in length, were used for recording burrows indicating the presence of pangolin. In total, 124 burrows were recorded, of which 38 were new and 86 were old, which indicated a clumped distribution. Based on the highest percentage frequency of occurrence, most burrows occurred between 650 and 800 m a.s.l., in areas with a south-facing aspect, with moderate canopy cover, in forest, red soil and gentle terrain. The logistic regression model revealed that habitat type, soil type, crown cover, terrain, and distance to water were the most important factors affecting pangolin presence. In total, 87 households and 9 key informants were interviewed using questionnaires to determine the people’s knowledge of pangolins and attitude to their conservation. More than 50% of the respondents had seen pangolin in the areas studied and had a general knowledge of their habitat and benefits. However, most of them were unaware that it was illegal to hunt pangolins and were involved in opportunistic hunting for meat consumption. Pangolins were mostly recorded in forest at altitudes 650–800 m a.s.l., with moderate canopy cover, red soil, and close to a source of water; habitat, soil, canopy cover, terrain, and distance to water were statistically significantly associated with the presence of pangolin burrows. This study revealed that an increase in public awareness (mainly through education) would help to increase the likelihood of pangolin survival. These results can also serve as guidelines for protecting pangolin habitats for use by local authorities.

Sobralia Ruiz & Pav. is a large and morphologically diverse neotropical orchid genus. It can be divided into four sections and some informal groups of species based mainly on the inflorescence architecture. While most of the species have strongly abbreviated, compact raceme, the section Racemosae is characterized by an elongated inflorescence with distinct internodes between flowers. Although the group is well-defined and easily distinguishable in terms of morphology, its species are often similar to each other and may be easily misidentified. Identification is especially difficult when considering herbarium specimens. Here, a taxonomic revision of Sobralia section Racemosae is presented. Apart from particular species’ morphological characteristics, keys for identification, ecological data, and distribution maps are presented. Sobralia gambitana is described as a species new to science. A neotype for S. hoppii Schltr. is proposed.

Population dynamics of a predator-prey system is usually simulated by the classical Lotka-Volterra models, which were successfully applied to the population dynamics of snowshoe hare and lynx and many other predator-prey systems. Attempts were made to apply them also to insect predator-prey systems, but in terms of biological control, they did not reveal the features of the predators that control the abundance of their prey. The most conspicuous example of failure of Lotka-Volterra models applied to insect predator-prey systems are ladybird-aphid systems, in which these models usually fail to fit empirical data. Because of their practical importance and because they are very well studied, we have chosen aphid-ladybird systems as a model. We summarize the results published on various aspects of the population dynamics of aphid-ladybird systems and present them in the context of empirical data. Using new data, we more closely specify the existing metapopulation model of aphid-ladybird interactions. Based on the arguments presented here, we conclude that the ladybird-aphid case can be generalized to insect (and maybe even other) predator-prey systems, where the ratio of the generation times of the predator to that of the prey (GTR) is large. In such systems, the main selection pressure on predators is choosing the best strategy to maximize survival of their offspring, rather than on maximization of the amount of prey eaten. Thus voracity, which is the main determinant of population dynamics in Lotka-Volterra models, loses its role and is replaced by optimization of the choice of oviposition sites in systems with large GTRs.

The presence of Orchids is declining worldwide, mostly due to habitat loss and other factors like climate change, which are likely to increase in severity in the coming decades [...]

The natural environment has been significantly altered by human activity over the past few decades. There is evidence we are now experiencing the sixth mass extinction, as many species of plants and animals are declining in abundance. We focused on the Orchidaceae because this plant family has experienced one of the biggest reductions in distribution. We investigated patterns in species richness and distribution of orchids, the rate and causes of their decrease and extinction, and factors influencing their occurrence in the Czech Republic and Greece. The key findings are: (i) Method of pollination and type of rooting system are associated with their distributions and they are different in the two countries. We assume that these differences might be due to the difference in the orography, distribution of suitable habitats and types of bedrock in these two countries. (ii) The greatest reduction in distribution was recorded for critically endangered taxa of orchids. The number of sites suitable for orchids in the Czech Republic declined by 8–92%. The most threatened orchid species are Spiranthes spiralis, Anacamptis palustris, Epipogium aphyllum and Goodyera repens. The distribution of orchids in the Czech Republic is mainly determined by the distribution of their habitats. (iii) The most important factor affecting the distribution of Czech orchids in South Bohemia is land cover. And the most important types of habitats (types in KVES) are oak and oak-hornbeam forests and agricultural meadows. Based on this information, it should be possible to improve the management that is crucial for maintaining orchid localities.

Recently, there has been a significant increase in number of land cover maps available to researchers and they are now more commonly used. The broad variety requires some system for determining the differences between maps and for estimating their applicability for specific research purposes. We focused on comparing land cover maps from the point of view of how the land cover categories used characterize potentially suitable habitats for species. This comparison includes only freely available global land cover projects with resolutions from 1 km to 10 m. The criteria chosen were temporal and spatial resolution, number of classes and map precision. To demonstrate the differences, two areas of different sizes were always chosen. Our results reveal that maps can significantly vary in their estimates of different types of land cover, even at the same spatial resolution. Results also revealed that one type of vegetation in this area is poorly recorded in all land cover maps. Copernicus CGLS-LC100 and ESA CCI-LC maps appear to be the most suitable for evaluating potentially suitable habitats.

Understanding patterns of species diversity along an altitudinal gradient is the major topic of much biogeographical and ecological research. The aim of this study was to explore how richness and density of orchid species and subspecies in terms of different categories of underground organ systems and pollination systems vary along an altitudinal gradient in the central Balkans. The altitudinal gradient of the study area was divided into 21 100-m vertical intervals. Data were analyzed using both non-linear and linear regressions with three data sets (total orchids, orchids of forest habitats, orchids of non-forest habitats) in the case of species richness and three data sets (total orchids—total area, forest orchids—forest area, and orchids of non-forest habitats—non-forest area) in the case of species density. The results showed a hump-shaped pattern of orchid richness and density, peaking at 900–1,000 m. The richness and density of orchids of forest habitats are generally slightly greater than the richness and density of orchids of non-forest habitats in lowland areas, whereas the orchids of herbaceous vegetation types dominating at high altitudes. Tuberous orchids dominate in low and mid-altitude areas, orchids with palmately lobed and fusiform tubers (“intermediate orchids”) dominate at high altitudes, while rhizomatous orchids are predominate in mid-altitude forest stands. Both deceptive and self-pollinated orchids show a unimodal trend with a peak at mid-altitude areas. This study underlines the importance of low and mid-altitude areas for the survival of deceptive orchids and the importance of mid- and high-altitude areas for the survival of rewarding orchids. In addition, forest habitats at mid-altitudes have been shown to be crucial for the survival of self-pollinated orchids. The results suggest that the altitudinal patterns of orchid richness and density in the central Balkans are determined by mechanisms related to land area size and habitat cover, partially confirming the species-area relationship (SAR) hypothesis. This study contributes significantly to a better understanding of the potential impacts of habitat changes on orchid diversity, thereby facilitating more effective conservation planning.

Barking deer is found in dense tropical and subtropical forests of Asia. It is listed as “least concerned” by the International Union of Conservation of Nature and as “vulnerable” in Nepal, where it is also protected. Due to the habitat loss and fragmentation by human activities, barking deer abundance is decreasing, which may even ultimately lead to its extinction. This in turn might negatively affect local ecosystem such as the abundance of the endangered common leopard, for which barking deer is the main prey species in the mid-hills of Nepal. We therefore need to know factors affecting barking deer abundance and its habitat preferences. To determine these factors, we recorded barking deer either by direct sighting or by any evidence of its indirect presence observed through transect surveys in January and February, 2019. To analyze habitat preference, the presence of barking deer was set to 1 if the barking deer or any sign of its presence were observed “used plots,” or to 0 if the barking deer or any sign of its presence were not observed (“habitat availability plot”). We measured main four ecological drivers such as forest management regime, microclimate, disturbance and food resources, which include 11 habitat characteristics in spots where barking deer was present, and in randomly selected spots. We found that elevation, slope, distance from settlement, presence of tree species, depth of leaf litter and percentage cover of leaf litter were most significantly affecting its presence. These results can serve as guidelines for local authorities to prevent decline in abundance of barking deer.

Alpine plants are perceived as some of the most vulnerable to extinction due to the global climate change. We expected that their life history strategies depend, among others, on the latitude they live in: those growing in temperate regions are likely to have a distinct phenology with short seasonal peaks, while tropical alpine plants can potentially exploit favorable year-round growing conditions and different individuals within a population may flower at different times of the year. In species, whose flowering is synchronized into short seasonal peaks, extraordinary climate events, which may become stronger and more frequent with climate change, can potentially destroy reproductive organs of all synchronized individuals. This may result in reducing fitness or even extinction of such species. We studied field populations of five groups of closely related Andean alpine plant species to test our expectations on their latitude-dependent synchronization of flowering. Our results confirmed these expectations: (i) Tropical alpine species were least synchronized and flowering peaks of different individuals in their populations were distributed across many months. Thus, in tropical alpine species, if an extraordinary event happens, only some individuals are affected and other members of the population successfully reproduce in other parts of the long season. (ii) Higher synchronicity in flowering of temperate and subtropical alpine plants resulted even in some of these species using only a part of the short growing season to reproduce, which increases their vulnerability to extraordinary climatic events. However, we did not find any unique pattern valid for all species, groups and regions. The diversity in flowering phenology (i.e., different levels of seasonality and synchronicity) that we found increases the likelihood of plants successfully coping with climate change.

Inappropriate forest management activities, above all clear-cutting, are recognized as the major threats to an iconic orchid species—the lady’s slipper orchid (Cypripedium calceolus), the flagship species of nature protection in Europe. Although clear-cutting in protected species’ localities is strongly regulated in many European countries, salvage logging is allowed in some circumstances (e.g., following windstorms, and insect outbreaks) and can threaten C. calceolus populations. In this paper, we review a database of recently registered populations of this species in the Czech Republic and study historical maps, to better understand the history of local habitat conditions and assess threats to C. calceolus populations by bark beetle outbreaks. We found that about one-third of the C. calceolus populations have suffered in coniferous or mixed tree plantations with a high proportion of spruce trees, which are forests with a high risk of bark beetle infestation. We review bark beetle management measures and distinguish management efforts in areas with known C. calceolus populations that result in no damage to the population and, at times, improve habitat conditions for the species. Thus, the bark beetle—usually understood as the enemy—can be transformed into a savior if smart management measures will replace the panic salvage logging.

In this study, we focus on factors affecting the socio-economic development within a protected zone and attempt to elucidate if being in a protected area significantly affects the development or whether other factors also have a role. We focused on population counts recorded in 1991 and 2011 in order to identify the changes in the economy following to the establishment of the Šumava National Park in 1991 and Český les Protected Landscape Area (PLA) in 2005. A total of 39 municipalities of similar size and history were included and 18 socio-economic indicators, which can be broadly categorized in terms of economy, landscape use and municipality income. We performed ANCOVA to determine the association between the size and location (outside or inside protected area) of a municipality and each of the18 socio-economic indicators. They did not vary significantly in 1991. After two decades the demography, economy and landscape usage were significantly different. However, they were not a result of being in a protected area but changes in the sizes of the municipalities. The municipalities located within protected areas may profit from their locality and it has positive rather than negative effects on the socioeconomic indicators.

The provoking title briefly represents the opinion of a number of politicians and lobbyists. The majority of biologists, however, do not agree with this statement and present several arguments for why such a change will not occur. We attempt to elucidate the current and future situation in the Šumava NP based on available data. We also compare the situation in the Šumava NP with that in the whole of the Czech Republic, where the situation is similar or even worse. The devastated spruce forests are regenerating from young seedlings, biodiversity is increasing and the national park is not threatened by drought any more than the surrounding landscape. Here we dismiss the alarming messages about a desert in the Šumava NP, as the opposite is true, with the drought level there lower than in the rest of the Czech Republic.

Studies on population dynamics are helpful for understanding the factors determining population development and predicting the effects of disturbances, such as harvesting of plant species. In an investigation of the demography of a terrestrial medicinal orchid known as Crepidium acuminatum, the effects of harvesting on its population dynamics were recorded. Data on recruitment, growth and survival were collected in three populations of C. acuminatum over a 6-year period (2012–2017) in central Nepal. A matrix modeling method was used to determine the effect of different harvesting regimes on the population growth and survival of this species. Population growth rates (λ) of unharvested populations were relatively similar and stable in different years of the study. Harvesting significantly reduced λ. The results of this study indicate that the sustainable survival of a population that is subject to harvesting can only occur when it is either selective (only flowering individuals or only small amounts of vegetative individuals) or rotational (once every 3–5 or more years). This study demonstrates the necessity of using a sustainable method when harvesting natural populations. Our results are useful for developing efficient management strategies for this species. As each species has a different biology, similar studies are needed for other rare and/or economically important species in the Himalayan region and in other understudied parts of the world.

Factors determining the spatial distribution of bird species along altitudinal gradients have been important in their ecological and biogeographical research. Here, have used the data on bird species recorded in Manang, central Nepal Himalayas and attempt to determine the drivers of bird species diversity. We also carried out indicator species analysis to observe if any bird species are associated with different altitudinal ranges and land use gradients. We recorded 1331 individuals belonging to 82 species of both resident and itinerant birds. In our study, altitude was the major factor determining species richness and abundance. Position of study localities is main factor determining bird community composition. Diversity of bird species were mainly found in habitats that were far human settlements, having high annual mean temperature and more roughness. Species diversity was high during July-August compared to September-October and in north-facing slopes, and also in shrub and tree covered areas than grassland and places with mostly snow and grassland. Indicator species analysis showed only 21 species were significantly associated with altitudinal gradients, mostly below 3000 m a.s.l. and only eight bird species were associated with two land use gradients (grassland and snow-glacier). In conclusion, position of sampled localities, altitude, aspect, land use types and different climatic factors were important determinants of bird diversity along altitudinal gradients in Manang. To protect bird diversity in Manang, we need to protect habitats that are located mainly in low altitudes for most of the bird species. However, high altitude habitats with snow and glaciers are also important for few bird species. Thus, a large area with heterogenous habitats is important for bird species management and conservation.

Diffusion tensor magnetic resonance imaging (DT-MRI) is a technique used to quantify the microstructural organization of biological tissues. Multiple images are necessary to reconstruct the tensor data and each acquisition is subject to complex thermal noise. As such, measures of tensor invariants, which characterize components of tensor shape, derived from the tensor data will be biased from their true values. Previous work has examined this bias, but over a narrow range of tensor shape. Herein, we define the mathematics for constructing a tensor from tensor invariants, which permits an intuitive and principled means for building tensors with a complete range of tensor shape and salient microstructural properties. Thereafter, we use this development to evaluate by simulation the effects of noise on characterizing tensor shape over the complete space of tensor shape for three encoding schemes with different SNR and gradient directions. We also define a new framework for determining the distribution of the true values of tensor invariants given their measures, which provides guidance about the confidence the observer should have in the measures. Finally, we present the statistics of tensor invariant estimates over the complete space of tensor shape to demonstrate how the noise sensitivity of tensor invariants varies across the space of tensor shape as well as how the imaging protocol impacts measures of tensor invariants.

By monitoring of 50 aphid colonies in 2017 and another 50 colonies in 2018 twice a week, we looked at how the aphid dynamics wasaffected by their natural enemies. This will help us to see, how much the presence of natural enemies shortens the duration of an aphidcolony, which may be one of the causes, why Harmonia axyridis is not very successful in the Mediterranean: the aphid colony may exist for aperiod of time too short in the Mediterranean conditions to enable successful development of H. axyridis.

The IPCC IS92a scenario predicts climate changes including within-year fluctuations in precipitation and a temperature increase of 1.7 °C by the year 2050 and a further 2.7 °C by the year 2100. We attempted to detect these changes in the Šumava Mts. and compare them with climate changes in the surrounding foothills. We used meteorological data records for the years 1961-2017, provided by the Czech Hydrometeorological Institute (CHMI). We recorded a decrease in precipitation, including snow cover, in the mountains and in the foothills during the last 15-20 years. Air temperature has also increased significantly in spring and summer over the last two decades. We assume that the increase in spring temperature negatively affects snow cover and causes it to melt earlier. We found that all these changes affect both the Šumava National Park and the surrounding foothills at the same rate; as a result, natural disturbances such as windstorm and bark beetle infestations occur more often and are more severe in both areas. Thus, changes in temperature and precipitation must be also considered in future management planning.

One of the key goals of conservation biology is to determine what causes declines in biodiversity and suggest ways of stopping or slowing them down. Studies on the temporal changes in the distributions of species provide critical information on temporal trends in local extinctions and information on what causes these changes. This is especially true for endangered groups of plants, such as orchids. Here we analysed changes in the distributions of orchids in the Czech Republic over three time periods when the agricultural practices differed. Orchids were divided into two groups based on whether they provide nectar to their pollinators. Moreover, we determined the effect of three different spatial resolutions on the interpretation of the results. Many species in the Czech orchid flora have become rarer over time and four became extinct. These changes are directly associated with changes in the agricultural practices in the Czech Republic that started in the 1950s, which especially resulted in the abandonment of traditional management. Mosaics of small fields were converted into huge fields and the application of artificial fertilizers increased dramatically, both of which resulted in loss of natural habitats and decline in many species of orchids - both nectariferous and nectarless species. Our results are important for conservation and are aimed at preventing further decline in orchid sites and recovery of orchid populations.

The structure of fiber tracts in DT-MRI data presents a challenging problem for visualization and analysis. We derive visualization of such traces from a local coherence measure and achieve much improved visual segmentation. We introduce a coherence measure defined for fiber tracts. This quantitative assessment is based on infinitesimal deviations of neighboring tracts and allows identification and segmentation of coherent fiber regions. We use a hardware-accelerated implementation to achieve interactive visualization on slices and provide several approaches to visualize coherence information. Furthermore, we enhance existing techniques by combining them with coherence. We demonstrate our method on both a canine heart, where the myocardial structure is visualized, and a human brain, where we achieve detailed visualization of major and minor fiber bundles in a quality similar to and exceeding fiber clustering approaches. Our approach allows detailed and fast visualization of important anatomical structures in DT-MRI data sets.

Species distribution models are a useful tool and are now often used in many branches of biology, especially when dealing with threatened organisms. In combination with GIS techniques, these models are especially important and valuable for predicting the occurrence of rare species, for example orchids. Orchids are an endangered plant group, protected worldwide. Questions about their conservation are therefore highly discussed, but not all factors affecting their survival and distribution are known. Here we present an example of using SDMs for analysing orchid species occurrence data from the Jeseniky Mountains in the Czech Republic. Our data were analysed using the MaxEnt program, which produces species distribution maps and thus allows the prediction of the potential occurrence of orchids at yet unknown localities. This program also determines the environmental factors affecting species distribution. This is important for the better protection of orchids, because only by knowing these factors can new localities be found or the management plans that are crucial for maintaining orchid localities be improved. We studied the most abundant orchid species in the given region. We determined the most important factors affecting their occurrence and also areas, where new sites are most likely to be discovered and depicted them in potential distribution maps. This approach can help in finding new localities of orchids and in understanding, which environmental factors influence the occurrence of endangered orchids.

Epiphytic orchids are common in subtropical forests, but little is known about the factors that determine their diversity. We surveyed two sites (north-facing Phulchowki and south-facing Shivapuri hills), in the sub-tropical forest in the Kathmandu valley, central Nepal. Along five transects per site, spanning an altitudinal gradient of 1525–2606 m a.s.l., we recorded all epiphytic orchids and the host species on which they were growing. The data were analyzed using a generalized linear model (GLM) and redundancy analysis (RDA). Species richness significantly decreased with increasing altitude and was higher in larger hosts and in places with high temperature. Species composition was affected by altitude, distance from the forest edge, host type, and precipitation. This study indicates that the most important factors affecting epiphytic orchid diversity was altitude, even if other factors were associated with patterns in composition. The low-altitude habitats with high species diversity are the best places for epiphytic orchids in this region. The altitudinal species richness and patterns in composition revealed by this study provide a baseline for further studies on epiphytic orchids.

Bohemian gentian (Gentianella praecox subsp. bohemica) is an endemic taxon that occurs on the Czech Massif and together with the Sturmian gentian (Gentianella obtusifolia subsp. sturmiana) are the only autumnal species of Gentianella with large flowers in central Europe. Both species have declined dramatically in both population size and numbers of populations. The Bohemian gentian rescue programme, which recommended appropriate management measures, was adopted in 2011. Here we study the ecology of this species, results of the rescue programme and explore the possibilities of using the experience resulting from this programme for improving the viability of the second species. Long-term monitoring of populations of the Bohemian gentian has shown that regular mowing or grazing together with careful litter removal and gap creation are necessary for its survival in the current climatic conditions. We found some ecological differences between these two closely related species of Gentianella. However, our empirical experience of the largest population of the Sturmian gentian at a site where it thrives, and general evidence that gaps are crucial for the successful establishment of Gentianella seedlings, indicate that regular mowing or grazing together with careful litter removal and creation of gaps, should also be recommended as in the case of the Bohemian gentian rescue programme. Artificial gaps are especially crucial for successful seedling regeneration in oligotrophic meadows with dense vegetation, where the last Sturmian gentian populations survive.

Understanding diversity patterns along altitudinal gradients and the effect of global change on abundance, distribution patterns and species survival are of the most discussed topics in biodiversity research. Here, we determined the associations of orchid species richness and the degree of their specialization to specific environmental conditions (expressed by species specialization index) with altitude in six floristic areas in the Czech Republic. We distinguished three basic trends in these relationships: linear, parabolic and cubic. We then determined whether these trends differ between three orchid groups classified by their rooting systems: rhizomatous, intermediate and tuberous. We used distributional data on 69 species and subspecies of terrestrial orchids recorded in the Czech Republic and interpolated them at 100-m intervals along an altitudinal gradient in each floristic area. The trends in both species richness and mean species specialization index differed between the six floristic areas within each of the three orchid groups studied. These patterns are probably strongly influenced by the orography of the country and the distribution of different habitats in the six floristic areas in the Czech Republic. We also found that the most widely distributed orchid group in the Czech Republic are the rhizomatous orchids, followed by intermediate and tuberous ones.

Dactylorhiza hatagirea is a terrestrial orchid listed in Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) and classified as threatened by International Union for Conservation of Nature (IUCN). It is endemic to the Hindu-Kush Himalayan region, distributed from Pakistan to China. The main threat to its existence is climate change and the associated change in the distribution of its suitable habitats to higher altitudes due to increasing temperature. It is therefore necessary to determine the habitats that are suitable for its survival and their expected distribution after the predicted changes in climate. To do this, we use Maxent modelling of the data for its 208 locations. We predict its distribution in 2050 and 2070 using four climate change models and two greenhouse gas concentration trajectories. This revealed severe losses of suitable habitat in Nepal, in which, under the worst scenario, there will be a 71–81% reduction the number of suitable locations for D. hatagirea by 2050 and 95–98% by 2070. Under the most favorable scenario, this reduction will be 65–85% by 2070. The intermediate greenhouse gas concentration trajectory surprisingly would result in a greater reduction by 2070 than the worst-case scenario. Our results provide important guidelines that local authorities interested in conserving this species could use to select areas that need to be protected now and in the future.

Understanding temporal changes in the distribution and abundance of various species is one of the key goals of conservation biology. During recent decades, the abundance and distribution of many species of plants and animals have declined dramatically, mainly because of habitat loss and fragmentation. The purpose of this study is to analyze the rate of extinction of orchids at various sites in different 20-year time intervals over the last 150 years, determined according to changes in society. Using the dataset of the orchid records of the Nature Conservation Agency of the Czech Republic, we determined the disappearance rate of orchids from sites using a grid of 1 × 1 km. We found that the vast majority of orchids disappeared from many of their historical localities in all time intervals analyzed. The number of sites suitable for Czech orchids declined by 8–92%, depending on the species. The most threatened orchid species in the Czech Republic are Spiranthes spiralis, Anacamptis palustris, Epipogium aphyllum and Goodyera repens. This all seems to be closely related with changes in agricultural practices in the open as well as in forest habitats. Preserving suitable orchid habitats seems to be the key for keeping Czech orchid flora alive.

Decline in wet grasslands, which in the past resulted particularly from the intensification of agriculture, was accompanied by the loss of a lot of populations of organisms, including protected and endangered species of plants and animals associated with these habitats e.g. terrestrial orchids. The survival of populations of many species of European orchids is strongly dependent on appropriate site management, especially regular mowing or grazing. In addition, humans can negatively affect the persistence of orchid populations in various ways, such as conversion of orchid meadows into building areas, dams, roads etc. or the intensive use of fertilizers and contamination of areas by fertilisers from nearby fields. Comparison of historical data with the present distribution of orchids can reveal a lot about the main reasons for the decline in this endangered group of plants. Here we present an extensive study of the persistence of 192 historical orchid sites in South Bohemia, with particular reference to the 5 commonest species of orchids, Anacamptis morio, Dactylorhiza majalis, Epipactis helleborine, Epipactis palustris and Platanthera bifolia. We show that the most abundant species at the sites studied was Dactylorhiza majalis. E. palustris, A. morio and P. bifolia are currently not present at any of the historical localities for these species. Considering more recent history, the situation regarding orchid localities in South Bohemia is not critical, but the fate of these species should be closely monitored. The majority of this loss is due to the cessation of mowing of the sites. Thus more attention should be paid to the management of the existing sites. During this study, some new sites were discovered.