German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig

Environmental sensor networks play a crucial role in monitoring key parameters essential for understanding Earth’s systems. To ensure the reliability and accuracy of collected data, effective quality control (QC) measures are essential. Conventional QC methods struggle to handle the complexity of environmental data. Conversely, advanced techniques such as neural networks, are typically not designed to process data from sensor networks with irregular spatial distribution. In this study, we focus on anomaly detection in environmental sensor networks using graph neural networks, which can represent sensor network structures as graphs. We investigate its performance on two datasets with distinct dynamics and resolution: commercial microwave link (CML) signal levels used for rainfall estimation and SoilNet soil moisture measurements. To evaluate the benefits of incorporating neighboring sensor information for anomaly detection, we compare two models: graph convolution network (GCN) and a graph-less baseline: long short-term memory (LSTM). Our robust evaluation through 5-fold cross-validation demonstrates the superiority of the GCN models. For CML, the mean area under receiver operating characteristic curve for the GCN was 0.941 compared to 0.885 for the baseline-LSTM, and for SoilNet, it was 0.858 for GCN and 0.816 for the baseline-LSTM. Visual inspection of CML time series revealed that the GCN proficiently classified anomalies and remained resilient against rain-induced events often misidentified by the baseline-LSTM. However, for SoilNet, the advantage of GCN was less pronounced, likely due to inconsistent and less precise labeling. Through interpretable model analysis, we demonstrate how feature attributions vividly illustrate the significance of neighboring sensor data, particularly in distinguishing between anomalies and expected changes in signal level in the time series.

Plant communities are composed of species that differ both in functional traits and evolutionary histories. As species’ functional traits partly result from their individual evolutionary history, we expect the functional diversity of communities to increase with increasing phylogenetic diversity. This expectation has only been tested at local scales and generally for specific growth forms or specific habitat types, for example, grasslands. Here we compare standardized effect sizes for functional and phylogenetic diversity among 1,781,836 vegetation plots using the global sPlot database. In contrast to expectations, we find functional diversity and phylogenetic diversity to be only weakly and negatively correlated, implying a decoupling between these two facets of diversity. While phylogenetic diversity is higher in forests and reflects recent climatic conditions (1981 to 2010), functional diversity tends to reflect recent and past climatic conditions (21,000 years ago). The independent nature of functional and phylogenetic diversity makes it crucial to consider both aspects of diversity when analysing ecosystem functioning and prioritizing conservation efforts.

South of 25°N, the rugged, riparian, mixed evergreen forests of eastern Bangladesh mark the western edge of the ranges of the globally Vulnerable Asiatic black bear Ursus thibetanus and sun bear Helarctos malayanus. According to the IUCN Red List, the distribution of bears in Bangladesh is unclear: black bears are described as ‘scattered’ and ‘likely to be very low in number’ and sun bears as ‘vagrants’ entering from the adjoining north-east Indian forests. These statements are not based on any population or habitat assessments, impeding focused research and conservation investment. We compiled recent evidence of bear presence in Bangladesh based on camera trapping, literature reviews and analysis of media reports. From peer-reviewed and grey literature published during 2010–2022 we traced 43 verifiable accounts of black bears in the country. Our camera-trap survey in Rajkandi Reserve Forest produced the first ever evidence of a small population of black bears in north-eastern Bangladesh. Two field studies (in 2016 and 2021) reported camera-trap observations and multiple incidents of poaching of sun bears in Kassalong Reserve Forest and Sangu-Matamuhuri Reserve Forest in south-eastern Bangladesh. Media reports on conflict incidents presented 83 human casualties (80 injured, three dead) and 13 bear casualties (six dead, seven rescued) during 2003–2023. The incidents peaked in the summer (17); 79% were reported during 2018–2023. Cognizant of the fact that the absence of evidence is not evidence of absence, our study calls for systematic conservation measures for both of these bear species in unprotected hill forests in eastern Bangladesh.

Conservation measures require accurate estimates of density and abundance and population trend assessments. The bonobo (Panpaniscus) is considered Endangered in the IUCN Red List. This classification assumes that available population data are representative. However, with only 30% of the bonobo’s historic geographical range surveyed, reliable information is needed to assess the species' population status. Here, we use information from 13 surveys conducted between 2002 and 2018 in an area of 42,000 km², representing ~27% of bonobo-suitable habitat: Salonga National Park and its corridor, Democratic Republic of the Congo (DRC). Using 8310 km of reconnaissance and transect walks and 27,045 days of camera trapping, we: (1) provide updated estimates of bonobo population density and distribution (42,000 km²; ~5,000 km² of which, to the best of our knowledge, have not been surveyed before by scientists), (2) assess population trends (15,758 km²; 2002–2008 vs 2012–2018), (3) compare estimates obtained with different methods, and (4) assess the factors driving bonobo density and distribution. Although we detected a non-significant population decline, our study suggests that Salonga is a bonobo stronghold, with a population ranging between 8244 and 18,308 mature individuals (density: 0.31 individuals/km²). Standing crop nest counts returned non-significantly lower density estimates than camera trap distance sampling. Nest count-estimates were higher in areas with Marantaceae understorey and those farther away from rivers, while camera trap-estimates were higher in areas with lower human presence. Regardless of the method, bonobos were rarer in proximity to villages. They occurred more often in areas of dense forest cover and in proximity to ranger posts. Our results point towards a declining bonobo population in Salonga, but do not provide sufficient evidence to confirm this statistically. Consequently, the continued monitoring of the bonobo population and preservation of the integrity of Salonga, considering its biological and cultural heritage, will be crucial in the preservation of this stronghold of wild bonobos.

Background Drug delivery to the brain is challenging due to the restrict permeability of the blood brain barrier (BBB). Recent studies indicate that BBB permeability increases over time during physiological aging likely due to factors (including extracellular vesicles (EVs)) that exist in the bloodstream. Therefore, inspiration can be taken from aging to develop new strategies for the transient opening of the BBB for drug delivery to the brain. Results Here, we evaluated the impact of small EVs (sEVs) enriched with microRNAs (miRNAs) overexpressed during aging, with the capacity to interfere transiently with the BBB. Initially, we investigated whether the miRNAs were overexpressed in sEVs collected from plasma of aged individuals. Next, we evaluated the opening properties of the miRNA-enriched sEVs in a static or dynamic (under flow) human in vitro BBB model. Our results showed that miR-383-3p-enriched sEVs significantly increased BBB permeability in a reversible manner by decreasing the expression of claudin 5, an important tight junction protein of brain endothelial cells (BECs) of the BBB, mediated in part by the knockdown of activating transcription factor 4 (ATF4). Conclusions Our findings suggest that engineered sEVs have potential as a strategy for the temporary BBB opening, making it easier for drugs to reach the brain when injected into the bloodstream. Graphical abstract

Forest restoration by planting tree seedlings is a crucial strategy to mitigate climate change and restore forest functions. The Intergovernmental Panel on Climate Change (IPCC) targets to remove around 70 Pg carbon (C) from the atmosphere via forest restoration. However, the impact of forest restoration on the recovery of soil organic carbon (SOC) and its driving factors remains unclear. Here, we conducted a global meta-analysis, based on 348 observations from 144 studies across 150 sites, to evaluate the recovery time of SOC and the driving factors of surface SOC recovery during forest restoration. We found that soil clay content and stand age were recognized as the dominant factors regulating SOC recovery during forest restoration. Overall, SOC recovery was lower in boreal and Mediterranean forests than that in tropical, subtropical, and temperate forests, lower in burned areas and mine sites than that in other sites, and lower in soils with 0%–20% clay contents than that in those with higher clay contents, and comparable among soils with different pH values. Across studies, surface SOC in restored forests with stand ages ranging from 1 to 200 years did not fully recover to the levels of reference forests. However, the SOC recovery rate was roughly twice as fast in tree polycultures (~ 10 years to plateau) as that in monocultures (~ 20 years). This global synthesis identifies critical drivers of SOC recovery during forest restoration and provides important insights into SOC management in forests. Graphical Abstract

Environmental filtering and dispersal history limit plant distributions and affect biogeographical patterns, but how their relative importance varies across evolutionary timescales is unresolved. Phylogenetic beta diversity quantifies dissimilarity in evolutionary relatedness among assemblages and might help resolve the ecological and biogeographical mechanisms structuring biodiversity. Here, we examined the effects of environmental dissimilarity and geographical distance on phylogenetic and taxonomic turnover for ~270,000 seed plant species globally and across evolutionary timescales. We calculated past and present dispersal barriers using palaeogeographical reconstructions and calculated geographical linear and least-cost distances, accounting for dispersal over water, mountains or areas with unsuitable climates. Environmental dissimilarity and geographical distance jointly explained most of the deviance in taxonomic (up to 86.4%) and phylogenetic turnover (65.6%). While environmental dissimilarity consistently showed strongly positive effects, the effect of geographical distance on phylogenetic turnover was less pronounced further back in evolutionary time. Past physiogeographical barriers explained a relatively low amount of the variation across all timescales, with a slight peak at intermediate timescales (20–50 Myr bp). Our results suggest that while old lineages have generally dispersed widely, the imprint of environmental filtering on range expansion persists, providing insights into biogeographical and evolutionary processes underlying global biodiversity patterns.

Effective conservation of migratory species relies on habitat protection throughout their annual cycle. Although protected areas (PAs) play a central role in conservation, their effectiveness at conserving habitats across the annual cycle of migratory species has rarely been assessed. We developed seasonal ecological niche models for 418 migratory butterfly species across their global distribution to assess whether they were adequately represented in the PAs across their full annual cycle. PA coverage was inadequate in at least one season for 84% of migratory butterflies, adequate for only 17% of species in one season, and inadequate for 45% of species in all seasons. There was marked geographic variation in PA coverage: 77% of species met representation targets in Sri Lanka, for example, but only 32% met targets in Italy. Our results suggest that coordinated efforts across multiple countries will be needed to develop international networks of PAs that cover the full annual cycle of migratory insects and that conservation measures, in addition to the establishment and maintenance of PAs, are likely to be needed to effectively conserve these species.

Increasing extreme climatic events threaten the functioning of terrestrial ecosystems1,2. Because soil microbes govern key biogeochemical processes, understanding their response to climate extremes is crucial in predicting the consequences for ecosystem functioning3,4. Here we subjected soils from 30 grasslands across Europe to four contrasting extreme climatic events under common controlled conditions (drought, flood, freezing and heat), and compared the response of soil microbial communities and their functioning with those of undisturbed soils. Soil microbiomes exhibited a small, but highly consistent and phylogenetically conserved, response under the imposed extreme events. Heat treatment most strongly impacted soil microbiomes, enhancing dormancy and sporulation genes and decreasing metabolic versatility. Microbiome response to heat in particular could be predicted by local climatic conditions and soil properties, with soils that do not normally experience the extreme conditions being imposed being most vulnerable. Our results suggest that soil microbiomes from different climates share unified responses to extreme climatic events, but that predicting the extent of community change may require knowledge of the local microbiome. These findings advance our understanding of soil microbial responses to extreme events, and provide a first step for making general predictions about the impact of extreme climatic events on soil functioning.

Over the course of human history, people have translocated plant and animal species, often with profound consequences. Understanding how endangered species adapt to human-mediated migration and novel environments is crucial to inform conservation strategies. The crested macaque (Macaca nigra), an endemic primate species of North Sulawesi (Indonesia), faces imminent extinction in its native range due to anthropogenic threats. While extensive research on this species has been conducted in the Duasudara Nature Reserve in North Sulawesi, critical knowledge gaps persist with regard to their distribution outside this protected area on Sulawesi and beyond. Previous studies report that crested macaques were introduced by humans to North Maluku ~200 hundred years ago. In 2023, we visited Bacan, Kasiruta, and southern Halmahera Island, conducting interviews, surveys, and direct observations of macaques to determine their presence or absence on these islands. We encountered wild crested macaques or their feces at 23 locations across these islands and pet macaques in 6 locations on Bacan. We confirm crested macaques on Bacan and also report them at Kasiruta and in the south of Halmahera, with results of our interviews suggesting that macaques might be present in North Maluku for ~500 years. We found no evidence of their presence on Mandioli. Additionally, we documented behavioral similarities, e.g., loud calls specific to male crested macaques. Our results extend the known distribution range of crested macaques by the islands of Kasiruta and Halmahera, shedding light on the potential for these populations to contribute to the survival of the species.

Analyzing the temporal dynamics of ecological communities can shed light on coexistence mechanisms and help understand how populations and communities will behave in the face of climate change. However, little is known about how frog communities respond to climate in urban ecosystems, especially in tropical countries. Here, we analyzed how frog species richness and abundance are influenced by weather variables both intra‐ and inter‐annually. We surveyed a peri‐urban area in central Brazil, monthly for 3 years. To test the effect of weather variables on species richness and abundance, we used Generalized Additive Mixed‐effects Models. We assessed seasonality using circular statistics. We also tested for differences in temporal beta diversity within and among years by estimating species disappearance and temporal rank shift, in addition to a multivariate model‐based method to test the effect of year on species composition. Finally, we tested how taxonomic and phylogenetic alpha diversity changed through time using a novel approach based on Hill numbers. We found that species richness varied little among years and was affected only by photoperiod, while species abundance was more variable both between and within years, being mostly affected by humidity, temperature, and photoperiod. Species composition varied little between years, mostly between the first and subsequent years. Conversely, beta diversity was highest within years. Only the effective number of species changed significantly through time. Our results help not only understand temporal mechanisms that allow species coexistence, but also allow to make inferences about the impact of urbanization on biodiversity in recently urbanized landscapes, showing that species composition in peri‐urban sites remains unaltered in a mid‐timescale, especially when climate conditions change little across years.

There remains considerable doubt, debate, and confusion regarding how biodiversity responds to gradients of important environmental drivers, such as habitat size, resource productivity, and disturbance. Here we develop a simple but comprehensive theoretical framework based on competition–colonization multispecies communities to examine the separate and interactive effects of these drivers. Using both numerical simulations and analytical arguments, we demonstrate that the critical trade‐off between competitive and colonization ability can lead to complex nonlinear, zig‐zag responses in both species richness and the inverse Simpson index along gradients of these drivers. Furthermore, we find strong interactions between these drivers that can dramatically shift the response of biodiversity to these gradients. The zig‐zag patterns in biodiversity along ecological gradients, together with the strong interactions between the drivers, can explain the mixed findings of empirical studies and syntheses, thereby providing a new paradigm that can reconcile debates on the relationships between biodiversity and multiple drivers.

Chromatin modeling enables the characterization of chromatin architecture at a resolution so far unachievable with experimental techniques. Polymer models fill our knowledge gap on a wide range of structures, from chromatin loops to nuclear compartments. Many physical properties already known for polymers can thus explain the dynamics of chromatin. With molecular simulations, it is possible to probe an ensemble of conformations, which attest to the variability observed in individual cells and the general behavior of a population of cells. In this review, we describe universal characteristics of polymers that chromatin carries. We introduce how these characteristics can be assessed with polymer simulations while also addressing specific aspects of chromatin and its environment. Finally, we give examples of plant chromatin models that, despite their paucity, augur well for the future of polymer simulations to plant chromosome biology.

In Europe, various conservation programs adopted to maintain or restore biodiversity have experienced differing levels of success. However, a synthesis about major factors for success of biodiversity-related conservation programs across ecosystems and national boundaries, such as incentives, subsidies, enforcement, participation, or spatial context, is missing. Using a balanced scorecard survey among experts, we analyzed and compared factors contributing to success or failure of three different conservation programs: two government programs (Natura 2000 and the ecological measures of the Water Framework Directive) and one conservation program of a non-governmental organization (NGO; Rewilding Europe), all focusing on habitat and species conservation. The experts perceived the NGO program as more successful in achieving biodiversity-related aims than governmental conservation legislation. Among the factors perceived to influence the success of biodiversity conservation, several stood out: Biodiversity-damaging subsidies, external economic interests competing with conservation goals or policies conflicting with biodiversity conservation were recognized as major factors for the lack of conservation success. Outreach to raise societal interest and awareness as well as stakeholder involvement were perceived as closely related to the success of programs. Our expert survey demonstrated that external factors from economy and policy often hinder success of conservation programs, while societal and environmental factors rather contribute to it. This study implies that conservation programs should be designed to be as inclusive as possible and provides a basis for developing a standardized methodology that explicitly considers indirect drivers from areas such as economy, policy and society.

Leaf dark respiration (Rdark), an important yet rarely quantified component of carbon cycling in forest ecosystems, is often simulated from leaf traits such as the maximum carboxylation capacity (Vcmax), leaf mass per area (LMA), nitrogen (N) and phosphorus (P) concentrations, in terrestrial biosphere models. However, the validity of these relationships across forest types remains to be thoroughly assessed. Here, we analyzed Rdark variability and its associations with Vcmax and other leaf traits across three temperate, subtropical and tropical forests in China, evaluating the effectiveness of leaf spectroscopy as a superior monitoring alternative. We found that leaf magnesium and calcium concentrations were more significant in explaining cross‐site Rdark than commonly used traits like LMA, N and P concentrations, but univariate trait–Rdark relationships were always weak (r² ≤ 0.15) and forest‐specific. Although multivariate relationships of leaf traits improved the model performance, leaf spectroscopy outperformed trait–Rdark relationships, accurately predicted cross‐site Rdark (r² = 0.65) and pinpointed the factors contributing to Rdark variability. Our findings reveal a few novel traits with greater cross‐site scalability regarding Rdark, challenging the use of empirical trait–Rdark relationships in process models and emphasize the potential of leaf spectroscopy as a promising alternative for estimating Rdark, which could ultimately improve process modeling of terrestrial plant respiration.

The increasing online availability of biodiversity data and advances in ecological modeling have led to a proliferation of open‐source modeling tools. In particular, R packages for species distribution modeling continue to multiply without guidance on how they can be employed together, resulting in high fidelity of researchers to one or several packages. Here, we assess the wide variety of software for species distribution models (SDMs) and highlight how packages can work together to diversify and expand analyses in each step of a modeling workflow. We also introduce the new R package ‘sdmverse' to catalog metadata for packages, cluster them based on their methodological functions, and visualize their relationships. To demonstrate how pluralism of software use helps improve SDM workflows, we provide three extensive and fully documented analyses that utilize tools for modeling and visualization from multiple packages, then score these tutorials according to recent methodological standards. We end by identifying gaps in the capabilities of current tools and highlighting outstanding challenges in the development of software for SDMs.