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The maximum entropy (MaxEnt) method has gained widespread use for distribution modelling, mostly because of the practical simplicity offered by the maxent.jar software. Whilst MaxEnt was originally described as a machine learning method, recent studies have shown that the method can be explained in terms of maximum likelihood estimation. This opens for using MaxEnt with new settings and options, such as new model selection and model assessment criteria, and improved user control of the variable selection process. New practical tools are needed to explore the new opportunities and assess if they enhance model performance and ecological interpretability of the models. We present a new conceptual framework, the Modular and functionally Integrated component-based Approach (MIA) framework for practical distribution modelling by which the core components of the DM process are decoupled and then wrapped together more flexibly into component-based functional modules. Computational object-oriented and workflow approaches are integrated with ecological, statistical and modelling theory in order to handle the complexity associated with the full modelling process in a practical way. Objects (variables, functions, results, etc.) are defined according to specific modelling parameters. Properties (e.g., identities and content) are inherited between objects and new objects are created in a flexible and automated, yet traceable way. We operationalise this framework for MaxEnt by the MIA Toolbox (MIAT), a set of flexible, modular R-scripts (available in supplementary appendices) wrapped around maxent.jar and existing R-functions. MIAT covers the full range of options and settings for the maximum likelihood implementation of MaxEnt and provide flexible guidance of users through the DM process. A trail of models of increasing complexity is built to enhance traceability and interpretability, and to suit different modelling purposes. We briefly outline research questions that can be addressed by the MIAT. [ABSTRACT FROM AUTHOR]

Question Why do plants grow where they grow? Prediction of species' occurrence and abundance in relation to the environment is a core aim of ecology, as is understanding the link between environmental stressors and adaptive traits. Community assembly may be viewed as a sequence of filters, sorting species according to their functional traits. We ask if the strength of filtering changes along a strong hydrological gradient? Can we predict species′ relative abundance using few, but biologically relevant traits? And are strongly filtered traits better predictors of community assembly? Location A hydrological gradient from pond to dry limestone pavements on the Island of Öland, South Sweden. Methods Plant community composition and six morpho-physiogical plant traits were measured along a pronounced gradient in water supply and soil depth. The strength of filtering was quantified using a trait dispersion index, while the prediction of species′ relative abundance and importance of individual traits was assessed with the community assembly by trait selection (CATS) model. Results We show that species are filtered by the hydrological environment through the traits root porosity, specific leaf area and resistance to water loss on drying. For individual traits, the strength of filtering waxes and wanes along the gradient. This strongly suggests that the mechanism, through which species are filtered into communities, acts through different traits as environmental conditions change along the gradient. The CATS model predicted 66% of the variation in species' relative abundances using six traits. In general, the traits subject to filtering also were most important in predicting species abundance. Conclusions Few plant traits are exposed to environmental filtering across the entire hydrological gradient, and most traits are strongly filtered only in parts of the gradient (e.g. root porosity in wet soils and water loss on drying on thin dry soils). Evidence for congruence between trait dispersion indices and the CATS model was established, underpinning the importance to plant community assembly of environmental filtering of species through their traits. New functional traits relevant to a specific environmental gradient - and not just some standard traits from a public database - can contribute significantly to resolve how plant communities are assembled. [ABSTRACT FROM AUTHOR]

Soil conditions and microclimate are important determinants of the fine-scale distribution of plant species in the Arctic, creating locally heterogeneous vegetation. We hypothesize that root-associated fungal ( RAF) communities respond to the same fine-scale environmental gradients as the aboveground vegetation, creating a coherent pattern between aboveground vegetation and RAF., We explored how RAF communities of the ectomycorrhizal ( ECM) plant Bistorta vivipara and aboveground vegetation structure of arctic plants were affected by biotic and abiotic variables at 0.3-3.0-m scales. RAF communities were determined using pyrosequencing. Composition and spatial structure of RAF and aboveground vegetation in relation to collected biotic and abiotic variables were analysed by ordination and semi-variance analyses., The vegetation was spatially structured along soil C and N gradients, whereas RAF lacked significant spatial structure. A weak relationship between RAF community composition and the cover of two ECM plants, B. vivipara and S. polaris, was found, and RAF richness increased with host root length and root weight., Results suggest that the fine-scale spatial structure of RAF communities of B. vivipara and the aboveground vegetation are driven by different factors. At fine spatial scales, neighbouring ECM plants may affect RAF community composition, whereas soil nutrients gradients structure the vegetation. [ABSTRACT FROM AUTHOR]

Questions Are Australian Sphagnum bogs compositionally stable or undergoing long-term change in response to grazing legacies or environmental change along a climatic gradient? Are these Sphagnum bogs resilient to discrete fire events, and over what time scales does recovery from disturbance take place? How does fire disturbance influence species composition in the assembly of fire-prone Australian bog communities? Location Alpine and subalpine bogs in mainland eastern Australia (Kosciuszko National Park). Method Full floristic sampling over ca. 50 yr (1960s, 1990, 2005, 2007, 2013) at 11 sites; each site sampled with 25 quadrats (0.1 m2) haphazardly placed during each successive survey. Sites were stratified over alpine and subalpine elevations, in burned and unburned areas. Changes in species composition over space and time were examined with multivariate and univariate analyses. Results The Sphagnum bogs of the subalpine and alpine regions show progressive increases in cover of Sphagnum over the last 40-50 yr. Overall species richness and frequency of dominant woody species declined. These trends were not strongly related to the climate gradient. Fire temporarily reduced the frequency of most species but initial floristic composition was regained a decade after fire. There was fire-dependent variation related to regeneration of hygrophyllous woody species through seed germination and seedling growth in open ground. Conclusion Our results show a degree of community resilience to both grazing and fire, although some observed changes appear directional and the recovery time for grazing was much longer than that for fire. The increase in Sphagnum frequency across subalpine and alpine bogs is likely to reflect progressive recovery of Sphagnum from the grazing era, possibly enhanced by the changing atmosphere. Concurrently, there have been declines in species richness and woody species frequency. The bogs exhibited resilience to infrequent pulse disturbance related to fires, which appear to drive community assembly through cycles of compositional change. [ABSTRACT FROM AUTHOR]

Maximum entropy (MaxEnt) modelling, as implemented in the Maxent software, has rapidly become one of the most popular methods for distribution modelling. Originally, MaxEnt was described as a machine-learning method. More recently, it has been explained from principles of Bayesian estimation. MaxEnt offers numerous options (variants of the method) and settings (tuning of parameters) to the users. A widespread practice of accepting the Maxent software's default options and settings has been established, most likely because of ecologists' lack of familiarity with machine-learning and Bayesian statistical concepts and the ease by which the default models are obtained in Maxent. However, these defaults have been shown, in many cases, to be suboptimal and exploration of alternatives has repeatedly been called for. In this paper, we derive MaxEnt from strict maximum likelihood principles, and point out parallels between MaxEnt and standard modelling tools like generalised linear models (GLM). Furthermore, we describe several new options opened by this new derivation of MaxEnt, which may improve MaxEnt practice. The most important of these is the option for selecting variables by subset selection methods instead of the ℓ1-regularisation method, which currently is the Maxent software default. Other new options include: incorporation of new transformations of explanatory variables and user control of the transformation process; improved variable contribution measures and options for variation partitioning; and improved output prediction formats. The new options are exemplified for a data set for the plant species Scorzonera humilis in SE Norway, which was analysed by the standard MaxEnt procedure in a previously published paper. We recommend that thorough comparisons between the proposed alternative options and default procedures and variants thereof be carried out. [ABSTRACT FROM AUTHOR]

An urgent aim of ecology is to understand how key species relate to climatic and environmental variation, to better predict their prospects under future climate change. The abundant dwarf shrub bilberry (Vaccinium myrtillus L.) has caught particular interest due to its uphill expansion into alpine areas. Species' performance under changing climate has been widely studied using the climatic space‐for‐time approach along elevation gradients, but potentially confounding, local environmental variables that vary along elevation gradients have rarely been considered. In this study, performed in 10 sites along an elevation gradient (200–875 m) in W Norway, we recorded species composition and bilberry performance, both vegetative (ramet size and cover) and reproductive (berry and seed production) properties, over one to 4 years. We disentangled effects of local environmental variables and between‐year, climatic variation (precipitation and temperature), and identified shared and unique contributions of these variables by variation partitioning. We found bilberry ramet size, cover and berry production to peak at intermediate elevations, whereas seed production increased upwards. The peaks were less pronounced in extreme (dry or cold) summers than in normal summers. Local environmental variables explained much variation in ramet size and cover, less in berry production, and showed no relation to seed production. Climatic variables explained more of the variation in berry and seed production than in ramet size and cover, with temperature relating to vegetative performance, and precipitation to reproductive performance. Bilberry's clonal growth and effective reproduction probably explain why the species persists in the forest and at the same time invades alpine areas. Our findings raise concerns of the appropriateness of the climatic space‐for‐time approach. We recommend including both climatic and local environmental variables in studies of variation along elevation gradients and conclude that variation partitioning can be a useful supplement to other methods for analysing variation in plant performance. [ABSTRACT FROM AUTHOR]

Questions What are the most important factors explaining present-day variation in species composition in a glacier foreland? Does the rate of species compositional change in glacier forelands decelerate through primary succession? How do data set properties and analytic methods influence our understanding of glacier foreland successional dynamics? Location Nigardsbreen glacier foreland, western Norway. Methods We sampled the species composition and recorded 21 explanatory variables in 74 plots, distributed on eight classes of terrain age (dated moraines). Gradients in species composition found using global non-metric multidimensional scaling ( GNMDS) ordination were interpreted with split-plot generalized linear models. Yearly succession rates were calculated from plot positions along a vector of maximum compositional change related to terrain age in the interpreted GNMDS ordination. Results We interpreted the main gradient in species composition as being related to a complex gradient with soil moisture and soil nutrients as primary constituents. Terrain age contributed to the second most important gradient. Succession rates were nonlinear with time. Terrain age explained variation in species composition only when plots from the two youngest terrain age classes were retained in the data set. Conclusions In contrast to the majority of studies of glacier foreland successions performed so far, we find that terrain age is not the principal factor that explains present-day variation in species composition. Instead, local environmental variables are the main determinants of species composition. This result emphasizes the importance of taking environmental gradients into account when variation in glacier foreland vegetation is studied. The limited importance of terrain age in our study is interpreted as likely due to this glacier foreland being situated below the tree line, the relatively long distance between the bulk of the studied foreland and the glacier snout, and inclusion of few plots from young terrain in our data set. The non-linearity of succession rates with time implies that a linear time-since-deglaciation variable is inappropriate for constrained ordination of glacier foreland vegetation. [ABSTRACT FROM AUTHOR]

Aim The rare lichen species Staurolemma omphalarioides is known mainly from the lowlands and coastal areas of the Mediterranean region but has also been found in coastal parts of central Norway. Despite extensive search efforts by experts for more than half a century, the species has been found nowhere in the gap. Our aim is to identify the most plausible explanation for this anomalous distribution by combining genetic analysis of archived specimens with distribution modelling. Location Europe, western Middle East and North Africa (but mainly the Mediterranean and Atlantic floristic regions). Methods We used multi-locus DNA sequencing of archived specimens and phylogenetic and network analyses to reveal potential genetic lineages within S. omphalarioides. We used georeferenced specimens and bioclimatic variables to model the distributions of the species and two genetic lineages, and to find the main environmental correlates of the distributions. Results Our phylogeographical results show that S. omphalarioides contains genetic variation that correlates with geographical distance, although with a few shared haplotypes across disjunct ranges. Distributions of the species as well as the two genetic lineages are non-random. Distribution models predict occurrences of the species as well as one of its genetic lineages outside the current range of the species. Main conclusions Our results indicate that neither the species nor its component genetic lineages have reached their potential distributions. Shared haplotypes across disjunct distributions, and absence from regions with suitable refugial habitats along the Atlantic coast of Western Europe, support long-distance dispersal, rather than vicariance, as the primary cause for the current distribution of the species. [ABSTRACT FROM AUTHOR]

Aims Cliff communities tend to be compositionally simple but taxonomically diverse at the phylum/division level. As a result, they provide a setting for examining the responses of distinct phyla (e.g. Anthophyta, Bryophyta and lichens), species within these phyla and communities comprised of these phyla, to the same environmental gradients. Our aims were both descriptive and hypothesis-driven. We sought to identify major community shifts across water-substrate gradients in a poorly studied system (inland North American cliffs), while considering extant hypotheses concerning the relationships of organisms to environments at different taxonomic scales. Location Sub-alpine cliffs in northeastern Yellowstone National Park. Methods Cliff faces on two mountains were blocked at nine waterfalls. At each block, community composition was recorded from random samples obtained for three levels of water availability (xeric, mesic and hygric) on two substrates (limestone and andesite). Patterns of cover and richness were compared using Friedman's Rank F-tests. Community patterns were discerned using permutation MANOVAs, ordinations, and cluster analyses. Results Phyletic composition varied in response to water availability. In general, lichens dominated dry sites, while vascular plants dominated wet sites. Anthophyta was the most narrowly specialized phylum, and Bryophyta was the most generalized. Beta diversity was higher at drier sites, due to the dominance of the diverse lichen group. As a result, communities on lime and andesitic substrates were indistinguishable in hygric environments, but significantly different at drier sites. This may have occurred because, while water is limiting for neither substrate in hygric environments, andesites are more likely to absorb and store atmospheric water in drier environments. Indicator species analyses identified 27 distinct species distinguishing water and substrate conditions, or their interactions. Conclusions Our experimental design uniquely accounted for extraneous variables in its examination of water and substrate effects on cliff communities. Water strongly controlled community composition both among and within phyla through both direct effects and interactions with substrate. [ABSTRACT FROM AUTHOR]

Questions We tested the relationship between total cover, species richness and composition of epiphytic lichens on trunks of Betula pubescens and ecosystem retrogression (i.e. prolonged absence of major disturbance). We then investigated how the relationships changed when also accounting for tree-scale factors (aspect, height and bark characteristics) and ecosystem-scale factors (e.g. light transmission, tree species diversity and soil fertility). Location Thirty forested islands in northern Sweden differing in fire history, which collectively represent a retrogressive chronosequence spanning ca. 5000 yr. Results Total lichen cover responded negatively to long-term absence of major disturbance, but only at exposed positions on the tree trunk, indicating that lichen cover on substrates with more favourable microclimates is less susceptible to environmental change at the ecosystem scale. Further, although there was no overall effect of island size on lichen species richness, we did find a significant interactive effect between island size and height on trunk on species richness. This emerged because species richness decreased with retrogression for lichen communities at breast height, but showed a hump-shaped response to retrogression at the trunk base. Shifts in ecosystem properties with retrogression explained some of the variation in lichen community composition, but most of the variation could be explained by tree-scale factors, notably height on the trunk. Conclusions While it has frequently been shown that lichens increase in abundance and richness during the first two or three centuries of succession, our results highlight that over a much longer time scale, encompassing soil aging and declining soil fertility, the lichen flora can be negatively affected. However, these effects are heavily mediated by tree-scale factors. These changes in the lichen community may be of potential importance for ecosystem processes and higher trophic level interactions driven by lichen communities. [ABSTRACT FROM AUTHOR]

Questions How much dead wood in the form of dead branches attached to living trees, compared to other types of dead wood, is present in managed boreal forests? Which lichen species grow on this substrate? Location Two areas of managed coniferous forest in southern Sweden. Methods We surveyed the numbers and surface areas of attached dead branches and all other major types of dead wood in 80 stands of managed coniferous forests of various ages and wooded mires. In total, we recorded 5546 dead branches attached to 480 living trees. We also recorded the species of lichens growing on 812 of these dead branches. Results The surface area of attached dead branches was generally of the same magnitude as that of all other wood types combined. Of the 46 lichen species identified growing on dead branches, 42 were generalist species characteristic of conifer bark and four were wood-dependent specialists. We found no significant difference in lichen species composition between dead branches of Picea abies and Pinus sylvestris, and only small differences in species composition between different stand types and between study areas. There were no clear differences in species composition between the study areas. Conclusions Although overlooked, attached dead branches constitute a significant proportion of all dead wood available in boreal forests. However, the lichen communities on these branches mainly consist of generalist species. Lichens on attached dead branches thus do not seem to contribute strongly to the species pool of wood-dependent lichens in managed boreal forests. [ABSTRACT FROM AUTHOR]

Questions What is the relative importance of topographic (elevation), edaphic (soil salinity, nitrogen and particle size) and hydrologic (estuarine river flow) gradients for variation in tidal wetland plant composition and diversity? Location Four Oregon estuaries: a marine-dominated lagoon, two tidal-driven bays, and a river-dominated site. Methods We surveyed species presence, cover and richness; and environmental factors (soil salinity, grain size, soil nitrogen and elevation) in plots in marsh and swamp. We assessed patterns of community structure and the relative importance of environmental gradients with hierarchical partitioning, ordination, species accumulation curves and path analysis. Results The relative importance of measured environmental gradients on plant occurrence differed by species. Soil salinity or elevation explained the most variation in the majority of common species. Estuarine hydrology, soil nitrogen and soil clay content were usually of secondary or minor importance. Assemblage composition and species richness varied most strongly with tidal elevation. Local soil salinity also affected composition, but differences in estuarine hydrology had comparatively less effect on composition and richness. Higher-elevation wetlands supported larger species pools and higher plot-level richness; fresher wetlands had larger species pools than salt marsh but plot-level richness was relatively invariant to differences in soil salinity. Conclusions Elevation and salinity tended to exert more influence on the vegetation structure of tidal wetlands than estuarine hydrology or other edaphic variables. With relative sea-level rise expected to increase both flooding intensity and salinity exposure in future wetlands, global climate change may lead to changes in species distributions, altered floristic composition and reduced plant species richness. [ABSTRACT FROM AUTHOR]

Questions As changing wildfire regimes modify North American deserts, can fires of greater severity and frequency negatively impact the recovery of native bryophyte communities, which are not adapted to such disturbances? Does post-fire recovery result from the survival of existing surface plants, dormant propagules in sub-surface soil banks (dispersal in time) or aerial immigration into burned sites (dispersal in space)? Do wildfires negatively affect the survival of propagules in bryophyte soil banks? Location Continental arid shrublands, Mojave Desert, southwestern US. Methods We characterized bryophyte communities along a post-fire chronosequence spanning three decades across sites where fires had different severities, ages and potential fuels. Three community profiles (surface, soil and aerial) were surveyed with a combination of on-site surveys and emergence germination techniques. We tested for differences in beta diversity, species composition and richness with PERMDISP, PERMANOVA and linear mixed models, respectively. Results Burn severity was associated with differences in beta diversity, species composition and richness, while burn age was associated only with different composition and richness. No effect of potential fuel availability was found. More variation in composition was explained by significant differences among profiles than by other fire attributes. Species richness (but not beta diversity) was higher in soil profiles than in aerial spore rain or existing surface communities. Soils from the oldest and least severe burns had a greater number of species than soils from recent and more severe burns. Conclusions Bryophyte soil banks are common elements of desert soils that facilitate post-disturbance recovery of communities, but soil banks are themselves threatened by the intensifying frequency and severity of wildfires in North American deserts. Recovery of desert bryophyte communities seems to begin (but not necessarily conclude) within 30 yr after wildfires. In the near future, communities may become perturbed from historical patterns as contemporary fire regimes undergo extensive changes. [ABSTRACT FROM AUTHOR]

Questions Do mortality rates of boreal bryophytes associated with leaf litter burial vary with degree of shelter on forest floor microsites in spruce-dominated forests? Do erect and prostrate species respond similarly? What is the relative importance of deciduous leaves (from aspen and birch) vs conifer needles as bryophyte mortality agents? Location Boreal spruce forests of central Sweden. Methods A transplant study examining mortality was set up with four different bryophyte species: two creeping, prostrate liverworts ( Calypogeia integristipula and Lepidozia reptans) and two more erect mosses ( Rhytidiadelphus triquetrus and Hylocomiastrum umbratum). We tested for differences in mortality rates associated with leaf litter burial in three microhabitats differing in degree of shelter on the forest floor, i.e. sheltered (large boulders, tree bases of spruce) and unsheltered (open forest floor). Results After two growing seasons, 12.7% of the bryophyte transplants (40 out of 316, of which 37 transplants were prostrate liverworts) were dead, presumably due to litter burial. These two prostrate liverworts displayed significantly higher mortality rates close to boulders and at tree bases compared to unsheltered forest floors. Furthermore, although only comprising a small portion of the canopy (<10%), deciduous litter accounted for 53% of all transplants that were buried by litter, compared to 47% for conifer needle litter. Conclusion We find fine-scale spatial patchiness in the responses of bryophytes to litter fall. Mortality of prostrate liverworts associated with litter burial varies among microhabitats on the forest floor, with significantly higher mortality at sheltered microsites (here exemplified by boulders and tree bases) compared to erect moss species. Bryophytes close to microtopographic structures (e.g. boulders and trees) are more strongly exposed to litter burial, but such structures can also function as refuges under disturbance events such as clear-cuts and windthrows. In addition, they may contain convex surfaces that accumulate less litter than flat or convex forest floor surfaces. The observed large effect of litter burial associated with bryophyte mortality, and the variation among microhabitats and species growth forms, suggest that incorporation of litter fall is of vital importance for our understanding of the dynamics of forest bryophyte communities. [ABSTRACT FROM AUTHOR]

Aims Our objective was to investigate how the after-effects of a heatwave interacted with nutrient addition in affecting the vegetation of an alpine mire. We also aimed to assess if the responses of vegetation to the environmental changes differed between mire habitats. Location A mire in the Dolomites (southeastern Alps, Italy, 1800 m a.s.l.). Methods We carried out an 8-yr (2002-2009) experiment of nutrient addition in an alpine mire that experienced, in summer 2003, an unprecedented heatwave. The cover of vascular plants and mosses was assessed non-destructively and the presence of all vascular plant and moss species was recorded in 60 plots. Results Interacting effects of the heatwave and experimental fertilization brought about profound changes in the vegetation of the mire. Patterns of change varied considerably between two habitats (hummocks and lawns). In the short term (2003-2005), the 2003 heatwave triggered a change in vegetation structure and PFT cover, with vascular plants expanding at the expense of mosses in both habitats. In the mid-term (2005-2009), moss cover increased in hummocks because Sphagnum mosses recovered and non- Sphagnum mosses expanded, especially under N addition. Conversely, in lawns vascular plants expanded while mosses did not recover. These trends were strengthened when N was added with no concomitant P addition. A decline in species richness was observed in lawns, most likely due to stronger interactions among species. Conclusions Hummocks have a greater ability than lawns to recover from extreme climatic events under higher levels of N influx. Conversely, a persistent increase in vascular plant cover at the expense of moss cover in lawns may jeopardize the carbon sink function of lawn habitats. [ABSTRACT FROM AUTHOR]

Questions Are topography-based forest types floristically consistent between sites in central Amazonia? Do broad landform and geological features control site-specific edaphic and floristic variation and therefore obfuscate the floristic classification based on local topographical classes? Is model-based clustering a useful tool for floristic classification? Location Non-inundated forest of central Amazonia, north of the Amazon River. Methods We analysed species presence-absence of a group of terrestrial monocot herbs ( Zingiberales) in 123 plots (250 × 2 m) concentrated in three sites of non-inundated forests. Distances between plots were 1-140 km. Floristic patterns were extracted by dimensionality reduction using geodesic floristic distance. We applied a model-based cluster analysis ( MC) coupled with the Bayesian information criterion to determine the best floristic classification. We used geometric and non-geometric internal evaluators to compare the performance of MC to the agglomerative hierarchical clustering method UPGMA. The floristic clusters were tested for differences in edaphic and topographic features. Landform-geological classes were defined based on geological maps and a digital elevation model. We used the Kappa index and ANOVA to evaluate the agreement between landform-geological classes, floristic clusters and environmental features. Results The best MC solution found four floristic clusters. Differences in soil chemical properties, which were linked with lithological classes and broad land-form features, explained abrupt floristic changes and floristic differences between the same topographical habitats of different sites. Within poor soils, floristic classes defined by elevation along the soil catena (upland and valley forests) were fuzzy. Valley sandy forest was not floristically consistent across sites due to subtle edaphic variation. Using a non-geometric internal evaluator, MC coupled with geodesic floristic distance estimation performed better overall than UPGMA. Main conclusions Geological classes defined by lithology and broad landform features control the major variation of edaphic and floristic patterns in central Amazonia. MC proved to be a useful method to classify and interpret floristic patterns. Revised vegetation maps that account for lithology, broad land-form features and edaphic conditions would therefore be a better proxy for regional floristic variation than the presently used simple classes based on position along the catena. [ABSTRACT FROM AUTHOR]

Several eukaryotic symbioses have shown to host a rich diversity of prokaryotes that interact with their hosts. Here, we study bacterial communities associated with ectomycorrhizal root systems of Bistorta vivipara compared to bacterial communities in bulk soil using pyrosequencing of 16S rRNA amplicons. A high richness of Operational Taxonomic Units (OTUs) was found in plant roots (3,571 OTUs) and surrounding soil (3,476 OTUs). The community composition differed markedly between these two environments. Actinobacteria, Armatimonadetes, Chloroflexi and OTUs unclassified at phylum level were significantly more abundant in plant roots than in soil. A large proportion of the OTUs, especially those in plant roots, presented low similarity to Sanger 16S rRNA reference sequences, suggesting novel bacterial diversity in ectomycorrhizae. Furthermore, the bacterial communities of the plant roots were spatially structured up to a distance of 60 cm, which may be explained by bacteria using fungal hyphae as a transport vector. The analyzed ectomycorrhizae presents a distinct microbiome, which likely influence the functioning of the plant-fungus symbiosis. [ABSTRACT FROM AUTHOR]

Question Does the abundance of keystone forest floor species change in response to changes in the forest structure? Location Sweden Methods We used data from the Swedish National Forest Inventory to investigate changes in the abundance of three common species, as well as the total abundance of all understorey vascular plants (the field layer) in forests in the boreal and temperate parts of Sweden. GLMs and GAMs were used to relate species abundance and temporal changes in abundances to forest structure and forest structural change. Results Productivity, measured as the site index, was the most important determinant of individual species' abundance. The volume of Picea abies, the density of tree stems and forest age were among the most important forest structural variables. We found that the dwarf shrub Vaccinium myrtillus, the narrow-leaved grasses (mainly Avenella flexuosa) and the total field layer cover decreased in boreal Sweden from 1994 through 2010 and that these changes coincided with an increase in forest density and with a reduction in forest age. Conclusions Changes in Swedish forests to higher tree layer density and younger age appear to contribute significantly to current changes in forest floor vegetation. The use of more intensive thinning practices to reduce the total density of the forest and to increase the proportion of broad-leaved tree species and Pinus sylvestris would favour the forest floor species in this study. Moreover, increasing forest age (i.e. the length of rotation periods) might favour V. myrtillus in particular, for which the time since disturbance is important for the recovery of pre-disturbance abundance. However, increased thinning intensity and forest age will reduce the potential for wood production, implying a trade-off between production of wood and maintenance of well-developed forest floor vegetation. [ABSTRACT FROM AUTHOR]

Although bryophytes are a dominant vegetation component of boreal and alpine ecosystems, little is known about their associated fungal communities. HPLC assays of ergosterol (fungal biomass) and amplicon pyrosequencing of the ITS2 region of rDNA were used to investigate how the fungal communities associated with four bryophyte species changed across an elevational gradient transitioning from conifer forest to the low-alpine. Fungal biomass and OTU richness associated with the four moss hosts did not vary significantly across the gradient ( P > 0.05), and both were more strongly affected by host and tissue type. Despite largely constant levels of fungal biomass, distinct shifts in community composition of fungi associated with Hylocomium, Pleurozium and Polytrichum occurred between the elevation zones of the gradient. This likely is a result of influence on fungal communities by major environmental factors such as temperature, directly or indirectly mediated by, or interacting with, the response of other components of the vegetation (i.e. the dominant trees). Fungal communities associated with Dicranum were an exception, exhibiting spatial autocorrelation between plots, and no significant structuring by elevation. Nevertheless, the detection of distinct fungal assemblages associated with a single host growing in different elevation zones along an elevational gradient is of particular relevance in the light of the ongoing changes in vegetation patterns in boreal and alpine systems due to global climate warming. [ABSTRACT FROM AUTHOR]

Spoil heaps of surplus rock from hydropower tunnel construction negatively impact alpine landscapes unless restored. Such spoil heaps have been created for more than 100 years, but we still lack knowledge about the relative importance of compensatory mitigation (seeding and fer-tilization), spoil-heap construction method, local environ-mental factors, and regional climatic factors for restoration success. We studied the species composition of 19 alpine spoil heaps in Western Norway and their undisturbed surroundings using ordination and statistical modeling. Substrate grain size was the principal factor explaining differences in species composition between spoil heaps and their surroundings. Soil characteristics, that is, organic matter content and pH, and reutilization of topsoil were also important. Seeding and fertilization had negligible effects on restoration success. Slow recovery was observed for total vegetation cover and species richness of vascu-lar plants and lichens while bryophyte cover recovered rapidly. Lower bryophyte cover and bryophyte and vas-cular plant species richness on older than on younger spoil heaps indicated recent changes in spoil-heap construction practices that favor plant colonization. Our results indi-cate that spoil-heap design is more important for restora-tion success than compensatory mitigation. We therefore suggest spoil heaps designed with a fine-grained top sub-strate preferably from stockpiled local topsoil, with uneven surface topography that mimics natural topographic vari-ation, and recommend discontinuation of seeding and fertilization. [ABSTRACT FROM AUTHOR]

Question It is an old notion that pattern and process are linked in plant communities. Spatial pattern may, therefore, be a valuable indicator of community processes in space and time. Obviously, spatial aggregation may arise as the result of clonal propagation and short-distance dispersal of seeds, but it is less well known how variation in the spatial aggregation links to plant community processes and to community responses to environmental stresses, such as eutrophication and acidification. We hypothesize that intra-specific spatial aggregation may prove a useful indicator of structure and function in plant communities and, more specifically, that spatial aggregation in semi-natural grasslands will increase with increasing eutrophication and acidification. Methods The intra-specific spatial aggregation at the level of the community was estimated using pin-point data for all observed species at a site with a single parameter using the PÓlya-Eggenberger distribution. Results Intra-specific spatial aggregation correlates with biotic and abiotic gradients in the form of pH, vegetation height, species richness and species composition. The results support the hypothesis that eutrophication and acidification not only cause loss of species, but also lead to increasing intra-specific aggregation of the component species. However, there was no significant effect of N deposition, which suggests that residual nutrients from former cultivation as well as sulphur deposition override the effect of N deposition on pH and productivity in Danish acidic grasslands. Conclusion We suggest that intra-specific spatial aggregation may be used as an indicator of structure and function in plant communities and as a possible early warning indicator of future species loss. [ABSTRACT FROM AUTHOR]

Jacobsen, J. A., Hansen, L. P., Bakkestuen, V., Halvorsen, R., Reddin, D. G., White, J., Ó Maoiléidigh, N., Russell, I.C., Potter, E. C. E., Fowler, M., Smith, G. W., Mork, K. A., Isaksson, A., Oskarsson, S., Karlsson, L., and Pedersen, S. 2012. Distribution by origin and sea age of Atlantic salmon (Salmo salar) in the sea around the Faroe Islands based on analysis of historical tag recoveries. – ICES Journal of Marine Science, 69: 1598–1608.A database of 2651 tags applied to Atlantic salmon (Salmo salar) smolts in 13 countries or jurisdictions and recovered in the Faroes longline salmon fishery from 1968 to 2000 was analysed for geographic distribution and origin of the salmon captured with respect to differences in sea age, season of the fishery, and hydrographic features in the Faroes area. The results indicated that salmon were not distributed randomly in the Faroes area by fishing season, sea age, or country of origin. The distribution of salmon in the Faroes zone partly depends on their geographic origin; salmon from countries in the northern European stock complex were distributed significantly farther northeast than those from countries in the southern European stock complex. Furthermore, the proportion of tag recoveries from southern European countries was higher in autumn, and the proportion recovered from northern European countries higher in winter. The apparent temporal and spatial segregation of stocks of different origin suggests that there may have been differential exploitation on these stocks, which provides information that could inform fishery management with regard to temporal and/or spatial fishery options for the Faroes commercial salmon fishery should it recommence in future. [ABSTRACT FROM PUBLISHER]

In terrestrial ecosystems, fungi are the major agents of decomposition processes and nutrient cycling and of plant nutrient uptake. Hence, they have a vital impact on ecosystem processes and the terrestrial carbon cycle. Changes in productivity and phenology of fungal fruit bodies can give clues to changes in fungal activity, but understanding these changes in relation to a changing climate is a pending challenge among ecologists. Here we report on phenological changes in fungal fruiting in Europe over the past four decades. Analyses of 746,297 dated and geo-referenced mushroom records of 486 autumnal fruiting species from Austria, Norway, Switzerland, and the United Kingdom revealed a widening of the annual fruiting season in all countries during the period 1970-2007. The mean annual day of fruiting has become later in all countries. However, the interspecific variation in phenological responses was high. Most species moved toward a later ending of their annual fruiting period, a trend that was particularly strong in the United Kingdom, which may reflect regional variation in climate change and its effects. Fruiting of both saprotrophic and mycorrhizal fungi now continues later in the year, but mycorrhizal fungi generally have a more compressed season than saprotrophs. This difference is probably due to the fruiting of mycorrhizal fungi partly depending on cues from the host plant. Extension of the European fungal fruiting season parallels an extended vegetation season in Europe. Changes in fruiting phenology imply changes in mycelia activity, with implications for ecosystem function. [ABSTRACT FROM AUTHOR]

The aim of this study is to examine the effect of individual canopy tree on the species composition and abundance of understorey vegetation in subtropical forests, by applying a model for tree influence on understorey vegetation of boreal spruce forests developed by Økland et al. (1999), according to the principles of Ecological Field Theory (EFT). The study was based upon five vegetation data sets, each with two subsets (vascular plants species and bryophytes species) from subtropical forests in south and southwest China. Optimal value of tree influence model parameters was found by maximizing the eigenvalue of a Constrained Ordination (CO) axis, obtained by use of the EFT-based tree influence index as the only constraining variable. One CO method, Redundancy Analysis (RDA), was applied to five vegetation data sets. The results showed that the optimal EFT tree influence models generally accounted for only a small part of the variation in species composition (the eigenvalues of RDA axes were low, amounted to 1-10% of total inertia). The higher eigenvalue-tototal- inertia ratio with RDA was interpreted as due mainly to the low species turnover along the tree influence gradient. Vascular plants and bryophytes species differed with respect to optimal parameters in the tree influence model, especially in a conifer dominated forest. Compositional turnover associated with tree influence indices was also generally low, although somewhat varies among study areas. Thus, it was concluded that single-tree EFT models may have limited suitability for studied subtropical forests; different optimal parameters in the tree influence model obtained for vascular plants and bryophytes species in two studied areas indicates that subtropical trees may impact vascular plants and bryophytes species in different ways; and trees may influence the understorey species composition more in a collective manner than through the influence of single individuals in studied subtropical forests. [ABSTRACT FROM AUTHOR]

Aim Theoretical models predict nurse plant facilitation enhances species richness by ameliorating stressful environmental conditions and expanding distributional ranges of stress-intolerant species into harsh environments. We studied the role of nurse facilitation on the recruitment of perennial plants along an arid scrubland-temperate rain forest boundary to test the following predictions: (1) nurse shrub canopy increases seedling abundance and species richness along the rain forest-scrubland boundary; (2) scrubland species are less dependent on facilitative interactions than temperate rain forest species, especially at the moister, upper end of the gradient. Location Bosque Fray Jorge National Park, north-central Chile, South America (30° 39′ S - 71° 40′ W). Methods We examined seedling abundance and species richness of perennial plants in the open and under different types of patches that may facilitate species recruitment (living shrubs, dead shrubs, perennial grasses and trees) along an arid scrubland-temperate rain forest boundary. To assess whether the potential role of the shrub canopy on seedling survival in the scrubland and forest differs, we designed a 2 × 2 factorial field experiment with shrub canopy (under shrub or open patch) and small mammal herbivory (access or closed) as factors. At both sides of the scrubland-forest gradient, we planted young seedlings of scrubland ( Senna cumingii) and forest ( Myrceugenia correifolia and Griselinia scandens) species under the four treatment combinations. Results Nurse living shrubs increased seedling abundance and diversity. Under living shrubs, the number of recruiting species was 100% and 30% larger than in open patches of the arid scrubland and temperate rain forest patches, respectively. Seedling abundance was 60% and 300% larger under living shrubs compared to open patches of the scrubland and the temperate rain forest, respectively. Despite their low cover, dead shrubs were particularly important for recruitment of young seedlings in the scrubland. Seedlings of forest species were extremely rare. The field experiment demonstrated the importance of nurse plant facilitation for the survival of the forest species at both sides of the boundary. In contrast, scrubland species were less dependent on nurse plants than forest and intermediate forest-scrubland species. Conclusions Our results show that facilitative interactions increase seedling abundance and species richness along an arid scrubland-temperate rain forest boundary, notably by enhancing seedling establishment of forest species. Despite increasing nurse shrub-seedling competition in the arid scrubland, shrubs have a net positive effect on plant community diversity. [ABSTRACT FROM AUTHOR]

Questions How are the fine-scale spatial distribution and abundance of epiphytic lichens explained by factors related to environmental filtering and local dispersal? Are spatial distribution and abundance explained by the same underlying factors across sites for: (1) each species separately; or (2) groups of species with similar dispersal strategies? Location Ten lowland deciduous forests at the southwest coast of Norway (60ºN, 5ºE). Methods We investigated the spatial distribution and abundance, given occurrence, of 15 epiphytic Lobarion lichens in ten forest sites: six 1800-m2 study sites and four 5000-m2 study sites. We divided each site into a grid of 1-m2 sampling units, marked all trees and recorded the abundance of individual lichen species. We assessed the relative impact of factors related to environmental filtering and local dispersal for each lichen species using multiple regressions and variation partitioning. Finally, to compare the results between species and between sites, we applied linear mixed effect models. Results We found that the occurrence of lichen species on a tree is explained primarily by factors related to environmental filtering. The abundance of lichen species that occur on a tree is explained by a combination of environmental filtering and local dispersal, but the relative importance of these factors was found to vary greatly between sites. We found no differences in this respect between species with different dispersal strategies. Conclusions Our results indicate that both environmental filtering and local dispersal dynamics are important processes explaining the distribution and abundance patterns of Lobarion lichens at fine spatial scales. However, spatial variations in environmental factors within sites interact with propagule distributions to produce a range of inter-site variation. Accordingly, the relative importance of these two structuring mechanisms varies among sites, particularly in the case of abundance patterns. Since single-site patterns are not readily generalized, we emphasize the importance of multiple study sites for evaluation of the role of different processes in shaping the spatial distribution patterns of species. [ABSTRACT FROM AUTHOR]

We investigated changes in the root-associated fungal communities associated with the ectomycorrhizal herb Bistorta vivipara along a primary succession gradient using 454 amplicon sequencing. Our main objective was to assess the degree of variation in fungal richness and community composition as vegetation cover increases along the chronosequence. Sixty root systems of B. vivipara were sampled in vegetation zones delimited by dated moraines in front of a retreating glacier in Norway. We extracted DNA from rinsed root systems, amplified the ITS1 region using fungal-specific primers and analysed the amplicons using 454 sequencing. Between 437 and 5063 sequences were obtained from each root system. Clustering analyses using a 98.5% sequence similarity cut-off yielded a total of 470 operational taxonomic units (OTUs), excluding singletons. Between eight and 41 fungal OTUs were detected within each root system. Already in the first stage of succession, a high fungal diversity was present in the B. vivipara root systems. Total number of OTUs increased significantly along the gradient towards climax vegetation, but the average number of OTUs per root system stayed unchanged. There was a high patchiness in distribution of fungal OTUs across root systems, indicating that stochastic processes to a large extent structure the fungal communities. However, time since deglaciation had impact on the fungal community structure, as a systematic shift in the community composition was observed along the chronosequence. Ectomycorrhizal basidiomycetes were the dominant fungi in the roots of B. vivipara, when it comes to both number of OTUs and number of sequences. [ABSTRACT FROM AUTHOR]

n improved understanding of population-level consequences of grazing on plants can be facilitated by an assessment of grazing effects on all stages in the life-cycle. In this study, 6 years of demographic data for three populations of the perennial herb Geranium sylvaticum were analysed. We examined the effects of sheep grazing (high sheep density, low sheep density and no sheep) and interannual climatic variability on vital rates and population growth rates (λ). Grazing did not affect survival or flowering rates, but reduced rates of growth and increased rates of clonal reproduction. At the population level, high contributions from retrogression and clonal reproduction buffered reduced rates of growth and stasis, and no consistent differences in λ between populations exposed to different sheep densities were found. Instead, large between-year variability in λ, independent of sheep density, was detected, related to variation in the local summer climate. The results indicated, however, that grazing effects on λ were more severe in unfavourable than in normal years. Our study highlights that increased clonal reproduction rates functioned as a tolerance mechanism towards grazing in this herb, which forms a mechanism to explain how moderate population responses to grazing in some herbs can arise. [ABSTRACT FROM AUTHOR]

We explored the effect of varying pseudo-absence data in species distribution modelling using empirical data for four real species and simulated data for two imaginary species. In all analyses we used a fixed study area, a fixed set of environmental predictors and a fixed set of presence observations. Next, we added pseudo-absence data generated by different sampling designs and in different numbers to assess their relative importance for the output from the species distribution model. The sampling design strongly influenced the predictive performance of the models while the number of pseudo-absences had minimal effect on the predictive performance. We attribute much of these results to the relationship between the environmental range of the pseudo-absences (i.e. the extent of the environmental space being considered) and the environmental range of the presence observations (i.e. under which environmental conditions the species occurs). The number of generated pseudo-absences had a direct effect on the predicted probability, which translated to different distribution areas. Pseudo-absence observations that fell within grid cells with presence observations were purposely included in our analyses. We discourage the practice of excluding certain pseudo-absence data because it involves arbitrary assumptions about what are (un)suitable environments for the species being modelled. [Copyright &y& Elsevier]

The article discusses results of a study that examines the relationships between morphological and ecological characteristics, time of fruiting and climate factors of autumn-fruiting species of mushroom-forming fungi, Agaricomycetidae in Norway. The study material and methods are discussed, including the use of data obtained from the Norwegian Mycological Database, University of Oslo. The study showed a significant relationship between the spore size and the day of fruiting of autumn-fruiting mushrooms.

Abstract: Human disturbances in the alpine region can have long-lasting ecosystem effects because biological recovery in harsh environments proceeds slowly. As a by-product of the exploitation of hydroelectricity, surplus masses from tunnel excavations are deposited as spoil heaps in the alpine landscape. The typical management goal for such spoil heaps is that their species composition converges towards that of their undisturbed surroundings. At present we lack knowledge of the rate as well as the direction of these successions. We examined the species composition of five alpine spoil heaps in western Norway at two points in time, after 6–16, and 24–34 years of succession, with regard to vegetation cover, species richness, species composition and soil conditions. We also compared the vegetation of spoil heaps with that of their surroundings. After ca. 30 years, bryophyte and lichen cover and species richness were similar to those of their surroundings, while cover of vascular plants and species richness recovered more slowly. The vegetation development of spoil heaps appears safe-site limited rather than dispersal limited. Topsoil development was slow, but some accumulation of organic matter was observed. The species composition followed a successional trajectory in direction of the vegetation of the surroundings. Estimated linear successional rates indicate that 35–48 years are needed from construction of spoil heaps till a species composition more or less similar to their surroundings has been reached. However, these estimates are likely to be over-optimistic because successional rates tend to decrease with time. Based on our results we propose three changes to the current spoil-heap construction practice that will improve their restoration: (1) to increase surface unevenness, by which the number of safe sites will increase and germination and establishment success will be enhanced; (2) to increase substrate variability, by adding more of fine-grained materials more species will establish in shorter time; and (3) to use seed from local sources or to let the spoil heaps regenerate naturally. [Copyright &y& Elsevier]