PADAPT 1.0 - the Pannonian Dataset of Plant Traits.

The existing plant trait databases' applicability is limited for studies dealing with the flora and vegetation of the eastern and central part of Europe and for large-scale comparisons across regions, mostly because their geographical data coverage is limited and they incorporate records from several different sources, often from regions with markedly different climatic conditions. These problems motivated the compilation of a regional dataset for the flora of the Pannonian region (Eastern Central Europe). PADAPT, the Pannonian Dataset of Plant Traits relies on regional data sources and collates data on 54 traits and attributes of the plant species of the Pannonian region. The current version covers approximately 90% of the species of the region and consists of 126,337 records on 2745 taxa. By including species of the eastern part of Europe not covered by other databases, PADAPT can facilitate studying the flora and vegetation of the eastern part of the continent. Although data coverage is far from complete, PADAPT meets the longstanding need for a regional database of the Pannonian flora.

Five times over: 42 new Angustopila species highlight Southeast Asia's rich biodiversity (Gastropoda, Stylommatophora, Hypselostomatidae).

The Southeast Asian genus Angustopila, currently comprising 13 nominal species, encompasses the world's tiniest land snails. This work shows that there are far more species than previously suspected, and that this genus is in fact, a very speciose group of tiny snails widely distributed in Southeast Asia. Angustopila is revised based on type material of known species as well as 211 samples newly collected in China, Laos, Myanmar, Thailand and Vietnam. Altogether, 53 species and one subspecies are recognised, of which 42 species and subspecies are new to science: A.akrodon Páll-Gergely & Hunyadi, sp. nov., A.apiaria Páll-Gergely & Hunyadi, sp. nov., A.apiostoma Páll-Gergely & Vermeulen, sp. nov., A.apokritodon Páll-Gergely & Hunyadi, sp. nov., A.antidomedon Páll-Gergely & Hunyadi, sp. nov., A.babel Páll-Gergely & Vermeulen, sp. nov., A.bathyodon Páll-Gergely & Hunyadi, sp. nov., A.bidentata Páll-Gergely & Jochum, sp. nov., A.cavicola Páll-Gergely & Dumrongrojwattana, sp. nov., A.cicatricosa Páll-Gergely & Vermeulen, sp. nov., A.coprologosuninodus Páll-Gergely & Grego, ssp. nov., A.erawanica Páll-Gergely & Dumrongrojwattana, sp. nov., A.fratermajor Páll-Gergely & Vermeulen, sp. nov., A.fraterminor Páll-Gergely & Vermeulen, sp. nov., A.gracilis Páll-Gergely & Hunyadi, sp. nov., A.halongensis Páll-Gergely & Vermeulen, sp. nov., A.hyron Páll-Gergely & Vermeulen, sp. nov., A.maasseni Páll-Gergely & Vermeulen, sp. nov., A.majuscula Páll-Gergely & Hunyadi, sp. nov., A.margaritarion Páll-Gergely & Hunyadi, sp. nov., A.megastoma Páll-Gergely & Vermeulen, sp. nov., A.occidentalis Páll-Gergely & Hunyadi, sp. nov., A.oostoma Páll-Gergely & Vermeulen, sp. nov., A.papaver Páll-Gergely & Hunyadi, sp. nov., A.parallela Páll-Gergely & Hunyadi, sp. nov., A.prolixa Páll-Gergely & Hunyadi, sp. nov., A.pusilla Páll-Gergely & Hunyadi, sp. nov., A.pustulata Páll-Gergely & Hunyadi, sp. nov., A.quadridens Páll-Gergely & Vermeulen, sp. nov., A.rara Páll-Gergely & Hunyadi, sp. nov., A.reticulata Páll-Gergely & Hunyadi, sp. nov., A.somsaki Páll-Gergely & Hunyadi, sp. nov., A.steffeki Páll-Gergely & Grego, sp. nov., A.tetradon Páll-Gergely & Hunyadi, sp. nov., A.thersites Páll-Gergely & Vermeulen, sp. nov., A.tonkinospiroides Páll-Gergely & Vermeulen, sp. nov., A.tridentata Páll-Gergely & Hunyadi, sp. nov., A.tweediei Páll-Gergely & Hunyadi, sp. nov., A.uvula Páll-Gergely & Hunyadi, sp. nov., A.vandevenderi Páll-Gergely & Jochum, sp. nov., A.vitrina Páll-Gergely & Hunyadi, sp. nov., A.vomer Páll-Gergely & Hunyadi, sp. nov., A.werneri Páll-Gergely & Hunyadi, sp. nov. Angustopilasubelevata Páll-Gergely & Hunyadi, 2015 is moved to the synonymy of Angustopilaelevata (F. G. Thompson & Upatham, 1997), and A.singuladentis Inkhavilay & Panha, 2016 is a junior synonym of A.fabella Páll-Gergely & Hunyadi, 2015. Three species, namely A.elevata, A.fabella and A.szekeresi, are widespread over several hundred kilometres while some other species (A.huoyani, A.parallelasp. nov., A.cavicolasp. nov.) are known from just two sites a few hundred kilometres apart. All others are small range or single-site endemics. The reproductive anatomy of A.erawanicasp. nov. is described.

Quartile coefficient of variation is more robust than CV for traits calculated as a ratio.

Comparing within-species variations of traits can be used in testing ecological theories. In these comparisons, it is useful to remove the effect of the difference in mean trait values, therefore measures of relative variation, most often the coefficient of variation (CV), are used. The studied traits are often calculated as the ratio of the size or mass of two organs: e.g. specific leaf area (SLA) is the ratio of leaf size and leaf mass. Often the inverse of these ratios is also meaningful; for example, the inverse of SLA is often referred to as LMA (leaf mass per area). Relative variation of a trait and its inverse should not considerably differ. However, it is illustrated that using the coefficient of variation may result in differences that could influence the interpretation, especially if there are outlier trait values. The alternative way for estimating CV from the standard deviation of log-transformed data assuming log-normal distribution and Kirkwood's geometric coefficient of variation free from this problem, but they proved to be sensitive to outlier values. Quartile coefficient of variation performed best in the tests: it gives the same value for a trait and its inverse and it is not sensitive to outliers.

Devil in the details: how can we avoid potential pitfalls of CATS regression when our data do not follow a Poisson distribution?

BACKGROUND: Community assembly by trait selection (CATS) allows for the detection of environmental filtering and estimation of the relative role of local and regional (meta-community-level) effects on community composition from trait and abundance data without using environmental data. It has been shown that Poisson regression of abundances against trait data results in the same parameter estimates. Abundance data do not necessarily follow a Poisson distribution, and in these cases, other generalized linear models should be fitted to obtain unbiased parameter estimates. AIMS: This paper discusses how the original algorithm for calculating the relative role of local and regional effects has to be modified if Poisson model is not appropriate. RESULTS: It can be shown that the use of the logarithm of regional relative abundances as an offset is appropriate only if a log-link function is applied. Otherwise, the link function should be applied to the product of local total abundance and regional relative abundances. Since this product may be outside the domain of the link function, the use of log-link is recommended, even if it is not the canonical link. An algorithm is also suggested for calculating the offset when data are zero-inflated. The relative role of local and regional effects is measured by Kullback-Leibler R2. The formula for this measure presented by Shipley (2014) is valid only if the abundances follow a Poisson distribution. Otherwise, slightly different formulas have to be applied. Beyond theoretical considerations, the proposed refinements are illustrated by numerical examples. CATS regression could be a useful tool for community ecologists, but it has to be slightly modified when abundance data do not follow a Poisson distribution. This paper gives detailed instructions on the necessary refinement.

Dimensions of invasiveness: Links between local abundance, geographic range size, and habitat breadth in Europe's alien and native floras.

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.

Trait convergence and trait divergence in lake phytoplankton reflect community assembly rules.

Environmental filtering and limiting similarity are those locally acting processes that influence community structure. These mechanisms acting on the traits of species result in trait convergence or divergence within the communities. The role of these processes might change along environmental gradients, and it has been conceptualised in the stress-dominance hypothesis, which predicts that the relative importance of environmental filtering increases and competition decreases with increasing environmental stress. Analysing trait convergence and divergence in lake phytoplankton assemblages, we studied how the concepts of 'limiting similarity' versus 'environmental filtering' can be applied to these microscopic aquatic communities, and how they support or contradict the stress-dominance hypothesis. Using a null model approach, we investigated the divergence and convergence of phytoplankton traits along environmental gradients represented by canonical axes of an RDA. We used Rao's quadratic entropy as a measure of functional diversity and calculated effect size (ES) values for each sample. Negative ES values refer to trait convergence, i.e., to the higher probability of the environmental filtering in community assembly, while positive values indicate trait divergence, stressing the importance of limiting similarity (niche partitioning), that is, the competition between the phytoplankters. Our results revealed that limiting similarity and environmental filtering may operate simultaneously in phytoplankton communities, but these assembly mechanisms influenced the distribution of phytoplankton traits differently, and the effects show considerable changes along with the studied scales. Studying the changes of ES values along with the various scales, our results partly supported the stress-dominance hypothesis, which predicts that the relative importance of environmental filtering increases and competition decreases with increasing environmental stress.

Silhouette width using generalized mean-A flexible method for assessing clustering efficiency.

Cluster analysis plays vital role in pattern recognition in several fields of science. Silhouette width is a widely used index for assessing the fit of individual objects in the classification, as well as the quality of clusters and the entire classification. Silhouette combines two clustering criteria, compactness and separation, which imply that spherical cluster shapes are preferred over others-a property that can be seen as a disadvantage in the presence of complex, nonspherical clusters, which is common in real situations. We suggest a generalization of the silhouette width using the generalized mean. By changing the p parameter of the generalized mean between -∞ and +∞, several specific summary statistics, including the minimum, maximum, the arithmetic, harmonic, and geometric means, can be reproduced. Implementing the generalized mean in the calculation of silhouette width allows for changing the sensitivity of the index to compactness versus connectedness. With higher sensitivity to connectedness, the preference of silhouette width toward spherical clusters should reduce. We test the performance of the generalized silhouette width on artificial data sets and on the Iris data set. We examine how classifications with different numbers of clusters prepared by different algorithms are evaluated, if p is set to different values. When p was negative, well-separated clusters achieved high silhouette widths despite their elongated or circular shapes. Positive values of p increased the importance of compactness; hence, the preference toward spherical clusters became even more detectable. With low p, single linkage clustering was deemed the most efficient clustering method, while with higher parameter values the performance of group average, complete linkage, and beta flexible with beta = -0.25 seemed better. The generalized silhouette allows for adjusting the contribution of compactness and connectedness criteria, thus avoiding underestimation of clustering efficiency in the presence of clusters with high internal heterogeneity.

Trait-based community assembly of epiphytic diatoms in saline astatic ponds: a test of the stress-dominance hypothesis.

The stress dominance hypothesis (SDH) postulates that strong environmental gradients drive trait convergence in communities over limiting similarity. Previous studies, conducted mostly with terrestrial plant communities, found controversial evidence for this prediction. We provide here the first test for SDH for epiphytic diatoms. We studied community assembly in diatom communities of astatic ponds. These water bodies serve as a good model system for testing SDH because they exhibit stress gradients of various environmental factors. Functional diversity of diatom communities was assessed based on four traits: (1) combined trait reflecting the trade-off between stress tolerance and competitive dominance, (2) cell size, (3) oxygen requirement and (4) N-uptake strategy. According to our results, salinity, pH and the width of the macrophyte belt appeared as significant predictors of the trait convergence/divergence patterns presumably acting through influencing the availability of carbon dioxide and turbidity. Lower trait diversity was found in turbid, more saline and more alkaline ponds and functional diversity was higher in transparent, less saline and less alkaline ponds. Overall, our results supported the stress dominance hypothesis. In habitats representing increased environmental stress, environmental filtering was the most important community assembly rule, while limiting similarity became dominant under more favourable conditions.

Aerobic anoxygenic phototrophs are highly abundant in hypertrophic and polyhumic waters.

Aerobic anoxygenic phototrophs (AAPs) are a group of photoheterotrophic bacteria common in natural waters. Here, AAP abundance and contribution to total bacterial abundance and biomass were investigated to test whether the trophic status of a lake or content of coloured dissolved organic matter (CDOM) play a role in determining AAP distribution and abundance in shallow inland lakes, with special focus on hypertrophic and polyhumic waters. Twenty-six different shallow lakes in Hungary were monitored. AAP abundance and biomass were determined by epifluorescence microscopy. The lakes exhibit a broad range of CDOM (2-7000 mg Pt L-1) and phytoplankton biomass (2-1200 µg L-1 chlorophyll a concentration). Very high AAP abundance (up to 3 × 107 cells mL-1) was observed in polyhumic and hypertrophic shallow lakes. AAP abundance was influenced by phytoplankton biomass and CDOM content, and these effects were interrelated. As determined, 40 µg L-1 chlorophyll a and 52 mg Pt L-1 CDOM are threshold levels above which these effects have a synergistic relationship. Hence, the observed high AAP abundance in some soda pans is a consequence of combined hypertrophy and high CDOM content. AAP contribution was influenced by total suspended solids (TSS) content: the success of AAP cells could be explained by high TSS levels, which might be explained by the decrease of their selective grazing control.

Global trait-environment relationships of plant communities.

Plant functional traits directly affect ecosystem functions. At the species level, trait combinations depend on trade-offs representing different ecological strategies, but at the community level trait combinations are expected to be decoupled from these trade-offs because different strategies can facilitate co-existence within communities. A key question is to what extent community-level trait composition is globally filtered and how well it is related to global versus local environmental drivers. Here, we perform a global, plot-level analysis of trait-environment relationships, using a database with more than 1.1 million vegetation plots and 26,632 plant species with trait information. Although we found a strong filtering of 17 functional traits, similar climate and soil conditions support communities differing greatly in mean trait values. The two main community trait axes that capture half of the global trait variation (plant stature and resource acquisitiveness) reflect the trade-offs at the species level but are weakly associated with climate and soil conditions at the global scale. Similarly, within-plot trait variation does not vary systematically with macro-environment. Our results indicate that, at fine spatial grain, macro-environmental drivers are much less important for functional trait composition than has been assumed from floristic analyses restricted to co-occurrence in large grid cells. Instead, trait combinations seem to be predominantly filtered by local-scale factors such as disturbance, fine-scale soil conditions, niche partitioning and biotic interactions.

The effect of abandonment on vegetation composition and soil properties in Molinion meadows (SW Poland).

Intermittently wet meadows of the Molinion alliance, as with many other grasslands of high-nature value, have become increasingly exposed to abandonment due to their low economic value. The potential consequences of land abandonment are the decrease in species diversity and environmental alterations. The issue of land-use induced changes in plant species composition and soil physico-chemical parameters have been rarely studied in species-rich intermittently wet grasslands. In this study we attempt to i) to identify determinants of plant species composition patterns and ii) to investigate the effect of cessation of mowing on vegetation composition and soil properties. The study was conducted in an area of 36 ha covered with Molinion meadows, comprising of mown sites and sites that were left unmown for 10 years. In total, 120 and 80 vegetation plots were sampled from mown and unmown sites, respectively. In these plots we measured plant community composition and soil physico-chemical parameters. The results have shown that the two groups of variables (soil properties and management) differ considerably in their ability to explain variation in plant species data. Soil variables explained four-fold more variation in plant species composition than management did. The content of soil organic matter, moisture, total nitrogen and exchangeable forms of potassium, calcium and magnesium were significantly higher in mown than in unmown grassland systems. The results revealed that soil organic matter was the component of the soil most strongly affected by management, followed by moisture, magnesium, calcium and potassium in that order. Each of these soil parameters was negatively correlated with the abundances of woody plants and invasive species. We concluded that low-intensity, late time of mowing is suitable grassland management practice to ensure high plant species diversity and sustainability of the grassland ecological system while cessation of mowing not only lead to reduced plant species richness and diversity, but also to reduced nutrient levels in grassland soils.

Unusual behaviour of phototrophic picoplankton in turbid waters.

Autotrophic picoplankton (APP) abundance and contribution to phytoplankton biomass was studied in Hungarian shallow lakes to test the effect of inorganic turbidity determining the size distribution of the phytoplankton. The studied lakes displayed wide turbidity (TSS: 4-2250 mg l-1) and phytoplankton biomass (chlorophyll a: 1-460 µg l-1) range, as well as APP abundance (0 and 100 million cells ml-1) and contribution (0-100%) to total phytoplankton biomass. Inorganic turbidity had a significant effect on the abundance and contribution of APP, resulting in higher values compared to other freshwater lakes with the same phytoplankton biomass. Our analysis has provided empirical evidence for a switching point (50 mg l-1 inorganic turbidity), above which turbidity is the key factor causing APP predominance regardless of phytoplankton biomass in shallow turbid lakes. Our results have shown that turbid shallow lakes are unique waters, where the formerly and widely accepted model (decreasing APP contribution with increasing phytoplankton biomass) is not applicable. We hypothesize that this unusual behaviour of APP in turbid waters is a result of either diminished underwater light intensity or a reduced grazing pressure due to high inorganic turbidity.

A higher-level classification of the Pannonian and western Pontic steppe grasslands (Central and Eastern Europe).

QUESTIONS: What are the main floristic patterns in the Pannonian and western Pontic steppe grasslands? What are the diagnostic species of the major subdivisions of the class Festuco-Brometea (temperate Euro-Siberian dry and semi-dry grasslands)? LOCATION: Carpathian Basin (E Austria, SE Czech Republic, Slovakia, Hungary, Romania, Slovenia, N Croatia and N Serbia), Ukraine, S Poland and the Bryansk region of W Russia. METHODS: We applied a geographically stratified resampling to a large set of relevés containing at least one indicator species of steppe grasslands. The resulting data set of 17 993 relevés was classified using the TWINSPAN algorithm. We identified groups of clusters that corresponded to the class Festuco-Brometea. After excluding relevés not belonging to our target class, we applied a consensus of three fidelity measures, also taking into account external knowledge, to establish the diagnostic species of the orders of the class. The original TWINSPAN divisions were revised on the basis of these diagnostic species. RESULTS: The TWINSPAN classification revealed soil moisture as the most important environmental factor. Eight out of 16 TWINSPAN groups corresponded to Festuco-Brometea. A total of 80, 32 and 58 species were accepted as diagnostic for the orders Brometalia erecti, Festucetalia valesiacae and Stipo-Festucetalia pallentis, respectively. In the further subdivision of the orders, soil conditions, geographic distribution and altitude could be identified as factors driving the major floristic patterns. CONCLUSIONS: We propose the following classification of the Festuco-Brometea in our study area: (1) Brometalia erecti (semi-dry grasslands) with Scabioso ochroleucae-Poion angustifoliae (steppe meadows of the forest zone of E Europe) and Cirsio-Brachypodion pinnati (meadow steppes on deep soils in the forest-steppe zone of E Central and E Europe); (2) Festucetalia valesiacae (grass steppes) with Festucion valesiacae (grass steppes on less developed soils in the forest-steppe zone of E Central and E Europe) and Stipion lessingianae (grass steppes in the steppe zone); (3) Stipo-Festucetalia pallentis (rocky steppes) with Asplenio septentrionalis-Festucion pallentis (rocky steppes on siliceous and intermediate soils), Bromo-Festucion pallentis (thermophilous rocky steppes on calcareous soils), Diantho-Seslerion (dealpine Sesleria caerulea grasslands of the Western Carpathians) and Seslerion rigidae (dealpine Sesleria rigida grasslands of the Romanian Carpathians).

Prevalence dependence in model goodness measures with special emphasis on true skill statistics.

It has long been a concern that performance measures of species distribution models react to attributes of the modeled entity arising from the input data structure rather than to model performance. Thus, the study of Allouche et al. (Journal of Applied Ecology, 43, 1223, 2006) identifying the true skill statistics (TSS) as being independent of prevalence had a great impact. However, empirical experience questioned the validity of the statement. We searched for technical reasons behind these observations. We explored possible sources of prevalence dependence in TSS including sampling constraints and species characteristics, which influence the calculation of TSS. We also examined whether the widespread solution of using the maximum of TSS for comparison among species introduces a prevalence effect. We found that the design of Allouche et al. (Journal of Applied Ecology, 43, 1223, 2006) was flawed, but TSS is indeed independent of prevalence if model predictions are binary and under the strict set of assumptions methodological studies usually apply. However, if we take realistic sources of prevalence dependence, effects appear even in binary calculations. Furthermore, in the widespread approach of using maximum TSS for continuous predictions, the use of the maximum alone induces prevalence dependence for small, but realistic samples. Thus, prevalence differences need to be taken into account when model comparisons are carried out based on discrimination capacity. The sources we identified can serve as a checklist to safely control comparisons, so that true discrimination capacity is compared as opposed to artefacts arising from data structure, species characteristics, or the calculation of the comparison measure (here TSS).

Conceptual frameworks and methods for advancing invasion ecology.

Invasion ecology has much advanced since its early beginnings. Nevertheless, explanation, prediction, and management of biological invasions remain difficult. We argue that progress in invasion research can be accelerated by, first, pointing out difficulties this field is currently facing and, second, looking for measures to overcome them. We see basic and applied research in invasion ecology confronted with difficulties arising from (A) societal issues, e.g., disparate perceptions of invasive species; (B) the peculiarity of the invasion process, e.g., its complexity and context dependency; and (C) the scientific methodology, e.g., imprecise hypotheses. To overcome these difficulties, we propose three key measures: (1) a checklist for definitions to encourage explicit definitions; (2) implementation of a hierarchy of hypotheses (HoH), where general hypotheses branch into specific and precisely testable hypotheses; and (3) platforms for improved communication. These measures may significantly increase conceptual clarity and enhance communication, thus advancing invasion ecology.

Alien species in a warmer world: risks and opportunities.

Climate change and biological invasions are key processes affecting global biodiversity, yet their effects have usually been considered separately. Here, we emphasise that global warming has enabled alien species to expand into regions in which they previously could not survive and reproduce. Based on a review of climate-mediated biological invasions of plants, invertebrates, fishes and birds, we discuss the ways in which climate change influences biological invasions. We emphasise the role of alien species in a more dynamic context of shifting species' ranges and changing communities. Under these circumstances, management practices regarding the occurrence of 'new' species could range from complete eradication to tolerance and even consideration of the 'new' species as an enrichment of local biodiversity and key elements to maintain ecosystem services.