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Question: How does restoration management affect vegetation diversity and composition in flooded meadows, and can plant species serve as indicators of management status? Location: Flooded meadows in Alam-Pedja Nature Reserve, central Estonia (26 ° 14' E, 58 ° 28' N). Methods: Plant community composition was described in 2000 and 2010 for restored and unmanaged stands of mesic, wet and tall sedge meadows, encompassing a survey of 280 vegetation plots of 1 m x I m. The impact of restoration management (mulching for first 5 yrs, mowing in Jul with hay removal in consecutive years) on vegetation diversity in different meadow types was estimated using general linear models, changes in plant community composition were described by NMDS ordination, multiple permutation tests and Indicator species analysis. Results: Restoration management resulted in an increase in species richness on mesic meadows in one of the study sites, and caused a decrease in spatial species turnover and significant changes in community composition in all sites. The effects of restoration on species composition were greater in drier, more elevated mesic meadows, and least prominent in tall sedge meadows in floodplain depressions. Indicator species analysis revealed Ranunculus auricomus as a common indicator of management in mesic and wet meadows, and Carex cespitosa and Calamagrostis canescens as indicators of abandonment in wet and tall sedge meadows, respectively. Conclusions: Restoration management was successful on flooded meadows that had been abandoned for 15-20 yrs, where water regime and soil fertility have not been altered by human activities, and where the local species pool is still available. The current community composition under different management regimes made it possible to propose several species as management status indicators, which may further be used in practical decision-making when evaluating the status of meadow communities.

Aim: Beta diversity can be partitioned into two components: dissimilarity due to species replacement and dissimilarity due to nestedness (Baselga, 2010, Global Ecology and Biogeography, 19, 134—143). Several contributions have challenged this approach or proposed alternative frameworks. Here, I review the concepts and methods used in these recent contributions, with the aim of clarifying: (1) the rationale behind the partitioning of beta diversity into species replacement and nestedness-resultant dissimilarity, (2) how, based on this rationale, numerators and denominators of indices have to match, and (3) how nestedness and nestedness-resultant dissimilarity are related but different concepts. Innovation: The rationale behind measures of species replacement (turnover) dictates that the number of species that are replaced between sites (numerator of the index) has to be relativized with respect to the total number of species that could potentially be replaced (denominator). However, a recently proposed partition of Jaccard dissimilarity fails to do this. In consequence, this partition underestimates the contribution of species replacement and overestimates the contribution of richness differences to total dissimilarity. I show how Jaccard dissimilarity can be partitioned into meaningful turnover and nestedness components, and extend these new indices to multiple-site situations. Finally the concepts of nestedness and nestedness-resultant dissimilarity are discussed. Main conclusions: Nestedness should be assessed using consistent measures that depend both on paired overlap and matrix filling, e.g. NODF, whereas beta-diversity patterns should be examined using measures that allow the total dissimilarity to be separated into the components of dissimilarity due to species replacement and dissimilarity due to nestedness. In the case of multiple-site dissimilarity patterns, averaged pairwise indices should never be used because the mean of the pairwise values is unable to accurately reflect the multiple-site attributes of dissimilarity.

Beta diversity (variation of the species composition of assemblages) may reflect two different phenomena, spatial species turnover and nestedness of assemblages, which result from two antithetic processes, namely species replacement and species loss, respectively. The aim of this paper is to provide a unified framework for the assessment of beta diversity, disentangling the contribution of spatial turnover and nestedness to beta-diversity patterns. I derive an additive partitioning of beta diversity that provides the two separate components of spatial turnover and nestedness underlying the total amount of beta diversity. I propose two families of measures of beta diversity for pairwise and multiple-site situations. Each family comprises one measure accounting for all aspects of beta diversity, which is additively decomposed into two measures accounting for the pure spatial turnover and nestedness components, respectively. Finally, I provide a case study using European longhorn beetles to exemplify the relevance of disentangling spatial turnover and nestedness patterns. Assigning the different beta-diversity patterns to their respective biological phenomena is essential for analysing the causality of the processes underlying biodiversity. Thus, the differentiation of the spatial turnover and nestedness components of beta diversity is crucial for our understanding of central biogeographic, ecological and conservation issues.

1. In 2003, 24 presence–absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. 2. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. 3. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B = βB,A), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. 4. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence–absence metric, βsim, performed well overall. Only βBaselga R turn, βBaselga B-C turn and βsim measured purely species turnover and were independent of nestedness. Among the other metrics, sensitivity to nestedness varied >4-fold. 5. Our results indicate large amounts of redundancy among existing β-diversity metrics, whilst the estimation of unseen shared and unshared species is lacking and should be addressed in the design of new abundance-based metrics.

Human activities have reorganized the earth's biota resulting in spatially disparate locales becoming more or less similar in species composition over time through the processes of biotic homogenization and biotic differentiation, respectively. Despite mounting evidence suggesting that this process may be widespread in both aquatic and terrestrial systems, past studies have predominantly focused on single taxonomic groups at a single spatial scale. Furthermore, change in pairwise similarity is itself dependent on two distinct processes, spatial turnover in species composition and changes in gradients of species richness. Most past research has failed to disentangle the effect of these two mechanisms on homogenization patterns. Here, we use recent statistical advances and collate a global database of homogenization studies (20 studies, 50 datasets) to provide the first global investigation of the homogenization process across major faunal and floral groups and elucidate the relative role of changes in species richness and turnover. We found evidence of homogenization (change in similarity ranging from −0.02 to 0.09) across nearly all taxonomic groups, spatial extent and grain sizes. Partitioning of change in pairwise similarity shows that overall change in community similarity is driven by changes in species richness. Our results show that biotic homogenization is truly a global phenomenon and put into question many of the ecological mechanisms invoked in previous studies to explain patterns of homogenization.

Aim: We tested whether the geographic variation in the proportion of beta diversity attributed to nestedness or turnover components was explained by the effect of past glaciation events. Specifically, we tested the hypothesis that most of the beta diversity in regions retaining ice until recent periods was due to nestedness. Additionally, we tested whether the variation was influenced by thermal tolerance and the dispersal ability of species. Location: This study analysed data from the New World. Methods: We used presence/absence data for amphibians, birds and mammals of the New World. We calculated beta diversity among each 1° x 1° cell and the adjacent cells using the Sorensen dissimilarity index that expresses the total beta diversity. Furthermore, we partitioned it into turnover and nestedness components. The relative importance of the two latter components was expressed as the proportion of total beta diversity explained by nestedness (ß ratio ). We calculated the correlation between p rat io and the time each cell was free of ice since the last glaciation (cell age). To control the effects of spatial autocorrelation, we calculated geographically effective degrees of freedom. Results: The proportion of beta diversity attributed to nestedness was negatively correlated with cell age. Moreover, this effect was stronger for amphibians than mammals, and stronger for mammals than birds. Main conclusions: Our results are in accordance with the hypothesis that the nestedness component of beta diversity is more important in areas affected by glaciations until recent time. The beta diversity in high latitudes is the result of past extinctions and recent recolonization, which result in higher levels of nestedness. This process is more evident for vertebrates with lower dispersal ability and lower temperature tolerance.

Aim The geographical range size of species is a strong predictor of vulnerability to global extinction. However, it remains unclear whether range size is also a good predictor of extinction risk at much smaller scales. Here, we reconstruct biodiversity time series to ask whether species with small ranges have declined preferentially with habitat loss at the local scale. Location Global. Time period 1500–2015. Major taxa studied Vascular plants. Method We collated 70 million occurrence records of 180,000 species of vascular plants from three biodiversity data‐sharing networks. We combined these with data on changes in global land use to find locations (0.25° grid cells) with biodiversity data before and after loss of natural habitat. First, we examined the change in community median range size before and after habitat loss. Second, we quantified the probabilities of local persistence of small‐ and large‐ranged species at different levels of habitat loss. Results Community median range size was higher after habitat loss, on average. Species with small ranges had lower probabilities of persistence than species with large ranges at already moderate habitat loss (≤50%). Main conclusions The loss of natural habitat has a differential effect on the local extinction risk of species with different range sizes. Given that species with small ranges decline preferentially, habitat loss can create a linkage between temporal and spatial species turnover, in that changes within communities decrease compositional differences between communities.

Aim Interactions with mycorrhizal fungi are increasingly recognized as an important factor underlying the distribution and abundance of orchid species. However, the geographical distribution of orchid mycorrhizal fungi (OMF) and how their communities vary over large geographical areas are less well understood. Because climatic and environmental similarity may decrease with geographical distance or because some OMF have limited dispersal capabilities, similarities in orchid mycorrhizal communities can be expected to decrease with increasing distances separating orchid populations. However, up till now empirical evidence is largely lacking. Location Eurasia. Taxa Gymnadenia conopsea (L.) R. Brown and Epipactis helleborine (L.) Crantz. Methods High‐throughput sequencing was used to perform a cross‐continental comparison of OMF that associate with two widespread Eurasian terrestrial orchids, Epipactis helleborine and Gymnadenia conopsea. Both phylogenetic and nonphylogenetic measures of community dissimilarity and their components were calculated and related to geographical distances using Mantel tests. Results Our results showed that in both orchid species similarity in mycorrhizal communities decreased significantly with geographical distance. Decomposing the contribution of spatial turnover and nestedness to overall dissimilarity showed that the observed dissimilarity was mainly the result of species replacement between regions, and not of species loss. Similarly, a strong relationship was observed between phylogenetic community dissimilarity and geographical distance. Decomposing PCD values into a nonphylogenetic and phylogenetic component showed that orchid populations located closely next to each other were likely to contain the same operational taxonomic units (OTUs), but that the non‐shared taxa came from different phylogenetic clades. Species indicator analyses showed that the majority of OMF OTUs were restricted to particular geographical areas. However, some OTUs occurred in both continents, indicating that some fungi have very wide distributions. Main conclusions Overall, these results demonstrate that orchid mycorrhizal communities differ substantially across large geographical areas, but that the distribution of orchids is not necessarily restricted by the distribution of particular OMF. Hence, widespread orchid species can be considered mycorrhizal generalists that are flexible in the OMF with which they associate across large geographical areas.

Plant invasions can cause biotic homogenisation which can have cascading effects on the diversity of invaded ecosystems. These impacts on diversity are likely to be scale-dependent and thus affect different aspects of diversity (i.e. beta, gamma and alpha). For example, the widespread invasion of non-native pine trees causes a loss of plant gamma diversity; however, the effects of this invasion and co-invasion by ectomycorrhizal fungi on belowground fungal communities remain unknown. We established thirteen 400 m2 plots across a Pinus nigra density gradient in Canterbury, New Zealand. We sampled twenty-four soil samples from each plot and extracted and sequenced DNA for fungi from each sample independently, allowing determination of within-sample (α) and plot-scale (γ) diversity and turnover (β-diversity). Pine invasion was associated with a positive unimodal response in soil fungal β-diversity, reflected by an increase in saprotroph diversity at low pine density following a loss of this group of fungi at high pine densities. Pine invasion was also associated with an overall 47.7% loss of fungal α-diversity and a 50% loss of γ-diversity. Loss of diversity correlated to a shift from a saprotroph-dominated fungal community in low pine density plots to an ectomycorrhizal-dominated community in high pine density plots. However, despite the resulting dominance of ectomycorrhizal fungi, there was no increase in γ-diversity of ectomycorrhizal fungi as pine density increased. Our results support the concept that low-density invasions increase ecosystem heterogeneity and therefore beta-diversity, but that as aboveground plant communities become more homogenised there is a dramatic loss of fungal diversity across all scales that could inhibit recovery and restoration of invaded ecosystems.

ABSTRACT Metabarcoding technologies for soil fungal DNA pools have enabled to capture the diversity of fungal community and the agreement of their β-diversity with plant β-diversity. However, processes underlying the synchrony of the aboveground–belowground biodiversity is still unclear. By using partitioning methods for plant β-diversity, this study explored the process driving synchrony in tundra ecosystems, in which drastic vegetation shifts are observed with climate warming. Our methods based on Baselga's partitioning enabled the division of plant β-diversity into two phenomena and three functional components. Correlation of fungal β-diversity with the components of plant β-diversity showed that the spatial replacement of fungi was promoted by plant species turnover, in particular, plant species turnover with functional exchange. In addition, spatial variety of graminoid or forbs species, rather than shrubs, enhanced fungal β-diversity. These results suggest the importance of small-scale factors such as plant–fungal interactions or local environments modified by plants for the fungal community assemblage. The process-based understanding of community dynamics of plants and fungi allows us to predict the ongoing shrub encroachment in the Arctic region, which could weaken the aboveground–belowground synchrony. Partitiong of plant β-diversity reveals that shrub encroachment of tundra ecosystems would affect belowground fungal diversity.