Joint species-trait distribution modeling: The role of intraspecific trait variation in community assembly.

The links between intraspecific trait variation and community assembly remain little studied, partially due to the lack of statistical methods to jointly model intraspecific trait variation and species abundances at the community level. Here, we extend the joint species distribution modeling (JSDM) framework into the joint species-trait distribution modeling (JSTDM) framework to explicitly link species abundances to phenotypic variation in traits for multiple species simultaneously. Using a case study of 65 tundra plant species abundances and 3 key functional traits measured across 325 sites, we show how the JSTDM approach (1) estimates the statistical associations among species abundances, species-level traits, and site-level traits, relative to environmental variation; (2) improves predictions on trait variation by using information on species abundances; and (3) generates hypotheses about trait-driven community assembly mechanisms.

Species traits and landscape structure can drive scale-dependent propagation of effects in ecosystems.

Species can directly and indirectly affect others across communities and habitats, yet the spatial scale over which such effects spread remains unclear. This uncertainty arises partly because the species traits and landscape structures allowing indirect effects to propagate may differ across scales. Here, we use a topological network metric, communicability, to explore the factors controlling spatial propagation of effects in a large-scale plant-frugivore network projected across the territory of Aotearoa New Zealand.

What lurks in the dark? An innovative framework for studying diverse wild insect microbiota.

Background: Symbiotic microorganisms can profoundly impact insect biology, including their life history traits, population dynamics, and evolutionary trajectories. However, microbiota remain poorly understood in natural insect communities, especially in 'dark taxa'-hyperdiverse yet understudied clades.

Results: Here, we implemented a novel multi-target amplicon sequencing approach to study microbiota in complex, species-rich communities.

Human contributions to global soundscapes are less predictable than the acoustic rhythms of wildlife.

Across the world, human (anthropophonic) sounds add to sounds of biological (biophonic) and geophysical (geophonic) origin, with human contributions including both speech and technophony (sounds of technological devices). To characterize society's contribution to the global soundscapes, we used passive acoustic recorders at 139 sites across 6 continents, sampling both urban green spaces and nearby pristine sites continuously for 3 years in a paired design. Recordings were characterized by bird species richness and by 14 complementary acoustic indices.

Idiosyncratic responses to biotic and environmental filters in wood-inhabiting fungal communities.

Quantification of different processes affecting the assembly of ecological communities remains challenging, especially in species-rich communities. While the role of environmental filtering has generally been well established, fewer studies have experimentally shown how other ecological assembly processes, such as biotic filtering, structure species-rich communities. Here, we studied the relative roles of biotic and environmental filtering in the colonization of wood-inhabiting fungi, a species-rich, highly interactive, and environment-sensitive group of species.

The role of stochasticity in fungal community assembly: explaining apparent stochasticity with field experiments.

Stochasticity is a main process in community assembly. However, experimental studies rarely target stochasticity in natural communities, and hence experimental validation of stochasticity estimates in observational studies is lacking. Here, we combine experimental and observational data to unravel the role of stochasticity in the assembly of wood-inhabiting fungi.

Restoration of forestry-drained boreal peatland ecosystems can effectively stop and reverse ecosystem degradation.

Ecosystem restoration will increase following the ambitious international targets, which calls for a rigorous evaluation of restoration effectiveness. Here, we present results from a long-term before-after control-impact experiment on the restoration of forestry-drained boreal peatland ecosystems. Our data comprise 151 sites, representing six ecosystem types.

Resolving biology's dark matter: species richness, spatiotemporal distribution, and community composition of a dark taxon.

Background: Zoology's dark matter comprises hyperdiverse, poorly known taxa that are numerically dominant but largely unstudied, even in temperate regions where charismatic taxa are well understood. Dark taxa are everywhere, but high diversity, abundance, and small size have historically stymied their study. We demonstrate how entomological dark matter can be elucidated using high-throughput DNA barcoding ("megabarcoding").

Understanding and applying biological resilience, from genes to ecosystems.

The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system's behaviour requires knowledge of its component parts and their interactions.

Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting.

Joint species distribution modelling (JSDM) is a widely used statistical method that analyzes combined patterns of all species in a community, linking empirical data to ecological theory and enhancing community-wide prediction tasks. However, fitting JSDMs to large datasets is often computationally demanding and time-consuming. Recent studies have introduced new statistical and machine learning techniques to provide more scalable fitting algorithms, but extending these to complex JSDM structures that account for spatial dependencies or multi-level sampling designs remains challenging.

Airborne DNA reveals predictable spatial and seasonal dynamics of fungi.

Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores.

Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA.

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world.

Global arthropod beta-diversity is spatially and temporally structured by latitude.

Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, plants, and other less diverse taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-diversity framework.

Landscape fragmentation overturns classical metapopulation thinking.

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood.

Experimental evidence that root-associated fungi improve plant growth at high altitude.

Unravelling how species communities change along environmental gradients requires a dual understanding: the direct responses of the species to their abiotic surroundings and the indirect variation of these responses through biotic interactions. Here, we focus on the interactive relationships between plants and their symbiotic root-associated fungi (RAF) along stressful abiotic gradients. We investigate whether variations in RAF community composition along altitudinal gradients influence plant growth at high altitudes, where both plants and fungi face harsher abiotic conditions.

Strategies for integrating scientific evidence in water policy and law in the face of uncertainty.

Understanding how human actions and environmental change affect water resources is crucial for addressing complex water management issues. The scientific tools that can produce the necessary information are ecological indicators, referring to measurable properties of the ecosystem state; environmental monitoring, the data collection process that is required to evaluate the progress towards reaching water management goals; mathematical models, linking human disturbances with the ecosystem state to predict environmental impacts; and scenarios, assisting in long-term management and policy implementation. Paradoxically, despite the rapid generation of data, evolving scientific understanding, and recent advancements in systems modeling, there is a striking imbalance between knowledge production and knowledge utilization in decision-making.

Recommendations for quantitative uncertainty consideration in ecology and evolution.

Ecological and evolutionary studies are currently failing to achieve complete and consistent reporting of model-related uncertainty. We identify three key barriers - a focus on parameter-related uncertainty, obscure uncertainty metrics, and limited recognition of uncertainty propagation - which have led to gaps in uncertainty consideration. However, these gaps can be closed.

Novel community data in ecology-properties and prospects.

New technologies for monitoring biodiversity such as environmental (e)DNA, passive acoustic monitoring, and optical sensors promise to generate automated spatiotemporal community observations at unprecedented scales and resolutions. Here, we introduce 'novel community data' as an umbrella term for these data. We review the emerging field around novel community data, focusing on new ecological questions that could be addressed; the analytical tools available or needed to make best use of these data; and the potential implications of these developments for policy and conservation.

LIES of omission: complex observation processes in ecology.

Advances in statistics mean that it is now possible to tackle increasingly sophisticated observation processes. The intricacies and ambitious scale of modern data collection techniques mean that this is now essential. Methodological research to make inference about the biological process while accounting for the observation process has expanded dramatically, but solutions are often presented in field-specific terms, limiting our ability to identify commonalities between methods.

The role of seasonality in shaping the interactions of honeybees with other taxa.

The Eltonian niche of a species is defined as its set of interactions with other taxa. How this set varies with biotic, abiotic and human influences is a core question of modern ecology. In seasonal environments, the realized Eltonian niche is likely to vary due to periodic changes in the occurrence and abundance of interaction partners and changes in species behavior and preferences.

Mixed effects of a national protected area network on terrestrial and freshwater biodiversity.

Protected areas are considered fundamental to counter biodiversity loss. However, evidence for their effectiveness in averting local extinctions remains scarce and taxonomically biased. We employ a robust counterfactual multi-taxon approach to compare occupancy patterns of 638 species, including birds (150), mammals (23), plants (39) and phytoplankton (426) between protected and unprotected sites across four decades in Finland.