Biodiversity Research Research Articles

Environmental DNA: The next chapter.

Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.

The Phyloperiodic Approach Removes the “Cryptic Species” and Puts forward Multilevel Organismal Diversity

The notion of the “cryptic species” has recently become an important agenda in biodiversity research. In this study, we show, by applying a periodic-like morphological and molecular framework to the nudibranch genus Cadlina from the world’s least explored locations in the Kuril Islands in the northwestern Pacific, including a description of six new species, that the term “cryptic species” should be removed from biodiversity research terminology. We explicitly show that different species of this complex have various degrees of molecular phylogenetic distances and morphological distinctness, revealing a truly multilevel system of fine-scale differences and similarities. Therefore, to designate any of these species as “cryptic” or “non-cryptic” would be completely arbitrary, non-operational, and generally meaningless. By this, we finally strongly propose to remove the notion of “crypticity” and the term “cryptic species” (in the sense of an “indistinguishable species”) from the arsenal of modern biology, including phylogeny and taxonomy. The importance of fine-scale species differentiation in the multilevel framework is shown for addressing conservation and global warming challenges. Six new species are named after scientists who have not always received the honours they deserve, including two women who did not receive their respective Nobel Prizes.

Too much diversity—Multiple definitions of geodiversity hinder its potential in biodiversity research

AbstractGeodiversity—the diversity of abiotic features and processes of the Earth's surface and subsurface—is an increasingly used concept in ecological research. A growing body of scientific literature has provided evidence of positive links between geodiversity and biodiversity. These studies highlight the potential of geodiversity to improve our understanding of biodiversity patterns and to complement current biodiversity conservation practices and strategies. However, definitions of geodiversity in ecological research vary widely. This can hinder the progress of geodiversity–biodiversity research and make it difficult to synthesize findings across studies. We therefore call for greater awareness of how geodiversity is currently defined and for more consistent use of the term ‘geodiversity’ in biodiversity research.

Navigating taxonomic complexity: A use-case report on FAIR scientific name-matching service usage in ENVRI Research Infrastructures

This paper presents a use-case conducted within the ENVRI FAIR project, examining challenges and opportunities in deploying FAIR-aligned (ensuring Findability, Accessibility, Interoperability and Reusability) scientific name-matching services across Environmental Research Infrastructures (RIs). Six services were tested using various name variations, revealing inconsistencies in match types, status reporting and handling of canonical forms and typos. These diversities pose challenges for RI data pipelines and interoperability. The paper underscores the importance of standardised tools, enhanced communication, training, collaboration and shared resources. Addressing these needs can facilitate more effective FAIR implementation within the ENVRI community and biodiversity research. This, in turn, will empower RIs to seamlessly integrate and leverage scientific names, unlocking the full potential of their data for research and policy implementation.

Refining taxonomic identification of microalgae through molecular and genetic evolution: a case study of Prorocentrum lima and Prorocentrum arenarium.

Species delimitation based on lineage definition has become increasingly popular. However, these methods have been limited, especially for species that lack genomic data and are morphologically similar. The trickiest part for the species identification is that the interspecific and intraspecific boundaries are vague. Taking Prorocentrum (Dinophyta) as an example, analysis of cell morphology, growth, and toxin synthesis in both species of P. lima and P. arenarium does not provide a reliable basis for species delineation. However, through phylogenetic and genetic distance analyses of their ITS and LSU sequences, establishment of evolutionary tree based on orthologous gene sequences, and combining the results of automatic barcode gap discovery and Poisson tree processes models, it was sustained that P. arenarium does not belong to the P. lima complex and should be considered as an independent species. Interspecies genetic evolution analysis revealed that P. lima and P. arenarium may contribute to evolutionary direction that favors combating reverse environmental factors. In P. lima, viral invasion may be one of the reasons for its large genome size. In the study, P. lima complex has been selected as an example to enhance the taxonomic identification of microalgae through molecular and genetic evolution, offering valuable insights into refining taxonomic identification and promoting microbial biodiversity research in other species.IMPORTANCEMicroalgae, especially the species known as Prorocentrum, have received significant attention due to their ability to trigger harmful algal blooms and produce toxins. However, the boundaries between species and within species are ambiguous. Clear and comprehensive species delineation indicates that Prorocentrum arenarium should be considered as an independent species, separate from the Prorocentrum lima complex. Improving the classification and identification of microalgae through molecular and genetic evolution will provide reference points for other cryptic species. Prorocentrum occupy multiple ecological niches in marine environments, and studying their evolutionary direction contributes to understanding their ecological adaptations and community succession.

Temporal β-Diversity Decomposition: Insights into Fish Biodiversity Dynamics in the Moroccan South Atlantic.

Understanding the various aspects of temporal β-diversity and their relationships can profoundly enhance the knowledge of the intricate dynamics of biodiversity over temporal scales. In this study, we examined extensive data on fish in the Moroccan South Atlantic, to quantify taxonomic and functional temporal β-diversity over three five-year periods, determine the relative contributions of turnover and nestedness to each facet, and elucidate the relationship between taxonomic and functional temporal β-diversity including their components using temporal and spatial comparisons. Our findings revealed a complex relationship between taxonomic and functional temporal β-diversity, with decoupled variation often observed. Furthermore, the predominant component of functional temporal β-diversity was functional nestedness, while species turnover had a greater impact on taxonomic temporal β-diversity. A noteworthy observation was the significant fluctuation in the turnover and nestedness components, despite consistent temporal β-diversity. These insights underscore the pivotal role of temporal β-diversity decomposition and advocate for the integration of functional aspects in temporal biodiversity research to provide additional key indicators for biodiversity sustainable management.

2018年浙江古田山24公顷亚热带常绿阔叶林动态监测样地林冠结构和地形数据集

The canopy structure and topographic variables jointly influence the spatiotemporal variation of habitats for important species. However, there remains a considerable scarcity of precise forest canopy structure and topographic data obtained from large-scale forest dynamic plots. LiDAR data, acquired via near-surface remote sensing platforms, facilitates precise computation of both canopy structure and topographic variables. This study selected a 24-hectare dynamic plot in the subtropical evergreen broadleaf forest, located in the core conservation area of Qianjiangyuan National Park, as its focal point for survey. We conducted an analysis and quality control process on the point cloud data in 2018 using a near-surface remote sensing platform for this area, aiming to acquire corresponding canopy structure and topography data. Ground data collected through Real-Time Kinematic (RTK) surveying were used to verify and validate the accuracy of the digital elevation model (DEM). The analysis revealed a mean square error of elevation of 0.07 meters, suggesting a high level of accuracy of the dataset. The 24-hectare subtropical evergreen broad-leaved forest dynamic plot represents a typical low-altitude evergreen broad-leaved forest in the central subtropical region. This dataset can provide essential data support for the monitoring and research of biodiversity in subtropical broadleaved evergreen forests.

Mapping an endangered living fossil's distribution, threats, and protection coverage

AbstractSpecies Distribution Models have emerged in recent decades as a powerful tool for biodiversity research, as they allow, for example, assessing the status of species in their whole distributions. These models have been particularly helpful in demonstrating that amphibian populations are at high risk, with many declining and others already extinct. Here, we assessed the potential distribution of the helmeted water toad (Calyptocephalella gayi), an endemic Chilean amphibian considered a living fossil and cataloged as vulnerable, which requires significant conservation efforts. We modeled the species' potential distribution using the Maximum Entropy (Maxent) approach and determined the overlap with national protected areas. In addition, we conducted a geospatial risk analysis to estimate the threat level to which this toad is being subjected. The potential distribution of C. gayi ranges from 28°S to 44°S, mainly explained by altitude, mean diurnal temperature range, slope, and distance to water bodies. Protected areas only cover 3.55% of the species' potential geographic distribution, which is of concern, considering that the geospatial risk analysis showed that 60.61% of C. gayi's distribution is subjected to extreme and high risks. We discuss how these results are relevant to focusing and directing efficient protection and conservation efforts for this species shortly.

Language matters for biodiversity

Abstract Language is central to the way people learn about the natural world. A salient concern of the biodiversity conservation arena has been to understand how language can be employed by scientists to communicate knowledge to nonexpert audiences and build ecological literacy. The use of analogy and narrative by scientists are prominent techniques. In this article, we consider how these two modes of language-based reasoning extend into ordinary conversational language use by the public, specifically when articulating everyday understanding and experiences of biodiversity. Drawing on a process of public engagement in a UK woodland environment, a typological framework based on principles of analogical and narrative reasoning is developed to characterize the precise character of processes of everyday biodiversity sense making. The implications of the framework are discussed in the context of future biodiversity research, particularly its participatory and educational dimensions.

Environmental DNA time series analysis of a temperate stream reveals distinct seasonal community and functional shifts

AbstractEnvironmental DNA (eDNA) extracted from water is routinely used in river biodiversity research, and via metabarcoding eDNA can provide comprehensive taxa lists with little effort and cost. However, eDNA‐based species detection in streams and rivers may be influenced by sampling season and other key factors such as water temperature and discharge. Research linking these factors and also informing on the potential of eDNA metabarcoding to detect shifts in ecological signatures, such as species phenology and functional feeding groups across seasons, is missing. To address this gap, we collected water samples every 2 weeks for 15 months at a long‐term ecological research (LTER) site and at three different positions in the river's cross section, specifically the water surface, riverbed, and riverbank. For these 102 samples, we analyzed macroinvertebrate species and molecular operational taxonomic unit (OTU) richness and temporal community turnover across seasons based on cytochrome c oxidase subunit I (COI) metabarcoding data. Using Generalized Additive Models, we found a significant influence of sampling season on species richness. Community turnover followed a cyclic pattern, reflecting the continuous change of the macroinvertebrate community throughout the year (“seasonal clock”). Although water temperature had no influence on the inferred species richness, higher discharge reduced the number of Annelida and Ephemeroptera species detectable with eDNA. Most macroinvertebrate taxa showed the highest species richness in spring, in particular merolimnic species with univoltine life cycles. Further, we detected an increase in the proportion of shredders in winter and parasites in summer. Our results show the usefulness of highly resolved eDNA metabarcoding time series data for ecological research and biodiversity monitoring in streams and rivers.

A new checklist of Slovenian leeches (Hirudinea: Euhirudinea): In memory of Boris Sket (1936–2023)

The new (as of 2023) checklist of Slovenian leeches (Euhirudinea) contains 33 species, which represents a 44% increase since the last published inventory in 2003. Notable new entries include Placobdella costata found parasitizing on European pond turtles, the marine fish leech Trachelobdella lubrica from the Slovenian Adriatic coast, the semi-terrestrial Haemopis elegans, the terrestrial Xerobdella praealpina – making Slovenia possibly the only country with confirmed occurrence of all three European land leeches – and a new, still undescribed highly troglomorphic cave leech from a deep Dinaric cave. The number of freshwater fish leeches is underwhelmingly low: two. This, and several unresolved taxonomic questions in erpobdellids suggest that more faunistic and taxonomic work is needed and that the list of Slovenian leech species is far from concluded. The authors dedicate this contribution to their teacher, Prof. Boris Sket (1936–2023), a leading figure in biodiversity research in the Dinaric Karst, including leeches and cave life.

A Survey and Analysis of the History of Ernest Henry Wilson’s Specimen Collections in China

Since the mid-17th century, Western plant collectors have explored Asia, particularly China, to collect native species for economic and botanical development. Ernest Henry Wilson (1876–1930) stands among the foremost figures in this pursuit. He conducted five plant collections in China between 1899 and 1918, gaining recognition for numerous valuable ornamental species. However, precise details such as the total number of specimens, a comprehensive species list, and the collection locations remained elusive, hindering a thorough assessment of his scientific contributions. To address this gap, we compiled data from various online databases and relevant publications, constructing a comprehensive dataset encompassing species names, collection dates, locations, and additional pertinent information. Employing Python, we organized and translated the species names and locations, facilitating analysis of families, genera, species, and the completeness and preferences of his collection. The conclusions drawn from the available data include 19,218 specimens, with 11,884 collection numbers, belonging to 200 families, 1046 genera, and 3794 species (including 342 infraspecific taxa). Wilson exhibited a preference for woody and flowering plants, resulting in a collection completeness of 25%. His collection spanned seven provinces, 28 prefecture-level cities, and 38 county-level areas, underscoring his significant contributions to the global dissemination of Chinese plant knowledge. This study conducts a comprehensive analysis of the plant specimens collected by Wilson in China, investigating their taxonomy, distribution, and historical context and evaluating Wilson’s contribution to plant dissemination. The findings serve as a valuable reference for subsequent biodiversity research endeavors.

Woody plant taxonomic, functional, and phylogenetic diversity decrease along elevational gradients in Andean tropical montane forests: environmental filtering and arrival of temperate taxa

Mountains are paramount for exploring biodiversity patterns due to the mosaic of topographies and climates encompassed over short distances. Biodiversity research has traditionally focused on taxonomic diversity when investigating changes along elevational gradients, but other facets should be considered. For first time, we simultaneously assessed elevational trends in taxonomic, functional, and phylogenetic diversity of woody plants in Andean tropical montane forests and explored their underlying ecological and evolutionary causes. This investigation covered four transects (traversing ca. 2,200 m a.s.l.) encompassing 114 plots of 0.1 ha across a broad latitudinal range (ca. 10°). Using Hill numbers to quantify abundance-based diversity among 37,869 individuals we observed a consistent decrease in taxonomic, functional, and phylogenetic diversity as elevation increased, although the decrease was less pronounced for higher Hill orders. The exception was a slight increase in phylogenetic diversity when dominant species were over-weighted. The decrease in taxonomic and functional diversity might be attributed to an environmental filtering process towards highlands, where the increasingly harsher conditions exclude species and functional strategies. Besides, the differences in steepness decrease between Hill orders suggest that rare species disproportionately contribute to functional diversity. For phylogenetic diversity the shifting elevational trend between Hill orders indicates a greater than previously considered influence in central Andean highlands of tropical lowlands originated species with strong niche conservatism relative to distantly related temperate lineages. This could be explained by a decreasing presence and abundance of temperate, extratropical taxa towards the central Andes relative to northern or southern Andes, where they are more prevalent.

Fostering biodiversity research in post-fire biology

The impacts of wildfire on vegetation and soil erosion have been studied for decades aiming to bring back ecosystems after fire perturbance. However, the influence of fires on above and belowground biodiversity remains far less understood. Biodiversity is critical for supporting ecosystem function, and this data scarcity is hampering managers in adopting effective practices for a proper restoration of burned ecosystems. This limitation could be overcome by future research that should focus post-fire diversity of plants and soil biota, by (i) analysing the environmental factors driving post-fire evolutionary trends; (ii) exploring their interrelations across different spatial and temporal scales; (iii) identifying the variability across fires of different severities and frequency; (iv) ascertaining the post-fire response of individual plant species and soil taxa to fire with or without application of post-fire restoration actions.

Treemendous: an R package for integrating taxonomic information across backbones.

Standardizing and translating species names from different databases is key to the successful integration of data sources in biodiversity research. There are numerous taxonomic name-resolution applications that implement increasingly powerful name-cleaning and matching approaches, allowing the user to resolve species relative to multiple backbones simultaneously. Yet there remains no principled approach for combining information across these underlying taxonomic backbones, complicating efforts to combine and merge species lists with inconsistent and conflicting taxonomic information. Here, we present Treemendous, an open-source software package for the R programming environment that integrates taxonomic relationships across four publicly available backbones to improve the name resolution of tree species. By mapping relationships across the backbones, this package can be used to resolve datasets with conflicting and inconsistent taxonomic origins, while ensuring the resulting species are accepted and consistent with a single reference backbone. The user can chain together different functionalities ranging from simple matching to a single backbone, to graph-based iterative matching using synonym-accepted relations across all backbones in the database. In addition, the package allows users to 'translate' one tree species list into another, streamlining the assimilation of new data into preexisting datasets or models. The package provides a flexible workflow depending on the use case, and can either be used as a stand-alone name-resolution package or in conjunction with existing packages as a final step in the name-resolution pipeline. The Treemendous package is fast and easy to use, allowing users to quickly merge different data sources by standardizing their species names according to the regularly updated database. By combining taxonomic information across multiple backbones, the package increases matching rates and minimizes data loss, allowing for more efficient translation of tree species datasets to aid research into forest biodiversity and tree ecology.

Aggregated time‐series features boost species‐specific differentiation of true and false positives in passive acoustic monitoring of bird assemblages

AbstractPassive acoustic monitoring (PAM) has gained increasing popularity to study behaviour, habitat preferences, distribution and community assembly of birds and other animals. Automated species classification algorithms like ‘BirdNET’ are capable of detecting and classifying avian vocalizations within extensive audio data, covering entire species assemblages. PAM reveals substantial potential for biodiversity monitoring that informs evidence‐based conservation. Nevertheless, fully realizing this potential remains challenging, especially due to the issue of false‐positive species detections. Here, we introduce an optimized thresholding framework, which incorporates contextual information extracted from the time‐series of automated species detections (i.e. covariates on quality and quantity of species' detections measured at varying time intervals) to improve the differentiation of true and false positives. We verified a sample of BirdNET detections per species and modelled species‐specific thresholds using conditional inference trees. These thresholds were designed to minimize false‐positive detections while maximizing the preservation of true positives in the dataset. We tested this framework for a large dataset of BirdNET detections (5760 h of audio data, 60 sites) recorded over an entire breeding season. Our results revealed considerable interspecific variability of precision (percentage of true positives) within raw BirdNET data. Our optimized thresholding approach achieved high precision (≥0.9) for 70% of the 61 detected species, while species‐specific thresholds solely relying on the BirdNET confidence scores achieved high precision for only 31% of the species. Conservative universal thresholds (not species‐specific) reached high precision for 48% of the species. Our thresholding approach outperformed previous thresholding approaches and enhanced interspecific comparability for bird community analyses. By incorporating contextual information from the time‐series of species detections, the differentiation of true and false positives was substantially improved. Our approach may enhance a straightforward application of PAM in biodiversity research, landscape planning and evidence‐based conservation.

Website Development on TNUK Biodiversity Material Based on Research Results to Improve Students Conservation Literacy

This study was prompted by the lack of maximization of the use of learning media, especially the use of information and communication technology (ICT) based media, resulting in the lack of learning resources on biodiversity topics and the lack of understanding of conservation education among 7th grade students. The purpose of the research is the determination of the level of validity of the developed web site. Research and development adapted from Thiagarajan's development model was used as the method. The research tools used in this study were interviewing and validating sheets. The steps of exploring potentials and problems, data collection, product design, product validation and product revision were used to develop the website learning media. The results showed that the validity level of biodiversity research website material to improve conservation literacy among seventh graders was 89% with a very valid category, so it can be used for learning.

Urban Green Connectivity Assessment: A Comparative Study of Datasets in European Cities

Urban biodiversity and ecosystem services depend on the quality, quantity, and connectivity of urban green areas (UGAs), which are crucial for enhancing urban livability and resilience. However, assessing these connectivity metrics in urban landscapes often suffers from outdated land cover classifications and insufficient spatial resolution. Spectral data from Earth Observation, though promising, remains underutilized in analyzing UGAs’ connectivity. This study tests the impact of dataset choices on UGAs’ connectivity assessment, comparing land cover classification (Urban Atlas) and spectral data (Normalized Difference Vegetation Index, NDVI). Conducted in seven European cities, the analysis included 219 UGAs of varying sizes and connectivity levels, using three connectivity metrics (size, proximity index, and surrounding green area) at different spatial scales. The results showed substantial disparities in connectivity metrics, especially at finer scales and shorter distances. These differences are more pronounced in cities with contiguous UGAs, where Urban Atlas faces challenges related to typology issues and minimum mapping units. Overall, spectral data provides a more comprehensive and standardized evaluation of UGAs’ connectivity, reducing reliance on local typology classifications. Consequently, we advocate for integrating spectral data into UGAs’ connectivity analysis to advance urban biodiversity and ecosystem services research. This integration offers a comprehensive and standardized framework for guiding urban planning and management practices.

Hierarchical-taxonomy-aware and attentional convolutional neural networks for acoustic identification of bird species: A phylogenetic perspective

The study of bird populations is crucial for biodiversity research and conservation. Deep artificial neural networks have revolutionized bird acoustic recognition; however, most methods overlook inherent relationships among bird populations, resulting in the loss of biological information. To address this limitation, we propose the Phylogenetic Perspective Neural Network (PPNN), which incorporates hierarchical multilevel labels for each bird. PPNN uses a hierarchical semantic embedding framework to capture feature information at different levels. Attention mechanisms are employed to extract and select common and distinguishing features, thereby improving classification accuracy. We also propose a path correction strategy to rectify inconsistent predictions. Experimental results on bird acoustic datasets demonstrate that PPNN outperforms current methods, achieving classification accuracies of 90.450%, 91.883%, and 89.950% on the Lishui-Zhejiang Birdsdata (100 species), BirdCLEF2018-Small (150 species), and BirdCLEF2018-Large (500 species) datasets respectively, with the lowest hierarchical distance of a mistake across all datasets. Our proposed method is applicable to any bird acoustic dataset and presents significant advantages as the number of categories increases.

Biodiversity, mental health and well-being: psychological mechanisms and moderators of a complex relationship (BIOWELL)

Human activities and their consequences, such as environmental pollution, the exploitation of resources or deforestation, are major causes of biodiversity loss. However, humans depend on a biologically diverse and healthy environment in many ways, as it provides access to clean water, air and food. The loss of biodiversity is an ecological crisis that threatens human health, and ultimately their very existence. At the same time, there is an unwavering interest in the positive effects of "nature" on mental health. Although these examples point to a connection between biodiversity and health, little is known about the causal effects of different facets of biodiversity on mental health. Exploring these relationships and the underlying psychological mechanisms is a major goal of this project. We will build on the expertise of an interdisciplinary team involving scholars from psychology, biodiversity research, human geography, and behavioural economics and combine this expertise with a variety of methods, with a focus on quantitative research, experimental and intervention designs, and investigate participants from different age groups to understand the causal effects of different environments with varying degrees of biological diversity on mental health, and to identify the physical, social, and psychological boundary conditions of these causal effects.