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In recent years, new technologies have emerged that can generate rapid and standardized biodiversity inventories without explicit human guidance (novel community data). The benefits as well as technical challenges of these technologies have been extensively reviewed, and ecologists are currently in the process of incorporating them into their observational studies. So far, however, large novel community datasets are still rare. Consequently, there are still many open questions about how these new data should be optimally used to address fundamental questions in community ecology, macroecology, and conservation. We review the state of the field, highlight the opportunities and analytical tools for advancing ecological research with novel community data, and discuss the implications of these emerging technologies for ecological theory, ecological study design, and environmental management. New technologies for monitoring biodiversity such as environmental (e)DNA, passive acoustic monitoring, and optical sensors promise to generate automated spatiotemporal community observations at unprecedented scales and resolutions. Here, we introduce 'novel community data' as an umbrella term for these data. We review the emerging field around novel community data, focusing on new ecological questions that could be addressed; the analytical tools available or needed to make best use of these data; and the potential implications of these developments for policy and conservation. We conclude that novel community data offer many opportunities to advance our understanding of fundamental ecological processes, including community assembly, biotic interactions, micro- and macroevolution, and overall ecosystem functioning. New technologies for monitoring biodiversity such as environmental (e)DNA, passive acoustic monitoring, and optical sensors promise to generate automated spatiotemporal community observations at unprecedented scales and resolutions. Here, we introduce 'novel community data' as an umbrella term for these data. We review the emerging fields around novel community data, focusing on new ecological questions that could be addressed; the analytical tools available or needed to make best use of these data; and the potential implications of these developments for policy and conservation. We conclude that novel community data offer many opportunities to advance our understanding of fundamental ecological processes, including community assembly, biotic interactions, micro- and macroevolution, and overall ecosystem functioning. [ABSTRACT FROM AUTHOR]

When comparing multiple models of species distribution, models yielding higher predictive performance are clearly to be favored. A more difficult question is how to decide whether even the best model is "good enough". Here, we clarify key choices and metrics related to evaluating the predictive performance of presence–absence models. We use a hierarchical case study to evaluate how four metrics of predictive performance (AUC, Tjur's R2, max‐Kappa, and max‐TSS) relate to each other, the random and fixed effects parts of the model, the spatial scale at which predictive performance is measured, and the cross‐validation strategy chosen. We demonstrate that the very same metric can achieve different values for the very same model, even when similar cross‐validation strategies are followed, depending on the spatial scale at which predictive performance is measured. Among metrics, Tjur's R2 and max‐Kappa generally increase with species' prevalence, whereas AUC and max‐TSS are largely independent of prevalence. Thus, Tjur's R2 and max‐Kappa often reach lower values when measured at the smallest scales considered in the study, while AUC and max‐TSS reaching similar values across the different spatial levels included in the study. However, they provide complementary insights on predictive performance. The very same model may appear excellent or poor not only due to the applied metric, but also how predictive performance is exactly calculated, calling for great caution on the interpretation of predictive performance. The most comprehensive evaluation of predictive performance can be obtained by evaluating predictive performance through the combination of measures providing complementary insights. Instead of following simple rules of thumb or focusing on absolute values, we recommend comparing the achieved predictive performance to the researcher's own a priori expectations on how easy it is to make predictions related to the same question that the model is used for. [ABSTRACT FROM AUTHOR]

Through their ephemeral reproductive structures (fruiting bodies), ectomycorrhizal forest soil fungi provide a resource for a plethora of organisms. Thus, resolving what biotic and abiotic factors determine the occurrence and abundance of fruiting bodies is fundamental for understanding the dynamics of forest trophic networks. While the influence of abiotic factors such as moisture and temperature on fungal fruiting are relatively well established, little is known about how these processes interact with the evolutionary history of fungal species to determine when, where, and in which abundance fungal fruiting bodies will emerge. A specific knowledge gap relates to whether species' responses to their environment are phylogenetically structured. Here, we ask whether related fungal taxa respond similarly to climatic factors and forest habitat characteristics, and whether such correlated responses will affect the assembly of fungal fruiting communities. To resolve these questions, we fitted joint species distribution models combining data on the species composition and abundance of fungal fruiting bodies, environmental variation, and phylogenetic relationships among fungal taxa. Our results show that both site‐level forest characteristics (dominant tree species and forest age) and climatic factors related to phenology (effective heat sum) greatly influence the occurrence and abundance of fruiting bodies. More importantly, while different fungal species responded unequally to their shared environment, there was a strong phylogenetic signal in their responses, so that related fungal species tended to fruit under similar environmental conditions. Thus, not only are fruiting bodies short‐lived and patchily distributed, but the availability of similar resources will be further aggregated in time and space. These strong constraints on resource availability for fungus‐associated taxa highlight the potential of fungus‐based networks as a model system for studies on the ecology and evolution of resource–consumer relations in ephemeral systems of high spatiotemporal patchiness. [ABSTRACT FROM AUTHOR]

Summary: Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity.We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition.We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity.We demonstrate that the Arctic harbours a relatively species‐rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change. [ABSTRACT FROM AUTHOR]

Interactions among fungi and insects involve hundreds of thousands of species. While insect communities on plants have formed some of the classic model systems in ecology, fungus‐based communities and the forces structuring them remain poorly studied by comparison. We characterize the arthropod communities associated with fruiting bodies of eight mycorrhizal basidiomycete fungus species from three different orders along a 1200‐km latitudinal gradient in northern Europe. We hypothesized that, matching the pattern seen for most insect taxa on plants, we would observe a general decrease in fungal‐associated species with latitude. Against this backdrop, we expected local communities to be structured by host identity and phylogeny, with more closely related fungal species sharing more similar communities of associated organisms. As a more unique dimension added by the ephemeral nature of fungal fruiting bodies, we expected further imprints generated by successional change, with younger fruiting bodies harboring communities different from older ones. Using DNA metabarcoding to identify arthropod communities from fungal fruiting bodies, we found that latitude left a clear imprint on fungus‐associated arthropod community composition, with host phylogeny and decay stage of fruiting bodies leaving lesser but still‐detectable effects. The main latitudinal imprint was on a high arthropod species turnover, with no detectable pattern in overall species richness. Overall, these findings paint a new picture of the drivers of fungus‐associated arthropod communities, suggesting that latitude will not affect how many arthropod species inhabit a fruiting body but, rather, what species will occur in it and at what relative abundances (as measured by sequence read counts). These patterns upset simplistic predictions regarding latitudinal gradients in species richness and in the strength of biotic interactions. [ABSTRACT FROM AUTHOR]

Identifying the spatial scales at which community assembly processes operate is fundamental for gaining a mechanistic understanding of the drivers shaping ecological communities. In this study, we examined whether and how traits and phylogenetic relationships structure fungal community assembly across spatial scales.We applied joint species distribution modelling to a European‐scale dataset on 215 wood‐inhabiting fungal species, which includes data on traits, phylogeny and environmental variables measured at the local (log‐level) and regional (site‐level) scales.At the local scale, wood‐inhabiting fungal communities were mostly structured by deadwood decay stage, and the trait and phylogenetic patterns along this environmental gradient suggested the lack of diversifying selection.At regional scales, fungal communities and their trait distributions were influenced by climatic and connectivity‐related variables. The fungal climatic niches were not phylogenetically structured, suggesting that diversifying selection or stabilizing selection for climatic niches has played a strong role in wood‐inhabiting communities. In contrast, we found a strong phylogenetic signal in the responses to connectivity‐related variables, revealing phylogenetic homogenization in small and isolated forests.Synthesis. Altogether, our results show that species‐level traits and phylogenies modulate the responses of wood‐inhabiting fungi to environmental processes acting at different scales. This result suggests that the evolutionary histories of fungal traits diverge along different environmental axes. [ABSTRACT FROM AUTHOR]

Species interactions are known to structure ecological communities. Still, the influence of climate change on biodiversity has primarily been evaluated by correlating individual species distributions with local climatic descriptors, then extrapolating into future climate scenarios. We ask whether predictions on arctic arthropod response to climate change can be improved by accounting for species interactions. For this, we use a 14‐year‐long, weekly time series from Greenland, resolved to the species level by mitogenome mapping. During the study period, temperature increased by 2°C and arthropod species richness halved. We show that with abiotic variables alone, we are essentially unable to predict species responses, but with species interactions included, the predictive power of the models improves considerably. Cascading trophic effects thereby emerge as important in structuring biodiversity response to climate change. Given the need to scale up from species‐level to community‐level projections of biodiversity change, these results represent a major step forward for predictive ecology. [ABSTRACT FROM AUTHOR]

In a warming world, changes in climate may result in species‐level responses as well as changes in community structure through knock‐on effects on ecological interactions such as predation and herbivory. Yet, the links between these responses at different levels are still inadequately understood. Assessing how microclimatic conditions affect each of them at local scales provides information essential for understanding the consequences of macroclimatic changes projected in the future.Focusing on the rapidly changing High Arctic, we examine how a community based on a common resource species (avens, Dryas spp.), a specialist insect herbivore (Sympistis zetterstedtii) and natural enemies of lepidopteran herbivores (parasitoids) varies along a multidimensional microclimatic gradient. We ask (a) how parasitoid community composition varies with local abiotic conditions, (b) how the community‐level response of parasitoids is linked to species‐specific traits (koino‐ or idiobiont life cycle strategy and phenology) and (c) whether the effects of varying abiotic conditions extend to interaction outcomes (parasitism rates on the focal herbivore and realized herbivory rates).We recorded the local communities of parasitoids, herbivory rates on Dryas flowers and parasitism rates in Sympistis larvae at 20 sites along a mountain slope. For linking community‐level responses to microclimatic conditions with parasitoid traits, we used joint species distribution modelling. We then assessed whether the same abiotic variables also affect parasitism and herbivory rates, by applying generalized linear and additive mixed models.We find that parasitism strategy and phenology explain local variation in parasitoid community structure. Parasitoids with a koinobiont strategy preferred high‐elevation sites with higher summer temperatures or sites with earlier snowmelt and lower humidity. Species of earlier phenology occurred with higher incidence at sites with cooler summer temperatures or later snowmelt. Microclimatic effects also extend to parasitism and herbivory, with an increase in the parasitism rates of the main herbivore S. zetterstedtii with higher temperature and lower humidity, and a matching increase in herbivory rates.Our results show that microclimatic variation is a strong driver of local community structure, species interactions and interaction outcomes in Arctic ecosystems. In view of ongoing climate change, these results predict that macroclimatic changes will profoundly affect arctic communities. [ABSTRACT FROM AUTHOR]

The regional origin of a food product commonly affects its value. To this, DNA-based identification of tissue remains could offer fine resolution. For honey, this would allow the usage of not only pollen but all plant tissue, and also that of microbes in the product, for discerning the origin. Here we examined how plant, bacterial and fungal taxa identified by DNA metabarcoding and metagenomics differentiate between honey samples from three neighbouring countries. To establish how the taxonomic contents of honey reflect the country of origin, we used joint species distribution modelling. At the lowest taxonomic level by metabarcoding, with operational taxonomic units, the country of origin explained the majority of variation in the data (70–79%), with plant and fungal gene regions providing the clearest distinction between countries. At the taxonomic level of genera, plants provided the most separation between countries with both metabarcoding and metagenomics. The DNA-based methods distinguish the countries more than the morphological pollen identification and the removal of pollen has only a minor effect on taxonomic recovery by DNA. As we find good resolution among honeys from regions with similar biota, DNA-based methods hold great promise for resolving honey origins among more different regions. [ABSTRACT FROM AUTHOR]

How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic rootassociated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities. [ABSTRACT FROM AUTHOR]

Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co‐occurrences that are not constrained by environmental conditions. In this study, we investigated co‐occurrences among root‐associated fungi, asking whether fungi co‐occur more or less strongly than expected based on the environmental conditions and the host plant species examined. We generated molecular data on root‐associated fungi of five plant species evenly sampled along an elevational gradient at a high arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co‐occurrences that could be explained by the environmental conditions and the host plant species, as well as those co‐occurrences that remained unexplained and thus more probably reflect interactive associations. Our results indicate that not only negative but also positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co‐occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root‐associated fungi are predominantly positive. [ABSTRACT FROM AUTHOR]

Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. In contrast, empirical studies report contrasting patterns: some find positive and others negative effects of fragmentation per se on species richness. To explain this apparent disparity, we devise a stochastic, spatially explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have complex effects on species diversity in competitive communities. When the total amount of habitat is large, fragmentation per se tends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentation per se decreases species diversity. [ABSTRACT FROM AUTHOR]

Aim: Forest fragmentation is among the principal causes of global biodiversity loss, yet how it affects mutualistic interactions between plants and animals at large spatial scale is poorly understood. In particular, tropical forest regeneration depends on animal‐mediated seed dispersal, but the seed‐dispersing animals face rapid decline due to forest fragmentation and defaunation. Here, we assess how fragmentation influences the pairwise interactions between 407 seed disperser and 1,424 tree species in a highly fragmented biodiversity hotspot. Location: Atlantic Forest, South America. Methods: We predicted interaction networks in 912 sites covering the entire biome by combining verified interaction data with co‐occurrence probabilities obtained from a spatially explicit joint species distribution model. We identified keystone seed dispersers by computing a species‐specific keystone index and by selecting those species belonging to the top 5% quantile. Results: We show that forest fragmentation affects seed dispersal interactions negatively, and the decreased area of functionally connected forest, rather than increased edge effects, is the main driver behind the loss of interactions. Both the seed disperser availability for the local tree communities and in particular the proportion of interactions provided by keystone seed dispersers decline with increasing degree of fragmentation. Importantly, just 21 keystone species provided >40% of all interactions. The numbers of interactions provided by keystone and non‐keystone species, however, were equally negatively affected by fragmentation, suggesting that seed dispersal interactions may not be rewired under strong fragmentation effects. Conclusions: We highlight the importance of understanding the fragmentation‐induced compositional shifts in seed disperser communities as they may lead to lagged and multiplicative effects on tree communities. Our results illustrate the utility of model‐based prediction of interaction networks as well as model‐based identification of keystone species as a tool for prioritizing conservation efforts. Similar modelling approaches could be applied to other threatened ecosystems and interaction types globally. [ABSTRACT FROM AUTHOR]

Aim: Beech forests comprise a globally unique temperate forest type in Europe. The dominance of beech in these forests developed during the ongoing post‐glacial northward re‐colonization, concurrently with intensified forest use by humans. We investigated how these two processes together with climate shaped the patterns of functional diversity of two major species groups involved in wood decomposition and whether functional diversity is determined on the local or regional species pool level. Location: European beech forest distribution range. Taxon: Saproxylic beetles and fungi. Methods: We analysed records of 532,496 saproxylic beetles of 788 species and 8,630 records of 234 saproxylic fungal species based on sets of traits similar to both groups. We tested how space, climate and landscape composition affect trait‐based functional diversity on local and regional scales. Using structural equation modelling, we tested whether functional diversity is shaped on the local or regional scale. Results: The response of local functional diversity of both saproxylic beetles and fungi followed a highly congruent pattern of decreasing functional diversity towards the north, with higher elevation and accounted for overall geographical gradients with higher temperature, while increasing with higher precipitation. Structural equation modelling revealed that local functional diversity is determined by community changes operating on the level of the regional species pool. Main conclusions: Our findings suggest that the functional diversity patterns of saproxylic organisms in European beech forests are mainly determined on the regional scale and driven by anthropogenic and biogeographical processes. To conserve the variation and hotspots of functional diversity in beech forests, activities have to focus on a broad spatial and climatic range of sites throughout Europe, including the primeval forests in the east, as started by the UNESCO World Heritage selection of "Ancient and Primeval Beech Forests of the Carpathians and Other Regions of Europe". [ABSTRACT FROM AUTHOR]

Analysing the structure and dynamics of biotic interaction networks and the processes shaping them is currently one of the key fields in ecology. In this paper, we develop a novel approach to gut content analysis, thereby deriving a new perspective on community interactions and their responses to environment. For this, we use an elevational gradient in the High Arctic, asking how the environment and species traits interact in shaping predator–prey interactions involving the wolf spider Pardosa glacialis. To characterize the community of potential prey available to this predator, we used pitfall trapping and vacuum sampling. To characterize the prey actually consumed, we applied molecular gut content analysis. Using joint species distribution models, we found elevation and vegetation mass to explain the most variance in the composition of the prey community locally available. However, such environmental variables had only a small effect on the prey community found in the spider's gut. These observations indicate that Pardosa exerts selective feeding on particular taxa irrespective of environmental constraints. By directly modelling the probability of predation based on gut content data, we found that neither trait matching in terms of predator and prey body size nor phylogenetic or environmental constraints modified interaction probability. Our results indicate that taxonomic identity may be more important for predator–prey interactions than environmental constraints or prey traits. The impact of environmental change on predator–prey interactions thus appears to be indirect and mediated by its imprint on the community of available prey. [ABSTRACT FROM AUTHOR]

Abstract: Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning and are important for human health, food production and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise. The method consists of using a cyclone sampler to acquire fungal spores directly from the air to an Eppendorf tube, and applying DNA barcoding with probabilistic species identification to generate a list of species from the sample. We tested the feasibility of the method by acquiring replicate air samples from different geographical regions within Finland. Our results show that air sampling is adequate for regional‐level surveys, with samples collected >100 km apart varying but samples collected <10 km apart not varying in their species composition. The data show marked phenology, and thus obtaining a representative species list requires aerial sampling that covers the entire fruiting season. In sum, aerial sampling combined with probabilistic molecular species identification offers a highly effective method for generating a species list of air‐dispersing fungi. The method presented here has the potential to revolutionize fungal surveys, as it provides a highly cost‐efficient way to include fungi as a part of large‐scale biodiversity assessments and monitoring programs. [ABSTRACT FROM AUTHOR]

Abstract: Protected areas are meant to preserve native local communities within their boundaries, but they are not independent from their surroundings. Impoverished habitat quality in the matrix might influence the species composition within the protected areas through biotic homogenization. The aim of this study was to determine the impacts of matrix quality on species richness and trait composition of bird communities from the Finnish reserve area network and whether the communities are being subject of biotic homogenization due to the lowered quality of the landscape matrix. We used joint species distribution modeling to study how characteristics of the Finnish forest reserves and the quality of their surrounding matrix alter species and trait compositions of forest birds. The proportion of old forest within the reserves was the main factor in explaining the bird community composition, and the bird communities within the reserves did not strongly depend on the quality of the matrix. Yet, in line with the homogenization theory, the beta‐diversity within reserves embedded in low‐quality matrix was lower than that in high‐quality matrix, and the average abundance of regionally abundant species was higher. Influence of habitat quality on bird community composition was largely explained by the species' functional traits. Most importantly, the community specialization index was low, and average body size was high in areas with low proportion of old forest. We conclude that for conserving local bird communities in northern Finnish protected forests, it is currently more important to improve or maintain habitat quality within the reserves than in the surrounding matrix. Nevertheless, we found signals of bird community homogenization, and thus, activities that decrease the quality of the matrix are a threat for bird communities. [ABSTRACT FROM AUTHOR]

The identification of traits that influence the responses of the species to environmental variation provides a mechanistic perspective on the assembly processes of ecological communities. While much research linking functional ecology with assembly processes has been conducted with animals and plants, the development of predictive or even conceptual frameworks for fungal functional community ecology remains poorly explored. Particularly, little is known about the contribution of traits to the occurrences of fungal species under different environmental conditions., Wood-inhabiting fungi are known to strongly respond to habitat disturbance, and thus provide an interesting case study for investigating to what extent variation in occurrence patterns of fungi can be related to traits. We apply a trait-based joint species distribution model to a data set consisting of fruit-body occurrence data on 321 wood-inhabiting fungal species collected in 22 460 dead wood units from managed and natural forest sites., Our results show that environmental filtering plays a big role on shaping wood-inhabiting fungal communities, as different environments held different communities in terms of species and trait compositions. Most importantly, forest management selected against species with large and long-lived fruit-bodies as well as late decayers, and promoted the occurrences of species with small fruit-bodies and early decayers. A strong phylogenetic signal in the data suggested the existence of also some other functionally important traits than the ones we considered., We found that those species groups that were more prevalent in natural conditions had more associations to other species than species groups that were tolerant to or benefitted from forest management. Therefore, the changes that forest management causes on wood-inhabiting fungal communities influence ecosystem functioning through simplification of interactive associations among the fungal species., Synthesis. Our results show that functional traits are linked to the responses of wood-inhabiting fungi to variation in their environment, and thus environmental changes alter ecosystem functions via promoting or reducing species with different fruit-body types. However, further research is needed to identify other functional traits and to provide conclusive evidence for the adaptive nature of the links from traits to occurrence patterns found here. [ABSTRACT FROM AUTHOR]

Research on mutualistic and antagonistic networks, such as plant-pollinator and host-parasite networks, has shown that species interactions can influence and be influenced by the responses of species to environmental perturbations. Here we examine whether results obtained for directly observable networks generalize to more complex networks in which species interactions cannot be observed directly. As a case study, we consider data on the occurrences of 98 wood-inhabiting fungal species in managed and natural forests. We specifically ask if and how much the positions of wood-inhabiting fungal species within the interaction networks influence their responses to forest management. For this, we utilize a joint species distribution model that partitions variation in species occurrences among environmental (i.e. resource availability) and biotic (i.e. species-to-species associations) predictors. Our results indicate that in addition to the direct loss of resource-specialised species, forest management has indirect effects mediated through interactive associations. In particular, species with strong associative links to other species are especially sensitive to forest management. [ABSTRACT FROM AUTHOR]

Reintroduction of locally extinct species is increasingly applied as a conservation tool for re-establishing species within their historical ranges. Thus far, this option has however not been investigated for fungi other than lichens. A large fraction of wood-inhabiting fungal species have declined because of forest loss and fragmentation, in addition to a decrease in dead wood. Here, we show the results from an experiment carried out in southern Finland, which demonstrates that inoculation is an effective method for reintroducing threatened wood-inhabiting fungi. All selected red-listed fungal species successfully established in the inoculated logs as mycelia, and three out of the seven produced fruit-bodies. Success rate was greater when the strains were inoculated in early-decay logs, including species that usually fruit in late decay stages. Inoculation can provide an effective tool for reintroducing fungal species, as the source populations remain intact and it is possible to produce massive amounts of inoculation-units with relatively low cost. Reintroductions of fungi should however be preceded by a risk assessment of the species to be reintroduced, by using source populations from nearby localities, and they should be considered complementary to the primary target of increasing the amount of their habitat. Our results suggest that the reintroductions of threatened fungi via inoculation in combination with other conservation measures can have important bearings for forest conservation and restoration. [ABSTRACT FROM AUTHOR]

Among the factors that affect the conservation efficiency of protected areas, lack of connectivity is considered as one of the main problems. In this study, we assessed the influence of connectivity of European beech forest reserves on wood-inhabiting fungal communities, compared to the influence of local factors. To address this topic, we used a data matrix consisting of 344 fungal species on 1571 resource units (i.e. fallen beech logs, including their standing snags) sampled in 42 European beech forest reserves. Our results show that connectivity has significant effects on wood-inhabiting fungal communities in European beech forest reserves, and that the effectiveness of reserves for maintaining the wood-inhabiting fungal diversity is compromised by habitat fragmentation. Connectivity at small scales (measured as the area of the reserve) had a strong influence on the occurrence of indicator species and was also critical for the number of species at a resource. Connectivity at larger scales (connectivity to surrounding beech forests) seemed to be particularly critical for the community composition both at resource and reserve levels. In line with previous research, we found other covariates such as size of the resource units and annual temperature range to positively influence wood-inhabiting fungal species richness. The effects of habitat fragmentation were especially strong in western and northern European regions where the smallest and more isolated reserves were located. We propose that an effective conservation strategy for wood-inhabiting fungi should focus on increasing the areas of the present reserves as well as conserving new reserves in the proximity of the existing ones. [ABSTRACT FROM AUTHOR]

For efficient use of conservation resources it is important to determine how species diversity changes across spatial scales. In many poorly known species groups little is known about at which spatial scales the conservation efforts should be focused. Here we examined how the community turnover of wood-inhabiting fungi is realised at three hierarchical levels, and how much of community variation is explained by variation in resource composition and spatial proximity. The hierarchical study design consisted of management type (fixed factor), forest site (random factor, nested within management type) and study plots (randomly placed plots within each study site). To examine how species richness varied across the three hierarchical scales, randomized species accumulation curves and additive partitioning of species richness were applied. To analyse variation in wood-inhabiting species and dead wood composition at each scale, linear and Permanova modelling approaches were used. Wood-inhabiting fungal communities were dominated by rare and infrequent species. The similarity of fungal communities was higher within sites and within management categories than among sites or between the two management categories, and it decreased with increasing distance among the sampling plots and with decreasing similarity of dead wood resources. However, only a small part of community variation could be explained by these factors. The species present in managed forests were in a large extent a subset of those species present in natural forests. Our results suggest that in particular the protection of rare species requires a large total area. As managed forests have only little additional value complementing the diversity of natural forests, the conservation of natural forests is the key to ecologically effective conservation. As the dissimilarity of fungal communities increases with distance, the conserved natural forest sites should be broadly distributed in space, yet the individual conserved areas should be large enough to ensure local persistence. [ABSTRACT FROM AUTHOR]

Unravelling how species communities change along environmental gradients requires a dual understanding: the direct responses of the species to their abiotic surroundings and the indirect variation of these responses through biotic interactions. Here, we focus on the interactive relationships between plants and their symbiotic root‐associated fungi (RAF) along stressful abiotic gradients. We investigate whether variations in RAF community composition along altitudinal gradients influence plant growth at high altitudes, where both plants and fungi face harsher abiotic conditions. We established a translocation experiment between pairs of Bistorta vivipara populations across altitudinal gradients. To separate the impact of shifting fungal communities from the overall influence of changing abiotic conditions, we used a root barrier to prevent new colonization by RAF following translocation. To characterize the RAF communities, we applied DNA barcoding to the root samples. Through the utilization of joint species distribution modelling, we assessed the relationship between changes in plant functional traits resulting from experimental treatments and the corresponding changes in the RAF communities. Our findings indicate that RAF communities influence plant responses to stressful abiotic conditions. Plants translocated from low to high altitudes grew more when they were able to associate with the resident high‐altitude RAF compared to those plants that were not allowed to associate with the resident RAF. We conclude that interactions with RAF impact how plants respond to stressful abiotic conditions. Our results provide experimental support that interactions with RAF improve plant stress tolerance to altitudinal stressors such as colder temperatures and less nutrient availability. [ABSTRACT FROM AUTHOR]

Aim: Understanding the variation in community composition and species abundances (i.e., β‐diversity) is at the heart of community ecology. A common approach to examine β‐diversity is to evaluate directional variation in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distance. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 148 datasets comprising different types of organisms and environments. Location: Global. Time period: 1990 to present. Major taxa studied: From diatoms to mammals. Method: We measured the strength of the decay using ranked Mantel tests (Mantel r) and the rate of distance decay as the slope of an exponential fit using generalized linear models. We used null models to test whether functional similarity decays faster or slower than expected given the taxonomic decay along the spatial and environmental distance. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm and organismal features. Results: Taxonomic distance decay was stronger than functional distance decay along both spatial and environmental distance. Functional distance decay was random given the taxonomic distance decay. The rate of taxonomic and functional spatial distance decay was fastest in the datasets from mid‐latitudes. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distance but a higher rate of decay along environmental distance. Marine ecosystems had the slowest rate of decay along environmental distances. Main conclusions: In general, taxonomic distance decay is a useful tool for biogeographical research because it reflects dispersal‐related factors in addition to species responses to climatic and environmental variables. Moreover, functional distance decay might be a cost‐effective option for investigating community changes in heterogeneous environments. [ABSTRACT FROM AUTHOR]

A large array of species distribution model (SDM) approaches has been developed for explaining and predicting the occurrences of individual species or species assemblages. Given the wealth of existing models, it is unclear which models perform best for interpolation or extrapolation of existing data sets, particularly when one is concerned with species assemblages. We compared the predictive performance of 33 variants of 15 widely applied and recently emerged SDMs in the context of multispecies data, including both joint SDMs that model multiple species together, and stacked SDMs that model each species individually combining the predictions afterward. We offer a comprehensive evaluation of these SDM approaches by examining their performance in predicting withheld empirical validation data of different sizes representing five different taxonomic groups, and for prediction tasks related to both interpolation and extrapolation. We measure predictive performance by 12 measures of accuracy, discrimination power, calibration, and precision of predictions, for the biological levels of species occurrence, species richness, and community composition. Our results show large variation among the models in their predictive performance, especially for communities comprising many species that are rare. The results do not reveal any major trade‐offs among measures of model performance; the same models performed generally well in terms of accuracy, discrimination, and calibration, and for the biological levels of individual species, species richness, and community composition. In contrast, the models that gave the most precise predictions were not well calibrated, suggesting that poorly performing models can make overconfident predictions. However, none of the models performed well for all prediction tasks. As a general strategy, we therefore propose that researchers fit a small set of models showing complementary performance, and then apply a cross‐validation procedure involving separate data to establish which of these models performs best for the goal of the study. [ABSTRACT FROM AUTHOR]

Deadwood can be recreated as a forest restoration measure to increase the amount of deadwood and assist deadwood‐dependent biodiversity. While deadwood restoration is known to have an overall positive effect on associated species in the long term, it remains poorly understood how and when wood‐inhabiting organisms colonize different kinds of deadwood, which is essential for developing efficient restoration frameworks. In this study, we use DNA metabarcoding to compare wood‐inhabiting fungal communities between fresh naturally fallen spruce logs and spruce logs felled for restoration. The results show that although pioneering fungal community composition greatly differs between natural and felled logs, with natural logs hosting more species‐rich and heterogeneous communities, felled logs still hold a relatively high fungal diversity. Responses to log type carried a strong phylogenetic signal, and orders Polyporales and Hymenochaetales including most species of conservation concern were more likely to occur in natural than in felled logs. Furthermore, we found that log type was more important for rarely recorded than commonly recorded taxa, suggesting that rare species might be more specialized in their habitat requirements than the common ones. Overall, while restored deadwood can hold a high fungal diversity, the results underline that freshly felled logs do not mimic fresh natural logs. Deadwood restoration should focus not only on increasing the quantity of deadwood but also on the quality of thereof, and most importantly, retaining the existing natural deadwood rather than artificially downing trees. [ABSTRACT FROM AUTHOR]

A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them. [ABSTRACT FROM AUTHOR]

The Eltonian niche of a species is defined as its set of interactions with other taxa. How this set varies with biotic, abiotic and human influences is a core question of modern ecology. In seasonal environments, the realized Eltonian niche is likely to vary due to periodic changes in the occurrence and abundance of interaction partners and changes in species behavior and preferences. Also, human management decisions may leave strong imprints on species interactions. To compare the impact of seasonality to that of management effects, honeybees provide an excellent model system. Based on DNA traces of interaction partners archived in honey, we can infer honeybee interactions with floral resources and microbes in the surrounding habitats, their hives, and themselves. Here, we resolved seasonal and management‐based impacts on honeybee interactions by sampling beehives repeatedly during the honey‐storing period of honeybees in Finland. We then use a genome‐skimming approach to identify the taxonomic contents of the DNA in the samples. To compare the effects of the season to the effects of location, management, and the colony itself in shaping honeybee interactions, we used joint species distribution modeling. We found that honeybee interactions with other taxa varied greatly among taxonomic and functional groups. Against a backdrop of wide variation in the interactions documented in the DNA content of honey from bees from different hives, regions, and beekeepers, the imprint of the season remained relatively small. Overall, a honey‐based approach offers unique insights into seasonal variation in the identity and abundance of interaction partners among honeybees. During the summer, the availability and use of different interaction partners changed substantially, but hive‐ and taxon‐specific patterns were largely idiosyncratic as modified by hive management. Thus, the beekeeper and colony identity are as important determinants of the honeybee's realized Eltonian niche as is seasonality. [ABSTRACT FROM AUTHOR]

Despite host‐fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life‐history studies. We assembled a spore morphology database covering over 26,000 species of free‐living to symbiotic fungi of plants, insects and humans and found more than eight orders of variation in spore size. Evolutionary transitions in symbiotic status correlated with shifts in spore size, but the strength of this effect varied widely among phyla. Symbiotic status explained more variation than climatic variables in the current distribution of spore sizes of plant‐associated fungi at a global scale while the dispersal potential of their spores is more restricted compared to free‐living fungi. Our work advances life‐history theory by highlighting how the interaction between symbiosis and offspring morphology shapes the reproductive and dispersal strategies among living forms. [ABSTRACT FROM AUTHOR]

Inferring interspecific interactions indirectly from community data is of central interest in community ecology. Data on species communities can be surveyed using different methods, each of which may differ in the amount and type of species detected, and thus produce varying information on interaction networks. Since fruit bodies reflect only a fraction of the wood‐inhabiting fungal diversity, there is an ongoing debate in fungal ecology on whether fruit body‐based surveys are a valid method for studying fungal community dynamics compared to surveys based on DNA metabarcoding. In this paper, we focus on species‐to‐species associations and ask whether the associations inferred from data collected by fruit‐body surveys reflect the ones found from data collected by DNA‐based surveys. We estimate and compare the association networks resulting from different survey methods using a joint species distribution model. We recorded both raw and residual associations that respectively do not and do correct for the influence of the abiotic predictors when estimating the species‐to‐species associations. The analyses of the DNA data yielded a larger number of species‐to‐species associations than the analyses of the fruit body‐based data as expected. Yet, we estimated unique associations also from the fruit‐body data. Our results show that the directions of estimated residual associations were consistent between the data types, whereas the raw associations were much less consistent, highlighting the need to account for the influence of relevant environmental covariates when estimating association networks. We conclude that even though DNA‐based survey methods are more informative about the total number of interacting species, fruit‐body surveys are also an adequate method for inferring association networks in wood‐inhabiting fungi. Since the DNA and fruit‐body data carry on complementary information on fungal communities, the most comprehensive insights are obtained by combining the two survey methods. [ABSTRACT FROM AUTHOR]

The ongoing global change and the increased interest in macroecological processes call for the analysis of spatially extensive data on species communities to understand and forecast distributional changes of biodiversity. Recently developed joint species distribution models can deal with numerous species efficiently, while explicitly accounting for spatial structure in the data. However, their applicability is generally limited to relatively small spatial data sets because of their severe computational scaling as the number of spatial locations increases. In this work, we propose a practical alleviation of this scalability constraint for joint species modeling by exploiting two spatial‐statistics techniques that facilitate the analysis of large spatial data sets: Gaussian predictive process and nearest‐neighbor Gaussian process. We devised an efficient Gibbs posterior sampling algorithm for Bayesian model fitting that allows us to analyze community data sets consisting of hundreds of species sampled from up to hundreds of thousands of spatial units. The performance of these methods is demonstrated using an extensive plant data set of 30,955 spatial units as a case study. We provide an implementation of the presented methods as an extension to the hierarchical modeling of species communities framework. [ABSTRACT FROM AUTHOR]

Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour‐intensive methods involving cultivation and morphology‐based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt–isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean‐up step using solid‐phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples—regardless of biomass or other properties—being successfully PCR‐amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus‐associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology‐based identifications, we find a species‐rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus‐associated interaction webs and communities. Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour‐intensive methods involving cultivation and morphology‐based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt–isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean‐up step using solid‐phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples—regardless of biomass or other properties—being successfully PCR‐amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus‐associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology‐based identifications, we find a species‐rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus‐associated interaction webs and communities. [ABSTRACT FROM AUTHOR]

Summary: Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed Protax‐fungi, a general tool for taxonomic placement of fungal internal transcribed spacer (ITS) sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. With empirical data on root‐ and wood‐associated fungi, Protax‐fungi reliably identified (with at least 90% identification probability) the majority of sequences to the order level but only around one‐fifth of them to the species level, reflecting the current limited coverage of the databases. Protax‐fungi outperformed the Sintax and Rdb classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. We applied Protax‐fungi to examine the internal consistencies of the Index Fungorum and UNITE databases. This revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. Protax‐fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships. [ABSTRACT FROM AUTHOR]

Abstract: Aim: Aphyllophoroid fungi are associated with plants, either using plants as a resource (as parasites or decomposers) or as symbionts (as mycorrhizal partners). In spite of their strong association with plants, it is unknown how much plant distributions determine their biogeographical patterns compared with environmental factors such as climate and human land use. In this study, our aims are to (1) describe the spatial diversity patterns of aphyllophoroid fungi in Europe and (2) identify the factors shaping these patterns. Location: Europe, as well as the adjacent Subarctic to Arctic islands (Greenland, Faroe Islands, Iceland, Svalbard), Palestine and the south‐east coast of the Caspian Sea. Methods: We compiled a dataset consisting of 14,030 fruitbody occurrences of 1,491 aphyllophoroid fungal species from 39 geographical areas (17 countries) belonging to eight biogeographical regions. We assessed the differences in fungal species richness and overall diversity and its nestedness and turnover components across biogeographical regions of Europe, as well as between southern and northern Europe (based on geographical latitude of 50° as threshold). We used cluster and ordination analyses to classify the European aphyllophoroid communities biogeographically and evaluated the importance of climate, host‐tree species, topography and human land‐use intensity in explaining biogeographical variation. Results: The importance of biogeographical regions in determining European aphyllophoroid fungal communities varies for different diversity components. Species richness and nestedness are best explained by plant‐based biogeographical regions, whereas overall beta diversity and species turnover are driven mostly by variation in climate, and nestedness mostly by tree species occupancy. Beta‐diversity patterns of aphyllophoroid fungi do not differ between southern and northern Europe. Main conclusions: At the continental scale, aphyllophoroid fungi are less shaped by historical legacies than vascular plant and animal communities, and trends of overall beta diversity in southern and northern Europe are similar to patterns found for bryophytes. [ABSTRACT FROM AUTHOR]

Estimation of intra- and interspecific interactions from time-series on species-rich communities is challenging due to the high number of potentially interacting species pairs. The previously proposed sparse interactions model overcomes this challenge by assuming that most species pairs do not interact. We propose an alternative model that does not assume that any of the interactions are necessarily zero, but summarizes the influences of individual species by a small number of community-level drivers. The community-level drivers are defined as linear combinations of species abundances, and they may thus represent e.g. the total abundance of all species or the relative proportions of different functional groups. We show with simulated and real data how our approach can be used to compare different hypotheses on community structure. In an empirical example using aquatic microorganisms, the community-level drivers model clearly outperformed the sparse interactions model in predicting independent validation data. [ABSTRACT FROM AUTHOR]

Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we propose Hierarchical Modelling of Species Communities ( HMSC) as a general, flexible framework for modern analysis of community data. While non-manipulative data allow for only correlative and not causal inference, this framework facilitates the formulation of data-driven hypotheses regarding the processes that structure communities. We model environmental filtering by variation and covariation in the responses of individual species to the characteristics of their environment, with potential contingencies on species traits and phylogenetic relationships. We capture biotic assembly rules by species-to-species association matrices, which may be estimated at multiple spatial or temporal scales. We operationalise the HMSC framework as a hierarchical Bayesian joint species distribution model, and implement it as R- and Matlab-packages which enable computationally efficient analyses of large data sets. Armed with this tool, community ecologists can make sense of many types of data, including spatially explicit data and time-series data. We illustrate the use of this framework through a series of diverse ecological examples. [ABSTRACT FROM AUTHOR]