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Theoretical 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 in mathematical oncology by modelling theoretical cancer cell populations comprising interacting growth factor-producing and non-producing cells. To formulate model equations, we use computational tools that enable the generation of STPPs, SCMs and mean-field population models (MFPMs) from user-defined model descriptions (Cornell et al., 2019). To calculate and compare STPP, SCM and MFPM-generated summary statistics, we develop an application-agnostic computational pipeline. Our results demonstrate that SCMs can capture STPP-generated population density dynamics, even when MFPMs fail to do so. From both MFPM and SCM equations, we derive treatment-induced death rates required to achieve non-growing cell populations. When testing these treatment strategies in STPP-generated cell populations, our results demonstrate that SCM-informed strategies outperform MFPM-informed strategies in terms of inhibiting population growths. We thus demonstrate that SCMs provide a new framework in which to study cell-cell interactions, and can be used to describe and perturb STPP-generated cell population dynamics. We, therefore, argue that SCMs can be used to increase IBMs’ applicability in cancer research.Statements and DeclarationsThe authors have no competing interests to declare that are relevant to the content of this article.

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 tall buildings) would be mostly occupied b,y a lower number of species sharing generalist traits. We also predicted to observe streets with similar community composition (profiles) shaped by environmental conditions and interspecific interactions. We applied hierarchical modelling of species communities as a flexible framework for analysis of community data. We observed that, increased noise exposure and reduced green cover were negatively related with species richness due to their negative relationships with most species’ occurrences. On the other hand, larger number of trees and higher proportion of green cover presented mostly positive relationships with occurrences, and thus with species richness. Throughout our streetscape, community composition was highly heterogeneous and similar conditions led to similar profiles. For example, noisy streets may favor the presence of omnivorous and large-bodied species, while wooded streets may allow for the presence of smaller-bodied forest specialist species that exploit lower vegetation strata. Our results indicate that streetscapes may have the potential to harbor functionally and taxonomically diverse bird communities.

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 perennial species, contrary to the commonly held view of autumn as the primary ?mushroom season?. Many species follow a diurnal pattern with a higher spore release rate during the night. Such patterns in release timing have important implications for dispersal, as shown by recent model simulations. 4. The overall level of spore release was negatively correlated with spore size, providing new evidence that fungi face the classic trade-off of investing either in the number or size of offspring. 5. We found that different species within the functional group of wood-inhabiting fungi display alternative strategies in spore release timing and along the trade-off between offspring size and number. Linking our findings to previously reported correlations between spore size and other traits, we propose a new conceptualization of life history strategies in wood-inhabiting fungi, with implications for species? ability to survive the ongoing biodiversity crisis.

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 profiles and investigate their temporal development. Results We demonstrate the emergence of novel and widespread community composition clusters in previously more compositionally homogeneous communities, with cluster-specific community trait profiles, indicating functional differences. A strong phylogenetic signal of species responses to the environment implies similar responses among closely related taxa. Community cluster-specific species prevalence indicates lower taxonomic dispersion within the current dominant clusters compared with the historically dominant cluster and an overall higher prevalence of smaller species sizes within communities. Our findings denote profound spatio-temporal structuring of species co-occurrence patterns and highlight functional differences of lake phytoplankton communities. Main conclusions Diverging community trajectories have led to a nationwide reshuffling of lake phytoplankton communities. At regional and national scales, lakes are not single entities but metacommunity hubs in an interconnected waterscape. The assembly mechanisms of phytoplankton communities are strongly structured by spatio-temporal dynamics, which have led to novel community types, but only a minor part of this reshuffling could be linked to temporal environmental change.

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 previous analyses in terms of identifying populations and scent compounds subject to stronger selection but also allowed us to evaluate and compare the strength of selection on scent across studies. Doing so revealed that selection on floral scent was highly variable, and overall about as common and as strong as selection on other phenotypic traits involved in pollinator attraction or pollen transfer. These results are consistent with an important role of floral scent in pollinator attraction. Our approach should be useful for further studies of plant-animal communication and for studies of selection on other high-dimensional phenotypes. In particular, our approach will be useful for studies of pollinator-mediated selection on complex scent blends comprising many volatiles, and when no prior information on the physiological responses of pollinators to scent compounds is available.

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, Malaysian Borneo. We used a mark–release–recapture study and a new Bayesian Joint Species Movement Modelling (JSMM) approach, extended to a continuous capture process model. 4. Dung beetle species were fairly generalist in their habitat use, but two species showed a statistically supported preference for riparian buffer forest over oil palm, and one species showed a strong preference for forest reserve over riparian buffer, indicating the importance of forested areas within oil palm landscapes for some species. 5. A land-use change simulation indicated that the loss of riparian buffers in oil palm will result in reduced movement by forest-dependent species. 6. Synthesis and applications. Our results provide evidence for the use of riparian buffers in oil palm plantations for forest-dependent dung beetle species, strengthening the case for their retention, restoration and re-establishment. Furthermore, our study demonstrates the wider applicability of the Joint Species Movement Modelling (JSMM) framework to assess movement behaviour of species in fragmented landscapes, a vital tool for future forest and landscape management and conservation prioritisation exercises.

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 improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.

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 threatened by increasing human disturbance. Using passive acoustic monitoring, we assessed how the species-rich aerial insectivorous bats—essential for insect suppression services—respond to chronic human disturbance in the Caatinga dry forests of Brazil, an area potentially harboring ca. 100 bat species (nearly 50% are insectivorous), but with > 60% its area composed of anthropogenic ecosystems under chronic pressure. Acoustic data for bat activity was collected at research sites with varying amounts of chronic human disturbance (e.g., livestock grazing and firewood gathering). The intensity of the disturbance is indicated by the global multi-metric CAD index (GMDI). Using Animal Sound Identifier (ASI) software, we identified 18 different bat taxon units. Using Hierarchical Modeling of Species Communities (HMSC), we found trends in the association of the disturbance gradient with species richness and bat activity: species richness was higher at sites with higher human disturbance, whereas bat activity decreased with increasing human disturbance. Additionally, we observed taxon-specific responses to human disturbance. We conclude that the effects of chronic anthropogenic disturbance on the insectivorous bat fauna in the Caatinga are not homogeneous and a species-specific approach is necessary when assessing the responses of local bats to human disturbances in tropical dry forests, and in other biomes under human pressure.

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, environmental fluctuations affect spatiotemporal differences in abundance. In contrast, species interactions had a minor impact on variation in abundance. Thus, important drivers of single-species dynamics are also strongly affecting dynamics of communities in time and space.

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) under the European Union's Horizon 2020 research and innovation programme (grant agreement no. 856506; ERC-synergy project LIFEPLAN); and Jianjun Wang was funded by CAS Key Research Program of Frontier Sciences (QYZDB-SSW-DQC043) and National Natural Science Foundation of China (91851117). The "sPlot" project was initiated by sDiv, the Synthesis Centre of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation (DFG FZT 118), and is now a platform of iDiv. The study was supported by the TRY initiative on plant traits (). We are also grateful to Jens Kattge and TRY database. TRY is hosted, developed and maintained at the Max Planck Institute for Biogeochemistry (MPI-BGC) in Jena, Germany, in collaboration with the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. The CESTES database of metacommunities is also an initiative of iDiv led by Alienor Jeliazkov. We thank sDiv for supporting the open science initiative., Aim: Understanding the variation in community composition and species abundances (i.e., β-diversity) is at the heart of community ecology. A common approach to examine β-diversity is to evaluate directional variation in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distance. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 148 datasets comprising different types of organisms and environments. Location: Global. Time period: 1990 to present. Major taxa studied: From diatoms to mammals. Method: We measured the strength of the decay using ranked Mantel tests (Mantel r) and the rate of distance decay as the slope of an exponential fit using generalized linear models. We used null models to test whether functional similarity decays faster or slower than expected given the taxonomic decay along the spatial and environmental distance. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm and organismal features. Results: Taxonomic distance decay was stronger than functional distance decay along both spatial and environmental distance. Functional distance decay was random given the taxonomic distance decay. The rate of taxonomic and functional spatial distance decay was fastest in the datasets from mid-latitudes. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distance but a higher rate of decay along environmental distance. Marine ecosystems had the slowest rate of decay along environmental distances. Main conclusions: In general, taxonomic distance decay is a useful tool for biogeographical research because it reflects dispersal-related factors in addition to species responses to climatic and environmental variables. Moreover, functional distance decay might be a cost-effective option for investigating community changes in heterogeneous environments., Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES) Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio De Janeiro (FAPERJ), Ella and Georg Erhnrooth Foundation, Ministry of Education, Youth & Sports - Czech Republic LTAUSA19137 Grant Agency of the Czech Republic 20-05840Y Czech Academy of Sciences RVO 67985939, Academy of Finland 309581, Jane and Aatos Erkko Foundation, Research Council of Norway through its Centres of Excellence Funding Scheme 223257, European Research Council (ERC) 856506, CAS Key Research Program of Frontier Sciences QYZDB-SSW-DQC043, National Natural Science Foundation of China (NSFC) 91851117, German Research Foundation (DFG) DFG FZT 118, TRY initiative on plant traits

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 nearly all prey killed. We then developed a model that assigns a spatially explicit value based on memory of predation success and territorial marking. The framework allows for estimation of multiple cognitive parameters, including temporal and spatial scales of memory. For most wolves, fitted memory-based models outperformed null models by 20 to 50% at predicting locations where wolves chose to forage. However, there was a high amount of individual variability among wolves in strength and even direction of responses to experiences. Some wolves tended to return to locations with recent predation success—following a strategy of foraging site fidelity—while others appeared to prefer a site switching strategy. These differences are possibly explained by variability in pack sizes, numbers of pups, and features of the territories. Our analysis points toward concrete strategies for incorporating spatial memory in the study of animal movements while providing nuanced insights into the behavioral strategies of individual predators.

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 the far-reaching impacts of global hazards, increases the risk of fish species loss, counteracting the benefits of remoteness. Hotspots of fish risk from fish-coral dependency are distinct from those caused by direct human impacts, increasing the number of risk hotspots by ~30% globally. These findings might apply to other ecosystems on Earth and depict a world where no place, no matter how remote, is safe for biodiversity, calling for a reconsideration of global conservation priorities., Coral reefs face both local and global stressors. Here, the authors show how a positive relationship between distance from human settlements and ecological specialisation makes remote coral reef fish communities more vulnerable to coral loss.

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

Individual-based models, ‘IBMs’, describe naturally the dynamics of interacting organisms or social or financial agents. They are considered too complex for mathematical analysis, but computer simulations of them cannot give the general insights required. Here, we resolve this problem with a general mathematical framework for IBMs containing interactions of an unlimited level of complexity, and derive equations that reliably approximate the effects of space and stochasticity. We provide software, specified in an accessible and intuitive graphical way, so any researcher can obtain analytical and simulation results for any particular IBM without algebraic manipulation. We illustrate the framework with examples from movement ecology, conservation biology, and evolutionary ecology. This framework will provide unprecedented insights into a hitherto intractable panoply of complex models across many scientific fields., Individual-based models are widely used to simulate complex systems of interacting agents. Here the authors provide a mathematical framework that automates the analysis of any model in a wide class, facilitating a deeper understanding of the scientific questions these models are used to address.

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, near-natural forest, and clear-cuts in southeastern Norway. We used joint species distribution models to estimate the strength of associations for 368 saproxylic beetle species (including 20 vulnerable, endangered, or critical red-listed species) for each forest management category and tree species. Tree species on which traps were mounted had the largest effect on beetle communities; oaks had the most highly associated beetle species, including most of the red-listed species, followed by Norway spruce and Eurasian aspen. Most beetle species were more likely to be captured in near-natural than in mature managed forest. Our estimated associations were compatible ? for many species ? with categorical classifications found in several existing databases of saproxylic beetle preferences. These quantitative beetle-habitat associations will improve future analyses that have typically relied on categorical classifications. Our results highlight the need to prioritize conservation of near-natural forests and oak trees in Scandinavia to protect the habitat of many red-listed species in particular. Furthermore, we underline the importance of carefully considering the species of trees on which traps are mounted in order to representatively sample beetle communities in forest stands.

Climate warming is predicted to have major impacts on the structure of terrestrial communities, particularly in high latitude ecosystems where growing seasons are short. Higher temperatures may dampen seasonal dynamics in community composition as a consequence of earlier snowmelt, with potentially cascading effects across all levels of biological organisation. Here, we examined changes in community assembly and structure along a natural soil temperature gradient in the Hengill geothermal valley, Iceland, during the summer of 2015. Sample collection over several time points within a season allowed us to assess whether temperature alters temporal variance in terrestrial communities and compositional turnover. We found that seasonal fluctuations in species richness, diversity and evenness were dampened as soil temperature increased, whereas invertebrate biomass varied more. Body mass was found to be a good predictor of species occurrence, with smaller species found at higher soil temperatures and emerging earlier in the season. Our results provide more in-depth understanding of the temporal nature of community and population-level responses to temperature, and indicate that climate warming will likely dampen the seasonal turnover of community structure that is characteristic of high latitude invertebrate communities.

The European Union adopted the Water Framework Directive (WFD) in the year 2000 to tackle the rapid degradation of freshwater systems. However, biological, hydromorphological, and physico-chemical water quality targets are currently not met, and identifying successful policy implementation and management actions is of key importance. We built a joint species distribution model for riverine fish in Flanders (Belgium) to better understand the response of fish communities to current environmental policy goals. Environmental covariates included physico-chemical variables and hydromorphological quality indices, while waterway distances accounted for spatial effects. We detected strong effects of physico-chemistry on fish species' distributions. Evaluation of fish community responses to simulated policy scenarios revealed that targeting a 'good' status, following the WFD, increases average species richness with a fraction of species (0.13-0.69 change in accumulated occurrence probabilities). Targeting a 'very good' status, however, predicted an increase of 0.17-1.38 in average species richness. These simulations indicated that riverbed quality, nitrogen, and conductivity levels should be the focal point of policy. However, the weak response of species to a 'good' quality together with the complexity of nutrient-associated problems, suggest a challenging future for river restoration in Flanders.

Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions., Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood’s properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood. IMPORTANCE Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.

Made available in DSpace on 2021-06-25T11:48:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-02-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) National Science Foundation Proyectos de Investigacion Cientifica y Tecnologica Academy of Finland Research Council of Norway (Centre of Excellence grant) The interaction between fruit chemistry and the physiological traits of frugivores is expected to shape the structure of mutualistic seed dispersal networks, but it has been understudied compared with the role of morphological trait matching in structuring interaction patterns. For instance, highly frugivorous birds (i.e., birds that have fruits as the main component of their diets), which characteristically have fast gut passage times, are expected to avoid feeding on lipid-rich fruits because of the long gut retention times associated with lipid digestion. Here, we compiled data from 84 studies conducted in the Neotropics that used focal plant methods to record 35,815 feeding visits made by 317 bird species (155 genera in 28 families) to 165 plant species (82 genera in 48 families). We investigated the relationship between the degree of frugivory of birds (i.e., how much of their diet is composed of fruit) at the genus level and their visits to plant genera that vary in fruit lipid content. We used a hierarchical modeling of species communities approach that accounted for the effects of differences in body size, bird and plant phylogeny, and spatial location of study sites. We found that birds with a low degree of frugivory (e.g., predominantly insectivores) tend to have the highest increase in visitation rates as fruits become more lipid rich, while birds that are more frugivorous tend to increase visits at a lower rate or even decrease visitation rates as lipids increase in fruits. This balance between degree of frugivory and visitation rates to lipid-poor and lipid-rich fruits provides a mechanism to explain specialized dispersal systems and the occurrence of certain physiological nutritional filters, ultimately helping us to understand community-wide interaction patterns between birds and plants. Univ Estadual Paulista, Dept Biodiversidade, Inst Biociencias, BR-13506900 Rio Claro, SP, Brazil Consejo Nacl Invest Cient & Tecn, Inst Invest Biodiversidad & Medioambiente, RA-8400 San Carlos De Bariloche, Rio Negro, Argentina Univ Nacl Comahue, RA-8400 San Carlos De Bariloche, Rio Negro, Argentina Univ Helsinki, Organismal & Evolutionary Biol Res Programme, POB 65, FI-00014 Helsinki, Finland Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, N-7491 Trondheim, Norway Penn State Univ, Dept Biol, University Pk, PA 16802 USA Penn State Univ, Ecol Program, University Pk, PA 16802 USA Univ Estadual Paulista, Dept Biodiversidade, Inst Biociencias, BR-13506900 Rio Claro, SP, Brazil CNPq: 304244/2016-3 National Science Foundation: DEB-1556719 Proyectos de Investigacion Cientifica y Tecnologica: 2015 0815 Academy of Finland: 1273253 Academy of Finland: 250444 Research Council of Norway (Centre of Excellence grant): 223257

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 climatic and forest covariates were also collected. We used Bayesian hierarchical joint species distribution models to estimate the influence of traits and phylogeny on species’ niches. We also tested for correlations between species associations and trait similarity. Finally, we compared species niches and the effects of traits among study regions. Results Traits explained some of the variability in species’ niches, but their effects differed among study regions. However, substantial phylogenetic signal in species niches implies that unmeasured but phylogenetically structured traits have a stronger effect. Degree of trait similarity was correlated with species associations but depended idiosyncratically on the trait and region. Species niches were much more consistent—widespread taxa often responded similarly to an environmental gradient in each region. Main conclusions The inconsistent effects of traits among regions limit their current use in understanding beetle community assembly. Phylogenetic signal in niches, however, implies that better predictive traits can eventually be identified. Consistency of species niches among regions means niches may remain relatively stable under future climate and land use changes; this lends credibility to predictive distribution models based on future climate projections but may imply that species’ scope for short-term adaptation is limited. ISSN:0305-0270 ISSN:1365-2699

Land-use changes are a main driver of modifications in tropical ecosystems, leading to the loss of species and ecological traits and affecting key ecological functions. Although much attention has been given to predict the effects of species loss on ecological processes, information on the large-scale effects of land-use changes over ecological functions is scarce. Here, we detected erosion in the prevalence of ecological functions performed by mammals in response to land-use changes in the Atlantic Forest of Brazil. By analyzing the loss of different ecological functions (vertebrate and invertebrate predation, seed dispersal, seed depredation, herbivory) performed by mammal assemblages in a deforestation gradient, we observed that vulnerable functions (performed by sensitive species, such as browsing, seed depredation, medium and large vertebrate predation) were positively related to patch size and forest cover and negatively related to anthropogenic cover. These relationships were reversed for persistent functions (performed by resilient species, such as grazing, small seed dispersal, small vertebrate and invertebrate predation). Vulnerable functions were virtually restricted to large forest remnants, while persistent functions were prevalent in human-modified landscapes. Disturbed forests are not necessarily empty of mammal species, but there is a substantial loss of ecological functions across most of the Atlantic Forest. Five out of ten ecological functions lose prevalence in small forest remnants. Nonetheless, these small remnants serve as refuges for the remaining biodiversity and are on the verge of the functional extinction of important processes. The erosion of ecological functions provided by mammals compromise the persistence of Atlantic Forest's biodiversity. (C) 2021 Associacao Brasileira de Ciencia Ecologica e Conservacao. Published by Elsevier B.V.

doi: 10.1111/oik.07502 Inferring interspecific interactions indirectly from community data is of central interest in community ecology. Data on species communities can be surveyed using different methods, each of which may differ in the amount and type of species detected, and thus produce varying information on interaction networks. Since fruit bodies reflect only a fraction of the wood-inhabiting fungal diversity, there is an ongoing debate in fungal ecology on whether fruit body?based surveys are a valid method for studying fungal community dynamics compared to surveys based on DNA metabarcoding. In this paper, we focus on species-to-species associations and ask whether the associations inferred from data collected by fruit-body surveys reflect the ones found from data collected by DNA-based surveys. We estimate and compare the association networks resulting from different survey methods using a joint species distribution model. We recorded both raw and residual associations that respectively do not and do correct for the influence of the abiotic predictors when estimating the species-to-species associations. The analyses of the DNA data yielded a larger number of species-to-species associations than the analyses of the fruit body?based data as expected. Yet, we estimated unique associations also from the fruit-body data. Our results show that the directions of estimated residual associations were consistent between the data types, whereas the raw associations were much less consistent, highlighting the need to account for the influence of relevant environmental covariates when estimating association networks. We conclude that even though DNA-based survey methods are more informative about the total number of interacting species, fruit-body surveys are also an adequate method for inferring association networks in wood-inhabiting fungi. Since the DNA and fruit-body data carry on complementary information on fungal communities, the most comprehensive insights are obtained by combining the two survey methods. This article is protected by copyright. All rights reserved.

1. According to metacommunity theories, the structure of natural communities is the result of both environmental filtering and spatial processes, with their relative importance depending on factors including local habitat characteristics, functional features of organisms, and the spatial scale considered. However, few studies have explored environmental and spatial processes in riverine systems at local scales, explicitly incorporating spatial coordinates into multi-taxa distribution models. To address this gap, we conducted a small-scale study to discriminate between abiotic and biotic factors affecting the distribution of aquatic macroin-vertebrates, applying metacommunity concepts.\ud \ud 2. We studied a mountain section in each of three perennial streams within the Po River Basin (northern Italy). We sampled macroinvertebrates both in summer and winter, using specific in situ 50-point random sampling grids. Environmental factors , including benthic organic matter (BOM), flow velocity, water depth, and sub-strate were recorded together with spatial coordinates for each sampling point. The relationships between community metrics (taxon richness, abundance, bio-mass, biomass-abundance ratio, and functional feeding groups) and explanatory variables (environmental and spatial) were assessed using generalised additive models. The influence of the explanatory variables on community structure was analysed with joint species distribution models.\ud \ud 3. Environmental variables-primarily BOM-were the main drivers affecting community metrics, whereas the effects of spatial variables varied among metrics, streams, and seasons. During summer, community structure was strongly affected by BOM and spatial position within the riverbed, the latter probably being a proxy for mass effects mediated by biotic and stochastic processes. In contrast, community structure was mainly shaped by hydraulic variables in winter.\ud \ud 4. Using macroinvertebrate communities as a model group, our results demonstrate that metacommunity concepts can explain small-scale variability in community structure. We found that both environmental filtering and biotic processes shape local communities, with the strength of these drivers depending on the season. These insights provide baseline knowledge that informs our understanding of ecological responses to environmental variability in contexts including restoration ecology, habitat suitability modelling, and biomonitoring.

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. Resupinate and pileate species were generally specialized in coniferous dead wood. Fungi inhabiting broadleaved trees had larger and more elongated spores than fungi in conifers. Spore size was larger and spore shape more spherical in species occupying large dead wood units. These results indicate the selective effect of dead wood quality, visible not only in species diversity, but also in reproductive and dispersal traits. (C) 2019 Elsevier Ltd and British Mycological Society. All rights reserved. peerReviewed

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

Spatially distinct pairs of sites may have similarly fluctuating population dynamics across large geographical distances, a phenomenon called spatial synchrony. However, species rarely exist in isolation, but rather as members of interactive communities, linked with other communities through dispersal (i.e. a metacommunity). Using data on Finnish moth communities sampled across 65 sites for 20 years, we examine the complex synchronous/anti-synchronous relationships among sites using the geography of synchrony framework. We relate site-level synchrony to mean and temporal variation in climatic data, finding that colder and drier sites—and those with the most drastic temperature increases—are important for spatial synchrony. This suggests that faster-warming sites contribute most strongly to site-level estimates of synchrony, highlighting the role of a changing climate to spatial synchrony. Considering the spatial variability in climate change rates is therefore important to understand metacommunity dynamics and identify habitats which contribute most strongly to spatial synchrony.

Contains fulltext : 217063.pdf (Publisher’s version ) (Open Access) Abstract Joint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analysing data in community ecology. Hierarchical Modelling of Species Communities (HMSC) is a general and flexible framework for fitting JSDMs. HMSC allows the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships and the spatio-temporal context of the study, providing predictive insights into community assembly processes from non-manipulative observational data of species communities. The full range of functionality of HMSC has remained restricted to Matlab users only. To make HMSC accessible to the wider community of ecologists, we introduce Hmsc 3.0, a user-friendly r implementation. We illustrate the use of the package by applying Hmsc 3.0 to a range of case studies on real and simulated data. The real data consist of bird counts in a spatio-temporally structured dataset, environmental covariates, species traits and phylogenetic relationships. Vignettes on simulated data involve single-species models, models of small communities, models of large species communities and models for large spatial data. We demonstrate the estimation of species responses to environmental covariates and how these depend on species traits, as well as the estimation of residual species associations. We demonstrate how to construct and fit models with different types of random effects, how to examine MCMC convergence, how to examine the explanatory and predictive powers of the models, how to assess parameter estimates and how to make predictions. We further demonstrate how Hmsc 3.0 can be applied to normally distributed data, count data and presence?absence data. The package, along with the extended vignettes, makes JSDM fitting and post-processing easily accessible to ecologists familiar with r.

Made available in DSpace on 2020-12-12T01:46:49Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-02-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Academy of Finland Norges Forskningsråd Aim: Forest fragmentation is among the principal causes of global biodiversity loss, yet how it affects mutualistic interactions between plants and animals at large spatial scale is poorly understood. In particular, tropical forest regeneration depends on animal-mediated seed dispersal, but the seed-dispersing animals face rapid decline due to forest fragmentation and defaunation. Here, we assess how fragmentation influences the pairwise interactions between 407 seed disperser and 1,424 tree species in a highly fragmented biodiversity hotspot. Location: Atlantic Forest, South America. Methods: We predicted interaction networks in 912 sites covering the entire biome by combining verified interaction data with co-occurrence probabilities obtained from a spatially explicit joint species distribution model. We identified keystone seed dispersers by computing a species-specific keystone index and by selecting those species belonging to the top 5% quantile. Results: We show that forest fragmentation affects seed dispersal interactions negatively, and the decreased area of functionally connected forest, rather than increased edge effects, is the main driver behind the loss of interactions. Both the seed disperser availability for the local tree communities and in particular the proportion of interactions provided by keystone seed dispersers decline with increasing degree of fragmentation. Importantly, just 21 keystone species provided >40% of all interactions. The numbers of interactions provided by keystone and non-keystone species, however, were equally negatively affected by fragmentation, suggesting that seed dispersal interactions may not be rewired under strong fragmentation effects. Conclusions: We highlight the importance of understanding the fragmentation-induced compositional shifts in seed disperser communities as they may lead to lagged and multiplicative effects on tree communities. Our results illustrate the utility of model-based prediction of interaction networks as well as model-based identification of keystone species as a tool for prioritizing conservation efforts. Similar modelling approaches could be applied to other threatened ecosystems and interaction types globally. Centre for Biodiversity Dynamics Norwegian University of Science and Technology Department of Agricultural Sciences University of Helsinki Departamento de Ecologia Instituto de Biociências Universidade de São Paulo Departamento de Ecologia Instituto de Biociências Universidade Estadual Paulista (UNESP) Departamento de Zoologia e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista (UNESP) Instituto de Ciências da Natureza Universidade Federal de Alfenas IPÊ – Instituto de Pesquisas Ecológicas Department of Natural Resources Management Texas Tech University Museum of Texas Tech University Department of Biology University of Miami Faculty of Biological and Environmental Sciences University of Helsinki Departamento de Ecologia Instituto de Biociências Universidade Estadual Paulista (UNESP) Departamento de Zoologia e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista (UNESP) FAPESP: #2013/08722-5 FAPESP: #2013/25441-0 FAPESP: #2013/50421-2 FAPESP: #2014/01986-0 FAPESP: #2014/14739-0 FAPESP: #2014/18800-6 FAPESP: #2015/17739-4 FAPESP: #2017/08440-0 FAPESP: #2017/09676-8 FAPESP: #2017/21816-0 Academy of Finland: 1273253 Norges Forskningsråd: 223257 Academy of Finland: 250444 Academy of Finland: 284601

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

Made available in DSpace on 2020-12-12T02:41:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-08-01 In a rapidly changing world, it is important to understand how environmental modifications by humans affect species behavior. This is not a simple task, since we need to deal with a multitude of species and the different external contexts that affect their behavior. Here, we investigate how interpatch short-distance movements of 73 common forest bird species can be predicted by forest cover and forest isolation. We modeled bird movement as a function of environmental covariates, species traits – body mass and feeding habit – and phylogenetic relationships using Joint Species Movement Models. We used field data collected in forest edges and open pastures of six 600 × 600 m plots in the Atlantic Forest biodiversity hotspot. We found that birds fly larger distances and visit more forest patches and remnant trees with decreasing forest cover. Increasing landscape isolation results in larger flight distances, and it increases the use of trees as stepping-stones for most species. Our results show that birds can adjust their behavior as a response to spatial modification in resource distribution and landscape connectivity. These adjusted behaviors can potentially contribute to ecosystem responses to habitat modification. Univ. Estadual Paulista (UNESP) Depto de Ecologia Inst. de Biociências Univ. Estadual Paulista (UNESP) Depto de Zoologia Inst. de Biociências Grupo de Ecología Cuantitativa INIBIOMA-CRUB CONICET S. C. de Bariloche Organismal and Evolutionary Biology Research Programme Univ. of Helsinki Centre for Biodiversity Dynamics Dept of Biology Norwegian Univ. of Science and Technology Univ. Estadual Paulista (UNESP) Depto de Ecologia Inst. de Biociências Univ. Estadual Paulista (UNESP) Depto de Zoologia Inst. de Biociências

International Scientific Symposium:Ecology and evolution: New challenges. Ekaterinburg, Russia, April 1–5, 2019, p. 67-68. The material for the report was compiled during eight years of operation of the international network of cooperation “Eurasian Chronicle of Nature - Large Scale Analysis of Changing Ecosystems” (“Chronicle of the nature of Eurasia: a large-scale analysis of changing ecosystems”). The material for the report was compiled during eight years of operation of the international network of cooperation “Eurasian Chronicle of Nature - Large Scale Analysis of Changing Ecosystems” (“Chronicle of the nature of Eurasia: a large-scale analysis of changing ecosystems”).

Scale-related assessment strategies are important contributions to successful ecosystem management. With varying impact of environmental drivers from local to regional scales, a focal task is to understand scale-de- pendent responses when assessing the state of an ecosystem. In this study we use large-scale monitoring data, spanning 40 years and including four aquatic bioindicator groups (phytoplankton, zooplankton, periphyton, zoobenthos) to expose the long-term changes of water quality across Russia. We include four hierarchical spatial scales (region, basin, waterbody and observation point) to identify the relative importance of different spatio- temporal scales for the variation of each bioindicator and patterns of co-variation among the bioindicators at different hierarchical levels. We analysed the data with Hierarchical Modelling of Species Communities (HMSC), an approach that belongs to the framework of joint species distribution models. We performed a cross validation to reveal the predictive power of modelled bioindicator variation, partitioned explained variance among the fixed effects (waterbody type, and influence of human population density) and the random effects (spatial and spatio-temporal variation at the four hierarchical scales), and examined the co-variation among bioindicators at each spatio-temporal scale. We detected generally decreasing water quality across Russian freshwaters, yet with region and bioindicator specific trends. For all bioindicators, the dominating part of the variation was attributed the largest (region) and smallest (observation point) hierarchical scales, the region particularly important for benthic and the observation point for pelagic bioindicators. All bioindicators captured the same spatial variation in water quality at the smallest scale of observation point, with phytoplankton, zooplankton and periphyton being associated positively to each other and negatively to zoobenthos. However, at larger spatial scales and at spatio-temporal scales, the associations among the bioindicators became more complex, with phytoplankton and zooplankton showing opposite trends over time. Our study reveals the sensitivity of bioindicators to spatial and temporal scales. While delivering unidirectional robust water quality assessments at the local scale, bioindicator co-variation is more complex over larger geographic scales and over time.

Functional traits are widely recognized as a useful framework for testing mechanisms underlying species community assemblage patterns and ecosystem processes. Functional trait studies in the plant and animal literature have burgeoned in the past 20 years, highlighting a need for standardized ways to measure ecologically meaningful traits across taxa and ecosystems. However, standardized measurements of functional traits are lacking for many organisms and ecosystems, including fungi. Basidiomycete wood fungi occur in all forest ecosystems world-wide, where they are decomposers and also provide food or habitat for other species, or act as tree pathogens. Despite their major role in the functioning of forest ecosystems, the understanding and application of functional traits in studies of communities of wood fungi lags behind other disciplines. As the research field of fungal functional ecology is growing, there is a need for standardized ways to measure fungal traits within and across taxa and spatial scales. This handbook reviews pre-existing fungal trait measurements, proposes new core fungal traits, discusses trait ecology in fungi and highlights areas for future work on basidiomycete wood fungi. We propose standard and potential future methodologies for collecting traits to be used across studies, ensuring replicability and fostering between-study comparison. Combining concepts from fungal ecology and functional trait ecology, methodologies covered here can be related to fungal performance within a community and environmental setting. This manuscript is titled "a start with" as we only cover a subset of the fungal community here, with the aim of encouraging and facilitating the writing of handbooks for other members of the macrofungal community, for example, mycorrhizal fungi. A is available for this article.

Made available in DSpace on 2019-10-06T17:06:53Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-04-01 Norges Forskningsråd Academy of Finland Joint species distribution modeling has enabled researchers to move from species-level to community-level analyses, leading to statistically more efficient and ecologically more informative use of data. Here, we propose joint species movement modeling (JSMM) as an analogous approach that enables inferring both species- and community-level movement parameters from multispecies movement data. The species-level movement parameters are modeled as a function of species traits and phylogenetic relationships, allowing one to ask how species traits influence movements, and whether phylogenetically related species are similar in their movement behavior. We illustrate the modeling framework with two contrasting case studies: a stochastic redistribution model for direct observations of bird movements and a spatially structured diffusion model for capture–recapture data on moth movements. In both cases, the JSMM identified several traits that explain differences in movement behavior among species, such as movement rate increasing with body size in both birds and moths. We show with simulations that the JSMM approach increases precision of species-specific parameter estimates by borrowing information from other species that are closely related or have similar traits. The JSMM framework is applicable for many kinds of data, and it facilitates a mechanistic understanding of the causes and consequences of interspecific variation in movement behavior. Organismal and Evolutionary Biology Research Programme University of Helsinki, P.O. Box 65 Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Departamento de Ecologia Instituto de Biociências Universidade Estadual Paulista (UNESP) Department of Zoology University of Oxford, South Parks Road Behavioural Ecology and Conservation Group Biodiversity Research Centre Earth and Life Institute UCLouvain, Croix du Sud 4-5, bte L7.07.04 Departamento de Zoologia Instituto de Biociências Universidade Estadual Paulista (Unesp) Grupo de Ecología Cuantitativa INIBIOMA-CRUB CONICET, Avenida Pioneros 2350, S.C. de Bariloche Departamento de Ecologia Instituto de Biociências Universidade Estadual Paulista (UNESP) Departamento de Zoologia Instituto de Biociências Universidade Estadual Paulista (Unesp) Norges Forskningsråd: 223257 Academy of Finland: 273253 Academy of Finland: 284601 Academy of Finland: 309581

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

Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning and are important for human health, food production and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise. The method consists of using a cyclone sampler to acquire fungal spores directly from the air to an Eppendorf tube, and applying DNA barcoding with probabilistic species identification to generate a list of species from the sample. We tested the feasibility of the method by acquiring replicate air samples from different geographical regions within Finland. Our results show that air sampling is adequate for regional‐level surveys, with samples collected >100 km apart varying but samples collected

1. Individual-based models (IBMs) allow realistic and flexible modelling of ecological systems, but their parameterization with empirical data is statistically and computationally challenging. Approximate Bayesian computation (ABC) has been proposed as an efficient approach for inference with IBMs, but its applicability to data on natural populations has not been yet fully explored. 2. We construct an IBM for the metapopulation dynamics of a species inhabiting a fragmented patch network, and develop an ABC method for parameterization of the model. We consider several scenarios of data availability from count data to combination of mark-recapture and genetic data. We analyse both simulated and real data on white-starred robin (Pogonocichla stellata), a passerine bird living in montane forest environment in Kenya, and assess how the amount and type of data affect the estimates of model parameters and indicators of population state. 3. The indicators of the population state could be reliably estimated using the ABC method, but full parameterization was not achieved due to strong posterior correlations between model parameters. While the combination of the data types did not provide more accurate estimates for most of the indicators of population state or model parameters than the most informative data type (ringing data or genetic data) alone, the combined data allowed robust simultaneous estimation of all unknown quantities. 4. Our results show that ABC methods provide a powerful and flexible technique forparameterizing complex IBMs with multiple data sources, and assessing the dynamics of the population in a robust manner.

Tropical forest loss and fragmentation are due to increase in coming decades. Understanding how matrix dynamics, especially secondary forest regrowth, can lessen fragmentation impacts is key to understanding species persistence in modified landscapes. Here, we use a whole-ecosystem fragmentation experiment to investigate how bat assemblages are influenced by the regeneration of the secondary forest matrix. We surveyed bats in continuous forest, forest fragments and secondary forest matrix habitats, ~15 and ~30 years after forest clearance, to investigate temporal changes in the occupancy and abundance of old-growth specialist and habitat generalist species. The regeneration of the second growth matrix had overall positive effects on the occupancy and abundance of specialists across all sampled habitats. Conversely, effects on generalist species were negligible for forest fragments and negative for secondary forest. Our results show that the conservation potential of secondary forests for reverting faunal declines in fragmented tropical landscapes increases with secondary forest age and that old-growth specialists, which are often of most conservation concern, are the greatest beneficiaries of secondary forest maturation. Our findings emphasize that the transposition of patterns of biodiversity persistence in island ecosystems to fragmented terrestrial settings can be hampered by the dynamic nature of human-dominated landscapes. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Background: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to ?spillover effects? on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures. Results: We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical?chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes. Conclusions: Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and ?spillover effects? of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology. Made available in DSpace on 2018-11-22T00:48:49Z (GMT). No. of bitstreams: 1 2018JosiMicrobiomeDirect.pdf: 1270795 bytes, checksum: aa05ddeb2cf5aa8b11561434538baf79 (MD5) Previous issue date: 2018-11-19

Accurate estimates of gamete and offspring dispersal range are required for the understanding and prediction of spatial population dynamics and species persistence. Little is known about gamete dispersal in fungi, especially in lichen-forming ascomycetes. Here, we estimate the dispersal functions of clonal propagules, gametes and ascospores of the epiphytic lichen Lobaria pulmonaria. We use hierarchical Bayesian parentage analysis, which integrates genetic and ecological information from multiannual colonization and dispersal source data collected in a large, oldgrowth forest landscape. The effective dispersal range of gametes is several hundred metres to kilometres from potential paternal individuals. By contrast, clonal propagules disperse only tens of metres, and ascospores disperse over several thousand metres. Our study reveals the dispersal distances of individual reproductive units; clonal propagules, gametes and ascospores, which is of great importance for a thorough understanding of the spatial dynamics of ascomycetes. Sexual reproduction occurs between distant individuals. However, whereas gametes and ascospores disperse over long distances, the overall rate of colonization of trees is low. Hence, establishment is the limiting factor for the colonization of new host trees by the lichen in old- growth landscapes.

1. The identification of traits that influence the responses of the species to environmental variation provides a mechanistic perspective on the assembly processes of ecological communities. While much research linking functional ecology with assembly processes has been conducted with animals and plants, the development of predictive or even conceptual frameworks for fungal functional community ecology remains poorly explored. Particularly, little is known about the contribution of traits to the occurrences of fungal species under different environmental conditions. 2. Wood-inhabiting fungi are known to strongly respond to habitat disturbance, and thus provide an interesting case study for investigating to what extent variation in occurrence patterns of fungi can be related to traits. We apply a trait-based joint species distribution model to a data set consisting of fruit-body occurrence data on 321 wood-inhabiting fungal species collected in 22 460 dead wood units from managed and natural forest sites. 3. Our results show that environmental filtering plays a big role on shaping wood-inhabiting fungal communities, as different environments held different communities in terms of species and trait compositions. Most importantly, forest management selected against species with large and long-lived fruit-bodies as well as late decayers, and promoted the occurrences of species with small fruit-bodies and early decayers. A strong phylogenetic signal in the data suggested the existence of also some other functionally important traits than the ones we considered. 4. We found that those species groups that were more prevalent in natural conditions had more associations to other species than species groups that were tolerant to or benefitted from forest management. Therefore, the changes that forest management causes on wood-inhabiting fungal communities influence ecosystem functioning through simplification of interactive associations among the fungal species. 5. Synthesis. Our results show that functional traits are linked to the responses of wood-inhabiting fungi to variation in their environment, and thus environmental changes alter ecosystem functions via promoting or reducing species with different fruit-body types. However, further research is needed to identify other functional traits and to provide conclusive evidence for the adaptive nature of the links from traits to occurrence patterns found here.

Stochastic models of closed populations predict eventual extinction with certainty. Consequently, their behavior is often characterized by the quasi-stationary state, i.e. the long-term distribution of population sizes conditional on non-extinction. In contrast, models which allow for immigration exhibit a regular stationary state. At the limit of a low immigration rate, a population is expected to alternate between three states: the quasi- stationary state of a closed population, the extinction state, and the transient phase during which a newly arrived immigrant either establishes a new population or fails to do so. We develop this argument into a simple and intuitive framework that can be used to assess the effect of immigration in a general class of population models. We exemplify the framework for models in which immigrants arrive either singly or in groups, for models with an Allee effect, for models with environmental stochasticity, and for models leading to metapopulation dynamics.

Phylogeny can provide information about the processes that have shaped extant diversity. Here, we complement existing comparative phylogenetic methods by developing a model that couples diversity-dependent diversification rate and range dynamics. Unlike many models, we used Approximate Bayesian Computation to fit the model to the data. We validated the inference by estimating known parameter values from simulated data, and found that within-region speciation and extinction rates cannot be simultaneously estimated most likely due to correlations among parameter values. Since the model can estimate a diversification rate, we applied the model to a monophyletic lineage of 74 species of dung beetles (Canthonini: Nanos and Apotolamprus) endemic to Madagascar. The estimated diversification rate is clearly higher in northern than in eastern or western Madagascar. The current species richness is highest in North where complex topography and a mixture of biomes likely favour ecological diversification. The approach we have developed here is a step towards examining weaknesses and strengths of phylogenetic comparative methods in an explicit spatial context. Further development and testing of the model is needed before its routine application to empirical data.

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

Autonomous audio recording is stimulating new field in bioacoustics, with a great promise for conducting cost-effective species surveys. One major current challenge is the lack of reliable classifiers capable of multi-species identification. We present PROTAX-Sound, a statistical framework to perform probabilistic classification of animal sounds. PROTAX-Sound is based on a multinomial regression model, and it can utilize as predictors any kind of sound features or classifications produced by other existing algorithms. PROTAX-Sound combines audio and image processing techniques to scan environmental audio files. It identifies regions of interest (a segment of the audio file that contains a vocalization to be classified), extracts acoustic features from them and compares with samples in a reference database. The output of PROTAX-Sound is the probabilistic classification of each vocalization, including the possibility that it represents species not present in the reference database. We demonstrate the performance of PROTAX-Sound by classifying audio from a species-rich case study of tropical birds. The best performing classifier achieved 68% classification accuracy for 200 bird species. PROTAX-Sound improves the classification power of current techniques by combining information from multiple classifiers in a manner that yields calibrated classification probabilities. © 2017 de Camargo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

The data set provided here includes 8,320 frugivory interactions (records of pairwise interactions between plant and frugivore species) reported for the Atlantic Forest. The data set includes interactions between 331 vertebrate species (232 birds, 90 mammals, 5 fishes, 1 amphibian, and 3 reptiles) and 788 plant species. We also present information on traits directly related to the frugivory process (endozoochory), such as the size of fruits and seeds and the body mass and gape size of frugivores. Data were extracted from 166 published and unpublished sources spanning from 1961 to 2016. While this is probably the most comprehensive data set available for a tropical ecosystem, it is arguably taxonomically and geographically biased. The plant families better represented are Melastomataceae, Myrtaceae, Moraceae, Urticaceae, and Solanaceae. Myrsine coriacea, Alchornea glandulosa, Cecropia pachystachya, and Trema micrantha are the plant species with the most animal dispersers (83, 76, 76, and 74 species, respectively). Among the animal taxa, the highest number of interactions is reported for birds (3,883) followed by mammals (1,315). The woolly spider monkey or muriqui, Brachyteles arachnoides, and Rufous-bellied Thrush, Turdus rufiventris, are the frugivores with the most diverse fruit diets (137 and 121 plants species, respectively). The most important general patterns that we note are that larger seeded plant species (>12 mm) are mainly eaten by terrestrial mammals (rodents, ungulates, primates, and carnivores) and that birds are the main consumers of fruits with a high concentration of lipids. Our data set is geographically biased, with most interactions recorded for the southeast Atlantic Forest.

We propose a numerical approach to study the invasion fitness of a mutant and to determine evolutionary singular strategies in evolutionary structured models in which the competitive exclusion principle holds. Our approach is based on a dual representation, which consists of the modeling of the small size mutant population by a stochastic model and the computation of its corresponding deterministic model. The use of the deterministic model greatly facilitates the numerical determination of the feasibility of invasion as well as the convergence-stability of the evolutionary singular strategy. Our approach combines standard adaptive dynamics with the link between the mutant survival criterion in the stochastic model and the sign of the eigenvalue in the corresponding deterministic model. We present our method in the context of a mass-structured individual-based chemostat model. We exploit a previously derived mathematical relationship between stochastic and deterministic representations of the mutant population in the chemostat model to derive a general numerical method for analyzing the invasion fitness in the stochastic models. Our method can be applied to the broad class of evolutionary models for which a link between the stochastic and deterministic invasion fitnesses can be established. (C) 2017 Elsevier Inc. All rights reserved.

Random encounter models can be used to estimate population abundance from indirect data collected by non-invasive sampling methods, such as track counts or camera-trap data. The classical Formozov–Malyshev–Pereleshin (FMP) estimator converts track counts into an estimate of mean population density, assuming that data on the daily movement distances of the animals are available. We utilize generalized linear models with spatio-temporal error structures to extend the FMP estimator into a flexible Bayesian modelling approach that estimates not only total population size, but also spatio-temporal variation in population density. We also introduce a weighting scheme to estimate density on habitats that are not covered by survey transects, assuming that movement data on a subset of individuals is available. We test the performance of spatio-temporal and temporal approaches by a simulation study mimicking the Finnish winter track count survey. The results illustrate how the spatio-temporal modelling approach is able to borrow information from observations made on neighboring locations and times when estimating population density, and that spatio-temporal and temporal smoothing models can provide improved estimates of total population size compared to the FMP method. © 2016 Jousimo, Ovaskainen. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Erratum to: Home-range use patterns and movements of the Siberian flying squirrel in urban forests: effects of habitat composition and connectivity The original article was published in Movement Ecology 2016 4:5 Non

Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.