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Constrained multivariate analysis is a common tool for linking ecological communities to environment. The follow-up is the development of the double-constrained correspondence analysis (dc-CA), integrating traits as species-related predictors. Further, methods have been proposed to integrate information on phylogenetic relationships and space variability. We expand this framework, proposing a dc-CA-based algorithm for decomposing variation in community structure and testing the simple and conditional effects of four sets of predictors: environment characteristics and space configuration as predictors related to sites, while traits and niche (dis)similarities as species-related predictors. In our approach, ecological niches differ from traits in that the latter are distinguished by and characterize the individual level, while niches are measured on the species level, and when compared, they are characteristics of communities and should be used as separate predictors. The novelties of this approach are the introduction of new niche parameters, niche dissimilarities, synthetic niche-based diversity which we related to environmental features, the development of an algorithm for the full variation decomposition and testing of the community–environment–niche–traits–space (CENTS) space by dc-CAs with and without covariates, and new types of diagrams for the results. Applying these methods to a dataset on freshwater mollusks, we learned that niche predictors may be as important as traits in explaining community structure and are not redundant, overweighting the environmental and spatial predictors. Our algorithm opens new pathways for developing integrative methods linking life, environment, and other predictors, both in theoretical and practical applications, including assessment of human impact on habitats and ecological systems. Supplementary Information The online version contains supplementary material available at 10.1007/s00442-021-05006-6.

Danube Delta shallow lakes experience cyanobacteria blooms that can negatively affect the aquatic ecosystem. Although there are several studies on Danube Delta cyanobacteria, little is known about their spatial–temporal patterns and the potential predictive role they can offer. We therefore analyzed the distribution of cyanobacteria in 19 lakes belonging to three lake complexes and tested whether their seasonal dynamics are in line with the predictions of the PEG model. Furthermore, we investigated to which extent cyanobacteria diversity and abundance were related to lake hydrogeomorphological characteristics such as surface, water level, connectivity, water retention, flood risk, and transparency. Although lakes had different seasonal cyanobacterial assemblages, the biovolume and genus richness had a geographical pattern, decreasing from south-east (lakes forming the fluvial delta) towards north-west (lakes forming the maritime delta). Cyanobacteria biovolume reflected largely the PEG model peaking in summer (the fluvial delta) and autumn (the maritime delta). Genus richness followed the same pattern. Cyanobacteria distribution was predicted by various abiotic (e.g., risk of flooding, connectivity) and biotic factors (e.g., submersed macrophytes, phytoplankton diversity, peat deposits). Our study contributes to the understanding of cyanobacteria diversity and distribution in shallow interconnected lakes by revealing the complexity of predictors for geographical and seasonal patterns.

Patterns of body size variation along geographical gradients have long been searched for and generalized into eco-geographical rules. However, no rodent species has yet been analyzed in relation to the 3 dimensions of latitude, longitude and altitude. We analyzed geographical clines and dimorphism of body and skull size in the herb field mouse (Apodemus uralensis) across the species range, based on field data and on data from the literature. Sexual dimorphism in adult A. uralensis was not expressed at a large scale, while local patterns were inconsistent. Age-dependent size changes were most expressed in adult individuals: most characters of adults exceeded in size those of subadults, while subadult-juvenile size differences were only significant in body weight and length, zygomatic skull width, length of cranial diastema and breadth of braincase. Despite central morphological niches along the clines being separated, A. uralensis populations showed a high degree of size overlap in morphological space. We found the species to be characterized by high size variability, with the largest individuals inhabiting the eastern and southern edges of the distribution range. Tail, hind foot and ear lengths were largest in the southern part of the range, in agreement with Allen's rule. The main measurements that we analyzed, namely body mass, zygomatic skull width and condylobasal skull length, show the presence of 3 clines in the size of adult A. uralensis: (i) a decreasing south-north cline, opposing Bergmann's rule; (ii) an increasing west-east cline, in accordance with Murphy's rule; and (iii) an increasing altitudinal cline.

Elevation is one of the most important natural gradients that is strongly shaping communities across relatively small areas. However, few studies have followed the temporal dynamics of elevational patterns, even in organisms for which population and community fluctuations have been extensively studied, such as rodents. Here we report the multiannual dynamics of small-mammal communities along an elevational gradient in the Southern Carpathians. During a 5-year survey, we conducted live-trapping in forested and shrubby habitats, at elevations between 820 and 2040 m. We used partial constrained multivariate analysis and mixed-effects models to test the effect of elevation, year, and their interaction. Community metrics differed significantly between even and odd years and temporal changes had stronger effect on small-mammal communities than elevation. The 2-year pattern of dynamics was especially marked in the yellow-necked field mouse (Apodemus flavicollis (Melchior, 1834)). Species abundance was predicted not only by year and elevation, but also by their interaction. The dominant rodent species, the bank vole (Myodes glareolus (Schreber, 1780)) and A. flavicollis, showed opposite annual patterns in relation to elevation, possibly as a strategy to avoid competition. Failure to consider the fluctuations in montane small-mammal communities may lead to wrong assessment of species’ state and distribution.

Intensification of agriculture is an increasing threat for biodiversity. Central Romania still preserves a traditional rural landscape with a matrix of small plots of crops and large surfaces covered by grasslands and forests, but its biodiversity is very poorly studied. Small mammals are key components of agrarian and semi-natural ecosystems but rodents are also viewed as major pests. Knowledge of the driving factors of small mammal communities in agricultural landscapes may enable taking management measures that pursue both conservation and economic goals. Here we evaluate the response of small mammals to environmental variables, including vegetation characteristics, land use and geographic position. We conducted live trapping between June and October in habitats with different environmental characteristics and land uses. We found that vegetation traits were the most important factors influencing small mammal communities. Species composition was shaped mainly by tree cover, shrub cover had strong effects on community diversity and abundance, while the height of the herbaceous layer significantly influenced all the parameters. Among the agrarian land uses maize crops stood out for the abundance of mice, especially Mus musculus, and hayfields for Microtus arvalis. Land fallowing was linked to the increase of diversity and total abundance to the maximum values but did not significantly alter species composition. Species with low tolerance to tree cover were more prone to be abundant in agricultural lands, whereas the habitat generalists prevailed in non-agrarian lands. Our results suggest that preservation of the mosaic of farmed and semi-natural habitats and actions targeted for vegetation management, such as interspersing woody vegetation in the crop matrix and mowing the herbaceous vegetation in semi-natural habitats adjacent to crops, may together achieve the balance between biodiversity conservation and crop protection.

Freshwaters are among the most imperilled habitats worldwide and Unionidae species are recognised as one of the most important and endangered parts of the communities they shelter. Understanding the changes in the structure of Unionidae communities and their responses to environmental variables are issues insufficiently studied and understood. We evaluated 35 naiad communities along geographical and ecological gradients in Romania, and measured 10 environmental factors at each sampling location. Using constrained ordination analysis, we learned that the most significant variables explaining the variance in species composition were flow, human impact and elevation. Among the levels of the habitat factorial variable the most explicative were the lower Danube habitats, which shelter the richest naiad assemblages. Unionids diversity decreases significantly with increases in elevation and human impact. By comparing some communities with those of two decades ago, a contrasting image emerges. In some rivers where the former heavy pollution has been greatly reduced, the naiads are recovering. However, the average diversity of the communities that we compared is statistically lower at present than two decades ago, indicating that in some areas the ecological state of the freshwater systems is slightly worsening. Main causes are pollution, hydrotechnical constructions, invasive species and climatic changes.

The survey of small mammal communities in the Lower Black River Basin was carried out between November 2005 and July 2012 in three locations. Using live traps several habitats have been investigated. During the study, we captured 199 individuals belonging to 9 species – 2 shrews and 7 rodents. Four other species were identified based on direct or indirect observations.

Small mammals are key components of forest ecosystems, playing vital roles for numerous groups of forest organisms: they exert bottom-up and top-down regulatory effects on vertebrate and invertebrate populations, respectively, they are fungus- and seed-dispersers and bioturbators. Therefore, preserving or restoring the diversity of small mammal communities may help maintain the functions of these ecosystems. In Romania, a country with low-intensity forest management and a high percentage of natural forests compared to other European countries, an overview of forest small mammal diversity and habitat type use is lacking, and our study aimed to fill this gap. We also aimed to partition the total small mammal diversity of Romanian forests into the alpha (plot-level), beta, and delta (among forest types) diversities, as well as further partition beta diversity into its spatial (among plots) and temporal (among years) components. We surveyed small mammals by live trapping in eight types of forest across Romania. We found that small mammal abundance was significantly higher in lowland than in mountain forests, but species richness was similar, being associated with the diversity of tree canopy, with the highest values in mixed forests. In contrast, small mammal heterogeneity was related to overall habitat heterogeneity. As predicted, community composition was most distinct in poplar plantations, where forest specialists coexist with open habitat species. Most of the diversity was represented by alpha diversity. Because of strong fluctuations in population density of dominant rodents, the temporal component of beta heterogeneity was larger than the spatial component, but species richness also presented an important temporal turnover. Our results show the importance of the time dimension in the design of the surveys aiming at estimating the diversity of small mammal communities, both at the local and regional scales.

[Questions] Species pools are the product of complex ecological and evolutionary mechanisms, operating over a range of spatial scales. Here, we focus on species absent from local sites but with the potential to establish within communities — known as dark diversity. Methods for estimating dark diversity are still being developed and need to be compared, as well as tested for the type, and amount, of reference data needed to calibrate these methods. [Location] South Bohemia (48°58′ N, 14°28′ E) and Železné Hory (49°52′ N, 15°34′ E), Czech Republic. [Method] We compared a widely accepted algorithm to estimate species pools (Beals smoothing index, based on species co-occurrence) against a novel method based on an unconstrained ordination (UNO). Following previous work, we used spatially nested sampling for target plots, with the dark diversity estimates computed from smaller plots validated against additional species present in larger plots, and a reference dataset (Czech National Phytosociological Database of >30,000 plots as global reference data). We determined which method provides the best estimate of dark diversity with an index termed the “Success Rate Index”. [Results] When using the whole reference dataset (national scale), both UNO and Beals provided comparable predictions of dark diversity that were better than null expectations based on species frequency. However, when predicting from regionally restricted spatial scales, UNO performed significantly better than Beals. UNO also tended to detect less common species better than Beals. The success rate of combining UNO and Beals slightly outperformed the results obtained from the single methods, but only with the largest reference dataset. [Conclusions] The UNO method provides a consistently reliable estimate of dark diversity, particularly when the reference dataset is size-limited. For future calculations, we urge caution regarding the choice of dark diversity methods with respect to the reference data available, and how different methods handle species of high, and low, occurrence frequency., Grant Agency of the Czech Republic grant (GA16‐15012S; to Francesco de Bello and Lars Götzenberger). Long‐term research development grant from the Czech Academy of Sciences (RVO 67985939; FdB and LG). Czech Science Foundation ‐ Centre of Excellence PLADIAS (14‐36079G; Petr Šmilauer and Jan Lepš).

The results of a one year study of bird communities from the Lotrioara River Basin (Lotru Mountains, Romania), using the transect method along the main valley, are presented. The study aimed to reveal the characteristics of the community’s dynamics, both from spatial and temporal point of view. During the research period 70 species belonging to 9 orders were identified in the investigated area. The number of species decreases with the altitude, but it is also related to the heterogeneity of habitats. During the year the species’ number varies from a minimum in winter to a maximum in spring. Insectivores are the prevailing feeding guild in the bird communities from Lotrioara basin, but during the cold season the dominance is taken over by omnivorous and granivorous species.

Small mammal communities were studied by live trapping during August-September 2010 and June-September 2011 in three localities from Hârtibaciu Plateau, in southern Transylvania. The area is situated between 420 and 550 m a.s.l., and represents a mosaic of small patches of different land use. 200 traps were set in lines for three consecutive nights, in 80 different habitats representing 12 habitat types, both cultivated and semi-natural. 1235 small mammals belonging to 15 species (four soricomorphs and 11 rodents) were captured. Abundance of small mammals was expressed by means of capture index (number of individuals caught per 100 active trap-nights). The community structure was strongly shaped by habitat type, even in case of small land patches. Microtus arvalis prevailed in the investigated area, being the dominant species in open fields with high grassy vegetation. The density of this species increased strongly from the beginning of summer to autumn, when the traps were occasionally saturated with field voles.