Wood-inhabiting fungi with tight associations with other species have declined as a response to forest management

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…

Contrasting Effects of Chronic Anthropogenic Disturbance on Activity and Species Richness of Insectivorous Bats in Neotropical Dry Forest

For prioritizing conservation actions, it is vital to understand how ecologically diverse species respond to environmental change caused by human activity. This is particularly necessary considering that chronic human disturbance is a threat to biodiversity worldwide. Depending on how species tolerate and adapt to such disturbance, ecological integrity and ecosystem services will be more or less affected. Bats are a species-rich and functionally diverse group, with important roles in ecosystems, and are therefore recognized as a good model group for assessing the impact of environmental change. Their populations have decreased in several regions, especially in the tropics, and are threatene…

Ten principles for conservation translocations of threatened wood-inhabiting fungi

Abstract Unlike for many other organism groups, conservation translocations of fungi are still rare. Encouraged by recent successful translocations, there is a growing interest in applying this conservation tool to threatened wood-inhabiting fungi. When combined with other conservation or restoration measures, translocation can be an effective measure for preventing further population decline in the short term, and species extinctions in the long term. Translocations can be appropriate for rare and specialist fungal species that occur as small local populations in isolated patches across fragmented landscapes, where there is a low likelihood of successful dispersal between distant host tree…

Spatial Memory Drives Foraging Strategies of Wolves, but in Highly Individual Ways

The ability of wild animals to navigate and survive in complex and dynamic environments depends on their ability to store relevant information and place it in a spatial context. Despite the centrality of spatial memory, and given our increasing ability to observe animal movements in the wild, it is perhaps surprising how difficult it is to demonstrate spatial memory empirically. We present a cognitive analysis of movements of several wolves (Canis lupus) in Finland during a summer period of intensive hunting and den-centered pup-rearing. We tracked several wolves in the field by visiting nearly all GPS locations outside the den, allowing us to identify the species, location and timing of ne…

The Ghost of the Hawk: Top Predator Shaping Bird Communities in Space and Time

Despite the wide recognition that strongly interacting species can influence distributions of other species, species interactions are often disregarded when assessing or projecting biodiversity distributions. In particular, it remains largely uncharted the extent to which the disappearance of a keystone species cast repercussions in the species composition of future communities. We tested whether an avian top predator can exert both positive and negative effects on spatial distribution of other species, and if these effects persist even after the predator disappeared. We acquired bird count data at different distances from occupied and non-occupied nests of Northern goshawks Accipiter genti…

Distance decay 2.0 – a global synthesis of taxonomic and functional turnover in ecological communities

AbstractUnderstanding 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 turnover in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distances. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 149 datasets comprising different types of organisms and environments. We modelled an exponential distance decay for each dataset using generalized linear models and extracted r2 and slope to analyse the streng…

Habitat area and local habitat conditions outweigh fragmentation effects on insect communities in vineyards

Fragmentation of habitat, for example by intensive agricultural practices, can be detrimental to local biodiversity. However, it often remains unclear whether such biodiversity declines are caused by loss of habitat area or increased fragmentation, and how habitat quality factors into it. In our study system, vegetated vineyards are typically small, and isolated from one another, potentially limiting the distribution and dispersal of organisms. In a full-factorial experiment of a priori selected vegetated vineyard patches of differing size and fragmentation, we aimed to disentangle the effects of habitat area (area of vegetated vineyards), habitat fragmentation (number of vegetated vineyard…

Morphological traits predict host-tree specialization in wood-inhabiting fungal communities

Tree species is one of the most important determinants of wood-inhabiting fungal community composition, yet its relationship with fungal reproductive and dispersal traits remains poorly understood. We studied fungal communities (total of 657 species) inhabiting broadleaved and coniferous dead wood (total of 192 logs) in 12 semi-natural boreal forests. We utilized a trait-based hierarchical joint species distribution model to examine how the relationship between dead wood quality and species occurrence correlates with reproductive and dispersal morphological traits. Broadleaved trees had higher species richness than conifers, due to discomycetoids and pyrenomycetoids specializing in them. Re…

Accounting for species interactions is necessary for predicting how arctic arthropod communities respond to climate change

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 degrees C and arthropod species richness halved. We show that with abiotic variables alone, we are essentially un…

Table S1;Table S2;Table S3;Table S4;Figure S1 from Scavenging in the realm of senses: smell and vision drive recruitment at carcasses in neotropical ecosystems

Scavenger species registered in the community. For each of them, we specified the common name, the scientific name and the taxonomic group (i.e., vulture, other bird, mammal or reptile).;Times of first arrival of each species from carcass placement and maximum abundance (i.e., average number of individuals present in each carcass size) of each species separately for large and small carcasses, both represented as the mean and standard deviation, i.e., X̅ ± SD.;Model coefficients for large carcasses by means generalized lineal models (GLMs) showing the influence of the linear predictor (L_ijt) and the biotic predictor (h_ijt: influence of heterospectifics) on each of the scavenging species. T…

Scavenging in the realm of senses: smell and vision drive recruitment at carcasses in Neotropical ecosystems

Social information, acquired through the observation of other individuals, is especially relevant among species belonging to the same guild. The unpredictable and ephemeral nature of carrion implies that social mechanisms may be selected among scavenger species to facilitate carcass location and consumption. Here, we apply a survival-modelling strategy to data obtained through the placement and monitoring of carcasses in the field to analyse possible information transmission cascades within a Neotropical scavenger community. Our study highlights how the use of different senses (smell and sight) within this guild facilitates carcass location through the transmission of social information bet…

A molecular-based identification resource for the arthropods of Finland

Publisher Copyright: © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the…

Choosy beetles : How host trees and southern boreal forest naturalness may determine dead wood beetle communities

Wood-living beetles make up a large proportion of forest biodiversity and contribute to important ecosystem services, including decomposition. Beetle communities in managed southern boreal forests are less species rich than in natural and near-natural forest stands. In addition, many beetle species rely primarily on specific tree species. Yet, the associations between individual beetle species, forest management category, and tree species are seldom quantified, even for red-listed beetles. We compiled a beetle capture dataset from flight intercept traps placed on Norway spruce (Picea abies), oak (Quercus sp.), and Eurasian aspen (Populus tremulae) trees in 413 sites in mature managed forest…

Effects of density, species interactions, and environmental stochasticity on the dynamics of British bird communities

Our knowledge of the factors affecting species abundances is mainly based on time-series analyses of a few well-studied species at single or few localities, but we know little about whether results from such analyses can be extrapolated to the community level. We apply a joint species distribution model to long-term time-series data on British bird communities to examine the relative contribution of intra- and interspecific density dependence at different spatial scales, as well as the influence of environmental stochasticity, to spatiotemporal interspecific variation in abundance. Intraspecific density dependence has the major structuring effect on these bird communities. In addition, envi…

Extending Joint Models in Community Ecology : A Response to Beissinger et al.

The joint modelling of many variables in community ecology is a new and technically challenging area with many opportunities for future developments. The possibility of extending joint models to deal with imperfect detection has been highlighted by Beissinger et al. as an important problem worthy of further investigation [1]. We agree, and previously pointed to this potential extension as an outstanding question [2], alongside models that can estimate phylogenetic repulsion or attraction, nonlinearity in the response to latent variables, and spatial or temporal correlation, because further developments in all these directions are needed.

Does trait-based joint species distribution modelling reveal the signature of competition in stream macroinvertebrate communities?

1. The occupancy and abundance of species are jointly driven by local factors, such as environmental characteristics and biotic interactions, and regional‐scale factors, such as dispersal and climate. Recently, it has been shown that biotic interactions shape species occupancies and abundances beyond local extents. However, for small ectothermic animals, particularly for those occurring in freshwater environments, the importance of biotic interactions remains understudied. Species‐to‐species associations from joint species distribution models (i.e. species associations while controlling for environmental characteristics) are increasingly used to draw hypotheses of which species possibly sho…

Habitat quality is more important than matrix quality for bird communities in protected areas

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 t…

Domain‐specific neural networks improve automated bird sound recognition already with small amount of local data

1. An automatic bird sound recognition system is a useful tool for collecting data of different bird species for ecological analysis. Together with autonomous recording units (ARUs), such a system provides a possibility to collect bird observations on a scale that no human observer could ever match. During the last decades, progress has been made in the field of automatic bird sound recognition, but recognizing bird species from untargeted soundscape recordings remains a challenge. 2. In this article, we demonstrate the workflow for building a global identification model and adjusting it to perform well on the data of autonomous recorders from a specific region. We show how data augmentatio…

Bayesian Modeling of Sequential Discoveries

We aim at modelling the appearance of distinct tags in a sequence of labelled objects. Common examples of this type of data include words in a corpus or distinct species in a sample. These sequential discoveries are often summarised via accumulation curves, which count the number of distinct entities observed in an increasingly large set of objects. We propose a novel Bayesian method for species sampling modelling by directly specifying the probability of a new discovery, therefore allowing for flexible specifications. The asymptotic behavior and finite sample properties of such an approach are extensively studied. Interestingly, our enlarged class of sequential processes includes highly tr…

Using latent variable models to identify large networks of species‐to‐species associations at different spatial scales

Summary We present a hierarchical latent variable model that partitions variation in species occurrences and co-occurrences simultaneously at multiple spatial scales. We illustrate how the parameterized model can be used to predict the occurrences of a species by using as predictors not only the environmental covariates, but also the occurrences of all other species, at all spatial scales. We leverage recent progress in Bayesian latent variable models to implement a computationally effective algorithm that enables one to consider large communities and extensive sampling schemes. We exemplify the framework with a community of 98 fungal species sampled in c. 22 500 dead wood units in 230 plot…

Movement of forest-dependent dung beetles through riparian buffers in Bornean oil palm plantations

1. Fragmentation of tropical forests is increasing globally, with negative impacts for biodiversity. In Southeast Asia, expansion of oil palm agriculture has caused widespread deforestation, forest degradation and fragmentation. 2. Persistence of forest-dependent species within these fragmented landscapes is likely to depend on the capacity of individuals to move between forest patches. In oil palm landscapes, riparian buffers along streams and rivers are potential movement corridors, but their use by moving animals is poorly studied. 3. We examined how six dung beetle species traversed riparian buffers connected to a continuous forest reserve area within an oil palm plantation in Sabah, Ma…

Nonlinear effects of climate on boreal rodent dynamics: mild winters do not negate high-amplitude cycles

Small rodents are key species in many ecosystems. In boreal and subarctic environments, their importance is heightened by pronounced multiannual population cycles. Alarmingly, the previously regular rodent cycles appear to be collapsing simultaneously in many areas. Climate change, particularly decreasing snow quality or quantity in winter, is hypothesized as a causal factor, but the evidence is contradictory. Reliable analysis of population dynamics and the influence of climate thereon necessitate spatially and temporally extensive data. We combined data on vole abundances and climate, collected at 33 locations throughout Finland from 1970 to 2011, to test the hypothesis that warming winte…

Macrosystem community change in lake phytoplankton and its implications for diversity and function

Aim We use lake phytoplankton community data to quantify the spatio-temporal and scale-dependent impacts of eutrophication, land-use and climate change on species niches and community assembly processes while accounting for species traits and phylogenetic constraints. Location Finland. Time period 1977–2017. Major taxa Phytoplankton. Methods We use hierarchical modelling of species communities (HMSC) to model metacommunity trajectories at 853 lakes over four decades of environmental change, including a hierarchical spatial structure to account for scale-dependent processes. Using a “region of common profile” approach, we evaluate compositional changes of species communities and trait profil…

Distance decay 2.0. A global synthesis of taxonomic and functional turnover in ecological communities

Caio Graco-Roza was funded by the Coordination for the Improvement of Higher Education Personnel (CAPES), the Carlos Chagas Filho Research Support Foundation (FAPERJ) and the Ella and Georg Erhnrooth Foundation; Jan Altman by research grants INTER-EXCELLENCE LTAUSA19137 provided by Czech Ministry of Education, Youth and Sports, 20-05840Y of the Czech Science Foundation, and long-term research development project no. RVO 67985939 of the Czech Academy of Sciences; Otso Ovaskainen was funded by Academy of Finland (grant no. 309581), Jane and Aatos Erkko Foundation, Research Council of Norway through its Centres of Excellence Funding Scheme (223257), and the European Research Council (ERC) unde…

Climate change reshuffles northern species within their niches

Climate change is a pervasive threat to biodiversity. While range shifts are a known consequence of climate warming contributing to regional community change, less is known about how species' positions shift within their climatic niches. Furthermore, whether the relative importance of different climatic variables prompting such shifts varies with changing climate remains unclear. Here we analysed four decades of data for 1,478 species of birds, mammals, butterflies, moths, plants and phytoplankton along a 1,200 km high latitudinal gradient. The relative importance of climatic drivers varied non-uniformly with progressing climate change. While species turnover among decades was limited, the …

Fruit body based inventories in wood-inhabiting fungi: Should we replicate in space or time?

We assessed the effect of survey design on the results when conducting fruit body surveys of wood-inhabiting fungi. Our results demonstrate that the optimal design depends on the ecological question to be addressed, as well as the group of fungal species under research. If the aim is to record the total species richness in a dead wood unit or to estimate the population size of a species, repeating the survey over time is generally necessary. However, if the aim is to estimate the total species richness in the forest or to assess how environmental covariates influence species richness or community composition, it is generally more efficient to increase the number of dead wood units than to r…

Ecological dependencies make remote reef fish communities most vulnerable to coral loss

Ecosystems face both local hazards, such as over-exploitation, and global hazards, such as climate change. Since the impact of local hazards attenuates with distance from humans, local extinction risk should decrease with remoteness, making faraway areas safe havens for biodiversity. However, isolation and reduced anthropogenic disturbance may increase ecological specialization in remote communities, and hence their vulnerability to secondary effects of diversity loss propagating through networks of interacting species. We show this to be true for reef fish communities across the globe. An increase in fish-coral dependency with the distance of coral reefs from human settlements, paired with…

Covariate-informed latent interaction models: Addressing geographic & taxonomic bias in predicting bird-plant interactions

Reductions in natural habitats urge that we better understand species' interconnection and how biological communities respond to environmental changes. However, ecological studies of species' interactions are limited by their geographic and taxonomic focus which can distort our understanding of interaction dynamics. We focus on bird-plant interactions that refer to situations of potential fruit consumption and seed dispersal. We develop an approach for predicting species' interactions that accounts for errors in the recorded interaction networks, addresses the geographic and taxonomic biases of existing studies, is based on latent factors to increase flexibility and borrow information acros…

Community Turnover of Wood-Inhabiting Fungi across Hierarchical Spatial Scales

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 richne…

The past and the present in decision-making: the use of conspecific and heterospecific cues in nest site selection

International audience; Nest site selection significantly affects fitness, so adaptations for assessment of the qualities of available sites are expected. The assessment may be based on personal or social information, the latter referring to the observed location and performance of both conspecific and heterospecific individuals. Contrary to large-scale breeding habitat selection, small-scale nest site selection within habitat patches is insufficiently understood. We analyzed nest site selection in the migratory Collared Flycatcher Ficedula albicollis in relation to present and past cues provided by conspecifics and by resident tits within habitat patches by using long-term data. Collared F…

Effects of a mobile disturbance pattern on dynamic patch networks and metapopulation persistence

Abstract Motivation Certain early-succession habitats may emerge only at restricted locations following disturbance. Therefore, whether disturbances tend to occur at certain sites or not can significantly affect habitat availability and metapopulation persistence of early-successional habitat specialists. Available models that combine metapopulation and landscape processes do not address how to model mobile, spatially shifting disturbance intensities independent of factors of site suitability. We present a model that allows the study on how a mobile disturbance pattern, of either natural or anthropogenic origin, affects patch network and metapopulation dynamics in realistic, heterogeneous l…

Local eukaryotic and bacterial stream community assembly is shaped by regional land use effects

With anticipated expansion of agricultural areas for food production and increasing intensity of pressures stemming from land-use, it is critical to better understand how species respond to land-use change. This is particularly true for microbial communities which provide key ecosystem functions and display fastest responses to environmental change. However, regional land-use effects on local environmental conditions are often neglected, and, hence, underestimated when investigating community responses. Here we show that the effects stemming from agricultural and forested land use are strongest reflected in water conductivity, pH and phosphorus concentration, shaping microbial communities a…

So Many Variables: Joint Modeling in Community Ecology

Technological advances have enabled a new class of multivariate models for ecology, with the potential now to specify a statistical model for abundances jointly across many taxa, to simultaneously explore interactions across taxa and the response of abundance to environmental variables. Joint models can be used for several purposes of interest to ecologists, including estimating patterns of residual correlation across taxa, ordination, multivariate inference about environmental effects and environment-by-trait interactions, accounting for missing predictors, and improving predictions in situations where one can leverage knowledge of some species to predict others. We demonstrate this by exa…

High‐resolution 3D forest structure explains ecomorphological trait variation in assemblages of saproxylic beetles

1. Climate, topography and the 3D structure of forests are major drivers affecting local species communities. However, little is known about how the specific functional traits of saproxylic (wood-living) beetles, involved in the recycling of wood, might be affected by those environmental characteristics. 2. Here, we combine ecological and morphological traits available for saproxylic beetles and airborne laser scanning (ALS) data in Bayesian trait-based joint species distribution models to study how traits drive the distributions of more than 230 species in temperate forests of Europe. 3. We found that elevation (as a proxy for temperature and precipitation) and the proportion of conifers p…

Traits mediate niches and co‐occurrences of forest beetles in ways that differ among bioclimatic regions

Aim The aim of this study was to investigate the role of traits in beetle community assembly and test for consistency in these effects among several bioclimatic regions. We asked (1) whether traits predicted species’ responses to environmental gradients (i.e. their niches), (2) whether these same traits could predict co-occurrence patterns and (3) how consistent were niches and the role of traits among study regions. Location Boreal forests in Norway and Finland, temperate forests in Germany. Taxon Wood-living (saproxylic) beetles. Methods We compiled capture records of 468 wood-living beetle species from the three regions, along with nine morphological and ecological species traits. Eight …

The legacy of human use in Amazonian palm communities along environmental and accessibility gradients

Aim: Palms are iconic and dominant elements of neotropical forests. In the Amazon region, palms have been used and managed by humans for food, material, medicine and other purposes for millennia. It is, however, debated to what extent the structure of modern palm communities reflects long-term human modification. Here, we investigate the complex interplay of ecological and societal factors that influence the distributions of both human-used and non-used palms in western Amazonia. Location: Amazonia. Time period: Present. Major taxa studied: Palms (Arecaceae). Methods: We used Bayesian hierarchical joint species distribution models to predict the distributions and environmental niche dimensi…

Fungal communities decline with urbanization : more in air than in soil

Increasing evidence suggests that degradation of biodiversity in human populated areas is a threat for the ecosystem processes that are relevant for human well-being. Fungi are a megadiverse kingdom that plays a key role in ecosystem processes and affects human well-being. How urbanization influences fungi has remained poorly understood, partially due to the methodological difficulties in comprehensively surveying fungi. Here we show that both aerial and soil fungal communities are greatly poorer in urban than in natural areas. Strikingly, a fivefold reduction in fungal DNA abundance took place in both air and soil samples already at 1 km scale when crossing the edge from natural to urban h…

Measuring, comparing and interpreting phenotypic selection on floral scent

Natural selection on floral scent composition is a key element of the hypothesis that pollinators and other floral visitors drive scent evolution. The measure of such selection is complicated by the high-dimensional nature of floral scent data and uncertainty about the cognitive processes involved in scent-mediated communication. We use dimension reduction through reduced-rank regression to jointly estimate a scent composite trait under selection and the strength of selection acting on this trait. To assess and compare variation in selection on scent across species, time and space, we reanalyse 22 datasets on six species from four previous studies. The results agreed qualitatively with prev…

Species distributions models may predict accurately future distributions but poorly how distributions change: A critical perspective on model validation

Aim: Species distribution models (SDMs) are widely used to make predictions on how species distributions may change as a response to climatic change. To assess the reliability of those predictions, they need to be critically validated with respect to what they are used for. While ecologists are typically interested in how and where distributions will change, we argue that SDMs have seldom been evaluated in terms of their capacity to predict such change. Instead, typical retrospective validation methods estimate model's ability to predict to only one static time in future. Here, we apply two validation methods, one that predicts and evaluates a static pattern, while the other measures change…

Multi-functionality and sustainability in the European Union’s forests

Spatial cumulant models enable spatially informed treatment strategies and analysis of local interactions in cancer systems

AbstractTheoretical and applied cancer studies that use individual-based models (IBMs) have been limited by the lack of a mathematical formulation that enables rigorous analysis of these models. However, spatial cumulant models (SCMs), which have arisen from theoretical ecology, describe population dynamics generated by a specific family of IBMs, namely spatio-temporal point processes (STPPs). SCMs are spatially resolved population models formulated by a system of differential equations that approximate the dynamics of two STPP-generated summary statistics: first-order spatial cumulants (densities), and second-order spatial cumulants (spatial covariances).We exemplify how SCMs can be used i…

Predation on two vole species by a shared predator: antipredatory response and prey preference

In prey communities with shared predators, variation in prey vulnerability is a key factor in shaping community dynamics. Conversely, the hunting efficiency of a predator depends on the prey community structure, preferences of the predator and antipredatory behavioural traits of the prey. We studied experimentally, under seminatural field conditions, the preferences of a predator and the antipredatory responses of prey in a system consisting of two Myodes species of voles, the grey-sided vole (M. rufocanus Sund.) and the bank vole (M. glareolus Schreb.), and their specialist predator, the least weasel (Mustela nivalis nivalis L.). To quantify the preference of the weasels, we developed a ne…

A Successful Crowdsourcing Approach for Bird Sound Classification

Automated recorders are increasingly used in remote sensing of wildlife, yet automated methods of processing the audio remains challenging. Identifying animal sounds with machine learning provides a solution, but optimizing the models requires annotated training data. Producing such data can require much manual effort, which could be alleviated by engaging masses to contribute to research and share the workload. Birdwatchers are experts on identifying bird vocalizations and form an ideal focal audience for a citizen science project aiming for the required multitudes of annotated avian audio data. For this purpose, we launched a web portal that was targeted and advertised to Finnish birdwatc…

Bryophyte Species Richness on Retention Aspens Recovers in Time but Community Structure Does Not

Green-tree retention is a forest management method in which some living trees are left on a logged area. The aim is to offer ‘lifeboats’ to support species immediately after logging and to provide microhabitats during and after forest re-establishment. Several studies have shown immediate decline in bryophyte diversity after retention logging and thus questioned the effectiveness of this method, but longer term studies are lacking. Here we studied the epiphytic bryophytes on European aspen (Populus tremula L.) retention trees along a 30-year chronosequence. We compared the bryophyte flora of 102 ‘retention aspens’ on 14 differently aged retention sites with 102 ‘conservation aspens’ on 14 d…

Give me a sample of air and I will tell which species are found from your region : Molecular identification of fungi from airborne spore samples

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 specie…

Spore production monitoring reveals contrasting seasonal strategies and a trade‐off between spore size and number in wood‐inhabiting fungi

1. Traits related to reproduction and dispersal drive the assembly and dynamics of species communities and can explain and predict how species respond to habitat loss and fragmentation and to the changing climate. For fungi, such links remain poorly known. 2. We examine how spore production rate, a key demographic trait, is influenced by the interaction between environmental conditions and species traits. We monitored the spore production of 97 wood-inhabiting fungal species on 107 decaying logs for two years and analyzed the data with a hierarchical community model. 3. Our analysis demonstrates clear species differences in seasonal patterns, with spring and summer release dominating in per…

The dual role of rivers in facilitating or hindering movements of the false heath fritillary butterfly

Background Species movement responses to landscape structures have been studied using a variety of methods, but movement research is still in need of simple methods that help predicting and comparing movements across structurally different landscapes. We demonstrate how habitat-specific movement models can be used to disentangle causes of differentiated movement patterns in structurally different landscapes and to predict movement patterns in altered and artificial landscapes. In our case study, we studied the role of riparian landscapes to the persistence of the endangered false heath fritillary butterfly (Melitaea diamina) in its newly discovered coastal distribution region in Finland. We…

Temporal turnover of the soil microbiome composition is guild-specific.

Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal deve…

A fungal perspective on conservation biology

Hitherto fungi have rarely been considered in conservation biology, but this is changing as the field moves from addressing single species issues to an integrative ecosystem-based approach. The current emphasis on biodiversity as a provider of ecosystem services throws the spotlight on the vast diversity of fungi, their crucial roles in terrestrial ecosystems, and the benefits of considering fungi in concert with animals and plants. We reviewed the role of fungi in ecosystems and composed an overview of the current state of conservation of fungi. There are 5 areas in which fungi can be readily integrated into conservation: as providers of habitats and processes important for other organisms…

Predator–vole interactions in northern Europe: the role of small mustelids revised

The cyclic population dynamics of vole and predator communities is a key phenomenon in northern ecosystems, and it appears to be influenced by climate change. Reports of collapsing rodent cycles have attributed the changes to warmer winters, which weaken the interaction between voles and their specialist subnivean predators. Using population data collected throughout Finland during 1986–2011, we analyse the spatio-temporal variation in the interactions between populations of voles and specialist, generalist and avian predators, and investigate by simulations the roles of the different predators in the vole cycle. We test the hypothesis that vole population cyclicity is dependent on predator…

Bayesian semiparametric long memory models for discretized event data

We introduce a new class of semiparametric latent variable models for long memory discretized event data. The proposed methodology is motivated by a study of bird vocalizations in the Amazon rain forest; the timings of vocalizations exhibit self-similarity and long range dependence. This rules out Poisson process based models where the rate function itself is not long range dependent. The proposed class of FRActional Probit (FRAP) models is based on thresholding, a latent process. This latent process is modeled by a smooth Gaussian process and a fractional Brownian motion by assuming an additive structure. We develop a Bayesian approach to inference using Markov chain Monte Carlo and show g…

Co‐occurrence patterns in a steppe bird community: insights into the role of dominance and competition

Spatial co-occurrence patterns are determined by environmental factors, such as food availability or habitat characteristics and by biotic associations. When resources are limited, competition which implies a dominant hierarchy can shape species assemblage. Here, we study space and time co-occurrence of steppe passerines during the breeding season in a natural steppe habitat, its modulation by environmental filtering, potential biotic interactions and random processes. We applied the joint species distribution model of hierarchical modelling of species community (HMSC) to data on species presence–absence and environmental, temporal and spatial covariates acquired from seven plots in a natur…

The relationships between urbanization and bird functional traits across the streetscape

Publisher Copyright: © 2023 The Authors The urbanization process leads to changes in bird communities’ taxonomic and functional compositions. Highly urbanized areas generally exhibit a reduced number of bird species sharing few functional traits. However, most urban bird studies focused on vegetation patches in temperate cities. In this study, we investigate how urban environmental attributes – noise, height of buildings, and urban vegetation characteristics – modulate species occurrences and the distribution of functional traits across the streetscape of a tropical metropolis. We predicted diverse trait-environment relationships, but that highly urbanized contexts (e.g., noisy streets with…

Experimentally induced community assembly of polypores reveals the importance of both environmental filtering and assembly history

The community assembly of wood-inhabiting fungi follows a successional pathway, with newly emerging resource patches being colonised by pioneer species, followed by those specialised on later stages of decay. The primary coloniser species have been suggested to strongly influence the assembly of the later-arriving community. We created an artificial resource pulse and studied the assembly of polypores over an 11yr period to ask how the identities of the colonising species depend on the environmental characteristics and the assembly history of the dead wood unit. Our results support the view that community assembly in fungi is a highly stochastic process, as even detailed description of the …

Appendix B. Treatment of missing data, special cases, and details of statistical analyses.

Treatment of missing data, special cases, and details of statistical analyses.

Data from: The dual role of rivers in facilitating or hindering movements of the false heath fritillary butterfly

Background: Species movement responses to landscape structures have been studied using a variety of methods, but movement research is still in need of simple methods that help predicting and comparing movements across structurally different landscapes. We demonstrate how habitat-specific movement models can be used to disentangle causes of differentiated movement patterns in structurally different landscapes and to predict movement patterns in altered and artificial landscapes. In our case study, we studied the role of riparian landscapes to the persistence of the endangered false heath fritillary butterfly (Melitaea diamina) in its newly discovered coastal distribution region in Finland. W…

Bayesian Modelling of Sequential Discoveries

We aim at modelling the appearance of distinct tags in a sequence of labelled objects. Common examples of this type of data include words in a corpus or distinct species in a sample. These sequential discoveries are often summarised via accumulation curves, which count the number of distinct entities observed in an increasingly large set of objects. We propose a novel Bayesian method for species sampling modelling by directly specifying the probability of a new discovery, therefore allowing for flexible specifications. The asymptotic behavior and finite sample properties of such an approach are extensively studied. Interestingly, our enlarged class of sequential processes includes highly tr…

Covariate-informed latent interaction models: Addressing geographic & taxonomic bias in predicting bird-plant interactions

Reductions in natural habitats urge that we better understand species’ interconnection and how biological communities respond to environmental changes. However, ecological studies of species’ interactions are limited by their geographic and taxonomic focus which can distort our understanding of interaction dynamics. We focus on bird-plant interactions that refer to situations of potential fruit consumption and seed dispersal. We develop an approach for predicting species’ interactions that accounts for errors in the recorded interaction networks, addresses the geographic and taxonomic biases of existing studies, is based on latent factors to increase flexibility and borrow information acros…

Appendix A. Illustration of the calculation of analyzed variables, supplemental results, parameter estimates, variable correlations and results of sensitivity analyses.

Illustration of the calculation of analyzed variables, supplemental results, parameter estimates, variable correlations and results of sensitivity analyses.

Data from: Predator–vole interactions in northern Europe: the role of small mustelids revised

The cyclic population dynamics of vole and predator communities is a key phenomenon in northern ecosystems, and it appears to be influenced by climate change. Reports of collapsing rodent cycles have attributed the changes to warmer winters, which weaken the interaction between voles and their specialist subnivean predators. Using population data collected throughout Finland during 1986–2011, we analyse the spatio-temporal variation in the interactions between populations of voles and specialist, generalist and avian predators, and investigate by simulations the roles of the different predators in the vole cycle. We test the hypothesis that vole population cyclicity is dependent on predator…

Data from: Give me a sample of air and I will tell which species are found from your region – molecular identification of fungi from airborne spore samples

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 spec…

Data from: Wood-inhabiting fungi with tight associations with other species have declined as a response to forest management

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…

Mutualistic interactions along a fragmentation gradient

Forest cover loss and fragmentation due to land use changes are one of the principal causes of global biodiversity loss. Indirectly, forest fragmentation can reduce biodiversity and ecosystem functioning by disrupting species interaction networks. Interaction networks, such as seed dispersal networks, are fundamental in maintaining ecosystem services. In tropical forests, frugivorous animals are the most important seed dispersers and thus the main agents of forest regeneration. In general, large tree species produce large seeds that are dispersed by large frugivores. Therefore, in absence of large frugivores, the average size in the tree community is hypothesized to eventually decrease whic…

Eurasian Chronicle of Nature as a basis for large-scale analysis of changing ecosystems.

At present, the study of the consequences of global climate change on ecosystems has become particularly relevant. "Chronicles of Nature" is a unique monitoring program unmatched in geographical (former USSR) and temporal scale (from early 1900s and still ongoing in most locations), that accumulated mostly on paper until early 2000s with no coordinated attempt to compile it in a common format. It has become the basis for international cooperation since 2011 in the framework of ECN project led by the University of Helsinki. ECN: Eurasian Chronicle of Nature - Large Scale Analysis of Changing Ecosystems, it has more than 450 participants (researchers) representing 176 organizations from 12 co…