Environmental heterogeneity predicts global species richness patterns better than area

Aim It is widely accepted that biodiversity is influenced by both niche‐related and spatial processes from local to global scales. Their relative importance, however, is still disputed, and empirical tests are surprisingly scarce at the global scale. Here, we compare the importance of area (as a proxy for pure spatial processes) and environmental heterogeneity (as a proxy for niche‐related processes) for predicting native mammal species richness world‐wide and within biogeographical regions. Location Global. Time period We analyse a spatial snapshot of richness data collated by the International Union for Conservation of Nature. Major taxa studied All terrestrial mammal species, including possibly extinct species and species with uncertain presence. Methods We applied a spreading dye algorithm to analyse how native mammal species richness changes with area and environmental heterogeneity. As measures for environmental heterogeneity, we used elevation ranges and precipitation ranges, which are well‐known correlates of species richness. Results We found that environmental heterogeneity explained species richness relationships better than did area, suggesting that niche‐related processes are more prevalent than pure area effects at broad scales. Main conclusions Our results imply that niche‐related processes are essential to understand broad‐scale species–area relationships and that habitat diversity is more important than area alone for the protection of global biodiversity

Advancing an interdisciplinary framework to study seed dispersal ecology

Although dispersal is generally viewed as a crucial determinant for the fitness of any organism, our understanding of its role in the persistence and spread of plant populations remains incomplete. Generalizing and predicting dispersal processes are challenging due to context dependence of seed dispersal, environmental heterogeneity and interdependent processes occurring over multiple spatial and temporal scales. Current population models often use simple phenomenological descriptions of dispersal processes, limiting their ability to examine the role of population persistence and spread, especially under global change. To move seed dispersal ecology forward, we need to evaluate the impact of any single seed dispersal event within the full spatial and temporal context of a plant’s life history and environmental variability that ultimately influences a population’s ability to persist and spread. In this perspective, we provide guidance on integrating empirical and theoretical approaches that account for the context dependency of seed dispersal to improve our ability to generalize and predict the consequences of dispersal, and its anthropogenic alteration, across systems. We synthesize suitable theoretical frameworks for this work and discuss concepts, approaches and available data from diverse subdisciplines to help operationalize concepts, highlight recent breakthroughs across research areas and discuss ongoing challenges and open questions. We address knowledge gaps in the movement ecology of seeds and the integration of dispersal and demography that could benefit from such a synthesis. With an interdisciplinary perspective, we will be able to better understand how global change will impact seed dispersal processes, and potential cascading effects on plant population persistence, spread and biodiversity

Emotional associations with soundscape reflect human-environment relationships

In line with the development of socio-ecological perspectives in conservation science, there is increasing interest in the role of soundscape perception in understanding human-environment interactions; the impact of natural soundscapes on human wellbeing is also increasingly recognized. However, research to date has focused on preferences and attitudes to western, urban locations. This study investigated individual emotional associations with local soundscape for three social groups living in areas with distinct degrees of urbanization, from pristine forest and pre-urban landscapes in Ecuador, to urban environments in UK and USA. Participants described sounds that they associated with a range of emotions, both positive and negative, which were categorized according to an adapted version of Schafer’s sound classification scheme. Analyses included a description of the sound types occurring in each environment, an evaluation of the associations between sound types and emotions across social groups, and the elaboration of a soundscape perception map. Statistical analyses revealed that the distribution of sound types differed between groups, reflecting essential traits of each soundscape and tracing the gradient of urbanization. However, some associations were universal: Natural Sounds were primarily associated with positive emotions, whereas Mechanical and Industrial Sounds were linked to negative emotions. Within nonurban environments, natural sounds were associated with a much wider range of emotions. Our analyses suggest that Natural Sounds could be considered as valuable natural resources that promotes human wellbeing. Special attention is required within these endangered forest locations, which should be classified as a ‘threatened soundscapes’, as well as ‘threatened ecosystems’, as we begin to understand the role of soundscape for the wellbeing of the local communities. The methodology presented in this paper offers a fast, cheap tool for identifying reactions towards landscape modification and identifying sounds of social relevance. The potential contribution of soundscape perception within the current conservation approaches is discussed

Employing plant functional groups to advance seed dispersal ecology and conservation

Seed dispersal enables plants to reach hospitable germination sites and escape natural enemies. Understanding when and how much seed dispersal matters to plant fitness is critical for understanding plant population and community dynamics. At the same time, the complexity of factors that determine if a seed will be successfully dispersed and subsequently develop into a reproductive plant is daunting. Quantifying all factors that may influence seed dispersal effectiveness for any potential seed-vector relationship would require an unrealistically large amount of time, materials and financial resources. On the other hand, being able to make dispersal predictions is critical for predicting whether single species and entire ecosystems will be resilient to global change. Building on current frameworks, we here posit that seed dispersal ecology should adopt plant functional groups as analytical units to reduce this complexity to manageable levels. Functional groups can be used to distinguish, for their constituent species, whether it matters (i) if seeds are dispersed, (ii) into what context they are dispersed and (iii) what vectors disperse them. To avoid overgeneralization, we propose that the utility of these functional groups may be assessed by generating predictions based on the groups and then testing those predictions against species-specific data. We suggest that data collection and analysis can then be guided by robust functional group definitions. Generalizing across similar species in this way could help us to better understand the population and community dynamics of plants and tackle the complexity of seed dispersal as well as its disruption

Converting Property Graphs to RDF: A Preliminary Study of the Practical Impact of Different Mappings

Today's space of graph database solutions is characterized by two main technology stacks that have evolved separate from one another: on one hand, there are systems that focus on supporting the RDF family of standards; on the other hand, there is the Property Graph category of systems. As a basis for bringing these stacks together and, in particular, to facilitate data exchange between the different types of systems, different direct mappings between the underlying graph data models have been introduced in the literature. While fundamental properties are well-documented for most of these mappings, the same cannot be said about the practical implications of choosing one mapping over another. Our research aims to contribute towards closing this gap. In this paper we report on a preliminary study for which we have selected two direct mappings from (Labeled) Property Graphs to RDF, where one of them uses features of the RDF-star extension to RDF. We compare these mappings in terms of the query performance achieved by two popular commercial RDF stores, GraphDB and Stardog, in which the converted data is imported. While we find that, for both of these systems, none of the mappings is a clear winner in terms of guaranteeing better query performance, we also identify types of queries that are problematic for the systems when using one mapping but not the other.This work was funded by the Swedish Research Council (Vetenskapsrådet, project reg. no. 2019-05655) and by the CENIIT program at Linköping University (project no. 17.05).The software related to this work can be found in the following repository on Github: https://github.com/LiUSemWeb/GRADES2022-paper</p

High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cells

Synthetic riboswitches mediating ligand-dependent RNA cleavage or splicing-modulation represent elegant tools to control gene expression in various applications, including next-generation gene therapy. However, due to the limited understanding of context-dependent structure-function relationships, the identification of functional riboswitches requires large-scale-screening of aptamer-effector-domain designs, which is hampered by the lack of suitable cellular high-throughput methods. Here we describe a fast and broadly applicable method to functionally screen complex riboswitch libraries (~1.8 × 104 constructs) by cDNA-amplicon-sequencing in transiently transfected and stimulated human cells. The self-barcoding nature of each construct enables quantification of differential mRNA levels without additional pre-selection or cDNA-manipulation steps. We apply this method to engineer tetracycline- and guanine-responsive ON- and OFF-switches based on hammerhead, hepatitis-delta-virus and Twister ribozymes as well as U1-snRNP polyadenylation-dependent RNA devices. In summary, our method enables fast and efficient high-throughput riboswitch identification, thereby overcoming a major hurdle in the development cascade for therapeutically applicable gene switches

Riboswitch-mediated Attenuation of Transgene Cytotoxicity Increases Adeno-associated Virus Vector Yields in HEK-293 Cells

Cytotoxicity of transgenes carried by adeno-associated virus (AAV) vectors might be desired, for instance, in oncolytic virotherapy or occur unexpectedly in exploratory research when studying sparsely characterized genes. To date, most AAV-based studies use constitutively active promoters (e.g., the CMV promoter) to drive transgene expression, which often hampers efficient AAV production due to cytotoxic, antiproliferative, or unknown transgene effects interfering with producer cell performance. Therefore, we explored artificial riboswitches as novel tools to control transgene expression during AAV production in mammalian cells. Our results demonstrate that the guanine-responsive GuaM8HDV aptazyme efficiently attenuates transgene expression and associated detrimental effects, thereby boosting AAV vector yields up to 23-fold after a single addition of guanine. Importantly, riboswitch-harboring vectors preserved their ability to express functional transgene at high levels in the absence of ligand, as demonstrated in a mouse model of AAV-TGFβ1-induced pulmonary fibrosis. Thus, our study provides the first application-ready biotechnological system-based on aptazymes, which should enable high viral vector yields largely independent of the transgene used. Moreover, the RNA-intrinsic, small-molecule regulatable mode of action of riboswitches provides key advantages over conventional transcription factor-based regulatory systems. Therefore, such riboswitch vectors might be ultimately applied to temporally control therapeutic transgene expression in vivo.publishe