Biodiversity Research Articles

Early warning system on harmful aquatic organisms at a regional sea scale: Components and mechanisms

The introduction of harmful aquatic organisms and pathogens (HAOP) via the ballast water of ships can endanger human health, the environment, economic resource-related systems, as well as impair biological diversity. Early warning systems (EWS) are highly effective instruments for mitigating risks and enhancing readiness in the face of potential disasters, including those resulting from HAOP. The establishment of a regional EWS for the identification and notification of harmful organisms is a complex marine policy process involving communication with stakeholders, technical development, engagement of regional knowledge, and, ultimately, harmonization between key authorities and Participating States. The purpose of EWS is to promptly communicate the findings of HAOP to the appropriate stakeholders, such as government agencies and commercial companies. The paper elucidates in detail the criteria and procedure for developing a regionally standardized EWS, including its mechanism, the technical information platform that is required, and the obligations of EWS data providers. It also discusses the decision-making process for issuing alerts and identifies the intended recipients of the warning signals. The system has been operational in the Baltic Sea region for over two years, and the knowledge and insights gathered during its development may prove beneficial in other areas as well.

Radiomic-Based Prediction of Lesion-Specific Systemic Treatment Response in Metastatic Disease.

Despite sharing the same histologic classification, individual tumors in multi metastatic patients may present with different characteristics and varying sensitivities to anticancer therapies. In this study, we investigate the utility of radiomic biomarkers for prediction of lesion-specific treatment resistance in multi metastatic leiomyosarcoma patients. Using a dataset of n=202 lung metastases (LM) from n=80 patients with 1648 pre-treatment computed tomography (CT) radiomics features and LM progression determined from follow-up CT, we developed a radiomic model to predict the progression of each lesion. Repeat experiments assessed the relative predictive performance across LM volume groups. Lesion-specific radiomic models indicate up to a 4.5-fold increase in predictive capacity compared with a no-skill classifier, with an area under the precision-recall curve of 0.70 for the most precise model (FDR = 0.05). Precision varied by administered drug and LM volume. The effect of LM volume was controlled by removing radiomic features at a volume-correlation coefficient threshold of 0.20. Predicting lesion-specific responses using radiomic features represents a novel strategy by which to assess treatment response that acknowledges biological diversity within metastatic subclones, which could facilitate management strategies involving selective ablation of resistant clones in the setting of systemic therapy.

Biosynthesis and Assembly Logic of Fungal Hybrid Terpenoid Natural Products.

In recent decades, fungi have emerged as significant sources of diverse hybrid terpenoid natural products, and their biosynthetic pathways are increasingly unveiled. This review mainly focuses on elucidating the various strategies underlying the biosynthesis and assembly logic of these compounds. These pathways combine terpenoid moieties with diverse building blocks including polyketides, nonribosomal peptides, amino acids, p-hydroxybenzoic acid, saccharides, and adenine, resulting in the formation of plenty of hybrid terpenoid natural products via C-O, C-C, or C-N bond linkages. Subsequent tailoring steps, such as oxidation, cyclization, and rearrangement, further enhance the biological diversity and structural complexity of these hybrid terpenoid natural products. Understanding these biosynthetic mechanisms holds promise for the discovery of novel hybrid terpenoid natural products from fungi, which will promote the development of potential drug candidates in the future.

New theoretical and analytical framework for quantifying and classifying ecological niche differentiation

AbstractEcological niche differentiation is a process that accompanies lineage diversification and community assembly. Traditionally, the degree of niche differentiation is estimated by contrasting niche hypervolumes of two taxa, reconstructed using ecologically relevant variables. These methods disregard the fact that niches can shift in different ways and directions. Without means of discriminating between different types of niche differentiation, important evolutionary and ecological patterns may go unrecognized. Herein, we introduce a new conceptual and methodological framework that allows quantification and classification of niche differentiation and divergence between taxa along single niche axis. This new method, the Niche Divergence Plane, is based on species' responses to an underlying environmental gradient, from which we derive a two‐dimensional plane defined by two indices, niche exclusivity and niche dissimilarity. These two indices identify the proportion of the environmental gradient that is unique to each species, that is, how much of the environmental gradient species do not share (niche breadth exclusivity) and how different the species' responses are along the environmental gradient (niche dissimilarity). Thus, the latter can also be seen as a measure of the differences in niche preference or importance, even when there is significant overlap in niche breadth (i.e., low niche exclusivity). Based on the position of the two indices on the divergence plane, we can distinguish niche conservatism from four other general types of niche divergence: hard, soft, weighted, and nested. We demonstrate that the Niche Divergence Plane complements traditional measures of niche similarity (e.g., Schoener's D or Hellinger's I). Additionally, we show an empirical comparison using the Niche Divergence Plane framework on two Ambystoma salamanders. Overall, we demonstrate that the Niche Divergence Plane is a versatile tool that can be used to complement and expand previous methods of ecological niche comparisons and the study of ecological niche divergence.

Three-dimensional ecological drought identification and evaluation method considering eco-physiological status of terrestrial ecosystems

Ecological drought is a complex process in terrestrial ecosystems where vegetation's eco-physiological functions are impaired due to water stress. However, there is currently a lack of long-term assessment of ecological drought from an eco-physiological perspective. In this study, the standardized ecological drought index (SESNDI) was developed using actual evaporation, root soil moisture, and kernel normalized difference vegetation index via the Euclidean distance method, reflecting ecosystem physiology, water supply capacity, and vegetation status. Solar-induced chlorophyll fluorescence validated SESNDI by reflecting vegetation photosynthesis. Using China as an example, severely impacted by climate change and ecological restoration, ecological drought's spatio-temporal variation and propagation characteristics was evaluated using clustering algorithms. The results demonstrated that (1) SESNDI showed superior performance over several other drought indices. (2) During 1982–2020, ecological drought was prevalent from 1990 to 2010, especially in the central and northeastern regions. (3) Compared to 1982–2000, the median duration and affected area of ecological drought events during 2001–2020 reduced by four months and 1.51 × 105 km2, respectively, while the median intensity increased by 0.06. (4) Decreased precipitation and increased temperature were the primary factors contributing to the frequent occurrence of ecological drought in China from 1990 to 2010. This study offers a crucial methodology for evaluating ecological drought, serving as a reference for developing effective terrestrial restoration strategies.

Annual-perennial lifespan variation in Chaenactis douglasii suggests a drought escape strategy in warm-arid environments.

Intraspecific variation in drought resistance traits, such as drought escape, appear to be frequent within wild, ruderal forb species. Understanding how these traits are arrayed across the landscape, particularly in association with climate, is critical to developing forbs for wildland restoration programs. Use of forbs is requisite for maintaining biological diversity and ecological services. Using 6074 greenhouse-grown Chaenactis douglasii seedlings from 95 wild, seed-sourced populations across the western United States, we recorded bolting phenology and estimated genome size using flow cytometry. Mixed-effects regression models were used to assess whether climate of seed origin was predictive for bolting phenology and genome size. Variation in bolting, reflecting an annual vs. perennial lifespan in this species, was observed in 8.7% of the plants, with bolting plants disproportionately occurring in locations with warm, arid climates. Populations with increasing heat and aridity were positively correlated with observed bolting (r = 0.61, p < 0.0001). About one-third (22%) of the total (61%) lifespan variation was attributed to seed source climate and annual heat moisture index, a measure of aridity. Genome size had no significant effect on bolting. Projected climate modeling for mid-century (2041-2070) supports an increasing occurrence of annual lifespan. Our analyses support a drought escape, bet-hedging strategy in C. douglasii. Populations exposed to greater aridity exhibited a higher proportion of individuals with an annual lifespan. Drought escape leading to an annual lifespan can affect how seeds are propagated and deployed for climate-informed restoration.

Understanding and achieving species elements in the Kunming-Montreal Global Biodiversity Framework.

The Kunming-Montreal Global Biodiversity Framework was adopted in December 2022 by the parties to the Convention on Biological Diversity. The framework states outcomes for species to be achieved by 2050 in goal A and establishes a range of targets to reduce pressures on biodiversity and halt biodiversity loss by 2030. Target 4 calls for urgent recovery actions for species where the implementation of other targets is insufficient to eliminate extinction risk. We analyze key species elements of goal A and target 4, examine their meaning and clarify implementation needs. We emphasize that target 4 should not be seen simply as the species target, because effective implementation of all targets is essential to achieve the species ambitions in goal A, but, rather, as a target for species that require urgent focused actions and emphasize that an indicator is needed to measure the implementation of urgent management actions. We conclude by considering next steps to identify priorities, undertake further research, make use of resources, ensure cooperation and capacity development.

The need to diversify genomic studies: Insights from Andean highlanders and Amazonians

More globally diverse perspectives are needed in genomic studies and precision medicine practices on non-Europeans. Here, we illustrate this by discussing the distribution of clinically actionable genetic variants involved in drug response in Andean highlanders and Amazonians, considering their environment, history, genetic structure, and historical biases in the perception of biological diversity of Native Americans.

Landscape structure influences the spatial distribution of urban bird attractiveness

ContextLandscape change affects biological diversity and the distribution of species traits related to spiritual, educational, and recreational benefits people derive from nature. These traits are associated with color, song and behavioral characteristics that influence people's perceptions of how attractive an assemblage is. However, the environmental variables that affect the spatial distribution of traits related to the attractiveness of biological diversity remain unexplored.ObjectivesWe tested how landscape structure influences patterns of perceived bird attractiveness (trait diversity associated with colorfulness, behavioral and song categories) across an urbanization gradient.MethodsWe used data from standardized surveys of birds and landscapes within 42 landscape units of 1km2 across the city of Brisbane in eastern Australia. We used structural equation modeling to test effects of landscape composition (built infrastructure, percentage of tree cover) and landscape configuration (fragmentation of tree cover) on mean bird community attractiveness. Relationships between individual traits and landscape structure were analyzed using multinomial logistic regression models.ResultsOur analysis across 82 bird species shows that the relative amount of built infrastructure in a landscape interacts with fragmentation to reduce the overall attractiveness of the landscape’s bird assemblage. However, built areas can exhibit high overall bird attractiveness where there is (1) reduced fragmentation and (2) increased diversity of vegetation structure that provides key habitats for many colorful species with a high diversity of calls. Relationships between bird attractiveness and landscape structure change when they are analyzed at the guild level (insectivores vs frugivores/nectarivores). In addition, body size moderates the effects of landscape structure on song complexity, personality, and color.ConclusionsSmall bodied, colorful and melodious species are negatively affected by built infrastructure and fragmentation. By learning how habitat loss and fragmentation affect the distribution of species-rich, attractive bird assemblages, our findings can inform how urban landscapes might be structured to increase people’s connection with nature.

Widespread changes in gene expression accompany body size evolution in nematodes.

Body size is a fundamental trait that drives multiple evolutionary and ecological patterns. Caenorhabditis inopinata is a fig-associated nematode that is exceptionally large relative to other members of the genus, including Caenorhabditis elegans. We previously showed that C. inopinata is large primarily due to postembryonic cell size expansion that occurs during the larval-to-adult transition. Here, we describe gene expression patterns in C. elegans and C. inopinata throughout this developmental period to understand the transcriptional basis of body size change. We performed RNA-seq in both species across the L3, L4, and adult stages. Most genes are differentially expressed across all developmental stages, consistent with C. inopinata's divergent ecology and morphology. We also used a model comparison approach to identify orthologues with divergent dynamics across this developmental period between the 2 species. This included genes connected to neurons, behavior, stress response, developmental timing, and small RNA/chromatin regulation. Multiple hypodermal collagens were also observed to harbor divergent developmental dynamics across this period, and genes important for molting and body morphology were also detected. Genes associated with transforming growth factor β signaling revealed idiosyncratic and unexpected transcriptional patterns given their role in body size regulation in C. elegans. This widespread transcriptional divergence between these species is unexpected and maybe a signature of the ecological and morphological divergence of C. inopinata. Alternatively, transcriptional turnover may be the rule in the Caenorhabditis genus, indicative of widespread developmental system drift among species. This work lays the foundation for future functional genetic studies interrogating the bases of body size evolution in this group.

Must we lose our biological connection to nature to endure changing times?

AbstractEarth has &gt;8 billion people. Scholarly publications number nearly 7 million annually with &gt;1 million in the life and biomedical sciences, and ≥52 professional journals specializing in conservation, ecology, or related disciplines. The challenges of applying ecological data to conservation and wildlife management can easily become overwhelming. Herein we offer reflective perspectives about the changing face of applied knowledge and engagement from our personal employment histories as ecologists working in agency, university, and non‐governmental organization (NGO) biologist positions. We suggest natural history will always be nature's glue, but knowledge steeped mostly in muddy boots and field biology are no longer the soup du jour of our profession. In many ways, new technologies have changed data collection and the scientific questions asked. Arguably, such change is not welcomed by all, but a change in overlap across decades is needed to sustain and improve upon how the planet's biological diversity can coexist with increasingly difficult human conditions. Given that 80% of the people in the United States live in urban areas, with similar numbers internationally, a future possibility may be an even greater divide between wild nature, ecological services, and enjoyment in the field. This is disturbing. Despite fundamental scientific insights that help understand critical components of the natural world, once society loses touch with nature, what will remain?

Ontogenetic, Sexual, and Monthly Niche Segregation of Sepia esculenta in the Northern East China Sea Revealed by Stable Carbon and Nitrogen Isotopes.

Golden cuttlefish play a significant role in the food web of the East and Yellow Seas and are a valuable fishery resource in Chinese coastal waters. Samples of golden cuttlefish were obtained from the northern East China Sea between September 2021 and March 2022, and stable isotope methods were utilized in this study to examine the variations in the forage ecology of golden cuttlefish. Our findings reveal dynamic shifts in carbon and nitrogen stable isotopes (δ13C and δ15N), highlighting intricate foraging strategies tailored to growth and environmental changes. A notable trend emerges: an initial growth-linked rise in δ13C and δ15N enrichment, followed by seasonal fluctuations mirroring seasonal food availability. The ontogenetic niche evolution displays striking habitat shifts and trophic level escalation in small mantle length stages, transitioning to niche overlap and subtle trophic shifts later on. Sex-specific differences emerge, with females occupying higher trophic levels than males in most samples. This comprehensive study underscores the complexity and adaptability of golden cuttlefish feeding ecology, inviting further inquiry into their intricate relationships within the marine ecosystem.

Conservation importance of non-threatened species through their direct linkages with nature's contributions to people

Over the last half-century, nature conservation has shifted through several steps from ‘nature for itself’ to ‘nature and people’, corresponding to a new perspective that all species count to ensure ecosystem functioning, and with them that nature's contributions to people (NCPs) are effective and maintained. Yet, despite these conceptual shifts in the academic literature, conservation practices have remained largely focused on threatened species and protected areas. The last Global Biodiversity Framework (GBF) of the Convention on Biological Diversity insisted on the need to use biodiversity sustainably and ensure nature's contributions to people, including ecosystem functions and services for the benefit of present and future generations by 2050. Here, using recently developed tables relating a large number of species observed in the Western Swiss Alps (vascular plants and vertebrates; n = 2066) to 17 key NCPs, we show that focusing on protecting threatened species only does not ensure the maintenance of key NCPs. Our results suggest that all species (threatened or not) need to be considered, in addition to strict conservation of threatened species, to support NCP provision. Similarly, considering all species better supports existing conservation programs. Developing such direct species-NCP relationships more broadly will be needed to support spatial prioritizations and help reach the 2050 GBF goals.

Lag in pollutant removal efficiency relative to microbial community dynamics in a denitrifying phosphorus removal bioreactor

Determining the system status in advance is critical for implementing timely control strategies, preventing wastewater treatment instability due to overload stress, and enhancing system resilience to impact loads. Unlike traditional instability monitoring methods, identifying temporal relationships between pollutant removal efficiency and microbial community dynamics can offer novel insights into identifying optimal intervention windows. Here, we chose nitrite, a vital intermediate of nitrogen reaction in wastewater treatment, as a stress factor. Then, we investigated the effects of nitrite stress on denitrifying phosphorus removal system performance and microbiome. By monitoring carbon, nitrogen, and phosphorus removal efficiency and analyzing microbiome information, we found that variations in bacterial ecology preceded pollutant removal efficiency. The lag in pollutant removal efficiency relative to microbial community dynamics reflects the complex dynamics of species traits, metabolic functions, and functional redundancy. Species in clusters may drove specific pollutant removal; e.g., Betaproteobacteria are more closely associated with nitrogen removal, while Gammaproteobacteria are more linked to phosphorus removal. The cellular secretion function displayed greater susceptibility to overload stress compared to the substrate conversion function, resulting in decreased stability observed after 30 cycles, preceding the decline in substrate conversion efficiency. The lag in performance relative to community stability can be attributed to functional redundancy. Under overload stress conditions, functional redundancy within the microbiome decreased by 30.77% from 60 cycles to 120 cycles. Our results support a novel strategy for system collapse prediction via changes in the microbiome,enabling proactive regulation and ensuring system stability before irreversible deterioration occurs.

Hybridization in the Anthropocene - how pollution and climate change disrupt mate selection in freshwater fish.

Chemical pollutants and/or climate change have the potential to break down reproductive barriers between species and facilitate hybridization. Hybrid zones may arise in response to environmental gradients and secondary contact between formerly allopatric populations, or due to the introduction of non-native species. In freshwater ecosystems, field observations indicate that changes in water quality and chemistry, due to pollution and climate change, are correlated with an increased frequency of hybridization. Physical and chemical disturbances of water quality can alter the sensory environment, thereby affecting chemical and visual communication among fish. Moreover, multiple chemical compounds (e.g. pharmaceuticals, metals, pesticides, and industrial contaminants) may impair fish physiology, potentially affecting phenotypic traits relevant for mate selection (e.g. pheromone production, courtship, and coloration). Although warming waters have led to documented range shifts, and chemical pollution is ubiquitous in freshwater ecosystems, few studies have tested hypotheses about how these stressors may facilitate hybridization and what this means for biodiversity and species conservation. Through a systematic literature review across disciplines (i.e. ecotoxicology and evolutionary biology), we evaluate the biological interactions, toxic mechanisms, and roles of physical and chemical environmental stressors (i.e. chemical pollution and climate change) in disrupting mate preferences and inducing interspecific hybridization in freshwater fish. Our study indicates that climate change-driven changes in water quality and chemical pollution may impact visual and chemical communication crucial for mate choice and thus could facilitate hybridization among fishes in freshwater ecosystems. To inform future studies and conservation management, we emphasize the importance of further research to identify the chemical and physical stressors affecting mate choice, understand the mechanisms behind these interactions, determine the concentrations at which they occur, and assess their impact on individuals, populations, species, and biological diversity in the Anthropocene.

Evolution of retrocopies in the context of HUSH silencing

Retrotransposition is one of the main factors responsible for gene duplication and thus genome evolution. However, the sequences that undergo this process are not only an excellent source of biological diversity, but in certain cases also pose a threat to the integrity of the DNA. One of the mechanisms that protects against the incorporation of mobile elements is the HUSH complex, which is responsible for silencing long, intronless, transcriptionally active transposed sequences that are rich in adenine on the sense strand. In this study, broad sets of human and porcine retrocopies were analysed with respect to the above factors, taking into account evolution of these molecules. Analysis of expression pattern, genomic structure, transcript length, and nucleotide substitution frequency showed the strong relationship between the expression level and exon length as well as the protective nature of introns. The results of the studies also showed that there is no direct correlation between the expression level and adenine content. However, protein-coding retrocopies, which have a lower adenine content, have a significantly higher expression level than the adenine-rich non-coding but expressed retrocopies. Therefore, although the mechanism of HUSH silencing may be an important part of the regulation of retrocopy expression, it is one component of a more complex molecular network that remains to be elucidated.

Historical and relative dominance of the convention on biological diversity agenda: a case analysis of decisions and recommendations

In contrast to the United Nations Convention to Combat Desertification (UNCCD) and the United Nations Framework Convention on Climate Change (UNFCCC), the Convention on Biological Diversity (CBD) gives developing countries greater bargaining power owing to their abundant natural resources. CBD negotiations tend to be increasingly dominated by agendas related to the CBD’s third objective: benefit sharing. The first and core objective of CBD is biodiversity conservation, but it is often neglected in favor of benefit sharing. To verify this tendency, this study used topic modeling to analyze the recommendations of the subsidiary bodies and decisions made by the Conference of the Parties (COP) over the past 30 years. The study identified the ten most frequently discussed agenda, then determined the relative dominant agenda between the COP and subsidiary bodies. By categorizing the negotiation agendas into strategic decision agendas and operational conservation agendas based on the level of the meeting which the agenda dominated, this study offers a new framework that can be used to understand how strategic and operational factors interact in CBD negotiations. The findings show that biodiversity conservation, the first objective of CBD, is no longer dominant, at least during negotiations. To the best of our knowledge, this is the first comprehensive investigation of all documents generated during CBD negotiations since its inception.

Exploring the uncharted seas: Metabolite profiling unleashes the anticancer properties of Oscillatoria salina

Marine cyanobacteria offer a rich source of varied natural products with both chemical and biological diversity. Oscillatoria salina (O. salina) is a filamentous non-heterocystous marine cyanobacterium from Oscillatoriaceae family. In this investigation, we have unveiled bioactive extracts from O. salina using two distinct solvent systems, revealing significant anticancer properties. Our assessment of the organic and aqueous extracts (MCE and AE) of O. salina demonstrated pronounced antiproliferative and antimetastatic effects. Notably, this study is the first to elucidate the anticancer and anti-metastatic potential of O. salina extracts in both 2D and 3D cell culture models. Both MCE and AE induced apoptosis, hindered cell proliferation, invasion, and migration in A549 non-small cell lung cancer cells, accompanied by alterations in cell morphology and cytoskeleton collapse. Moreover, MCE and AE induced spheroid disintegration in A549 cells. Transcriptomics analysis highlighted the significant involvement of Rap1 and p53 signaling pathways in mediating the observed antitumor effects. Mass spectroscopy characterization of these extracts identified 11 compounds, some known for their anticancer potential. HPLC analysis of AE revealed six peaks with UV absorption spectra resembling phycocyanin, a cyanobacterial pigment with well-known anticancer activity. Collectively, these findings underscore the anticancer potential of MCE and AE, containing bioactive metabolites with anticancer and antimetastatic properties.

Environmental aspects of digitalization of phytosanitary examination of agricultural crops

Abstract The article provided discusses the environmental aspects of digitalizing phytosanitary examination in plant cultivation. The authors highlight the negative environmental consequences resulting from the irrational use of natural resources and the increasing impact of powerful anthropogenic factors, such as the depletion of entomofauna composition, disruption of self-regulation mechanisms, and increased mass reproduction of phytophagous insects. Digitalization based on mathematical modeling is identified as a highly effective tool for phytosanitary monitoring. It involves a software module that allows dynamic changes in the number of research objects and the input of initial data about the studied objects and their parameters. The proposed method of comprehensive assessment enables a balanced consideration of parameters and criteria, encompassing both quantitative and qualitative evaluations. It facilitates the simultaneous maximization and minimization of various parameters, contributing to the mobilization of natural biota resources and the enhancement of biological diversity in agrolandscapes while considering the complexity of relationships within these landscapes. This approach is crucial for addressing the need to balance conflicting requirements or goals in the digitalization of phytosanitary expertise in agricultural crops.

Discordance between taxonomy and population genomic data: An avian example relevant to the United States Endangered Species Act.

Population genomics can reveal cryptic biological diversity that may impact fitness while simultaneously serving to delineate relevant conservation units. Here, we leverage the power of whole-genome resequencing for conservation by studying 433 individual lesser prairie-chicken (Tympanuchus pallidicinctus; LEPC, a federally endangered species of conservation concern in the United States) and greater prairie-chicken (Tympanuchus cupido; GRPC, a legally huntable species throughout much of its range). The genomic diversity of two formally recognized distinct population segments (DPSs) of LEPCs is similar, but they are genetically distinct. Neither DPS is depleted of its genomic diversity, neither is especially inbred, and temporal diversity is relatively stable in both conservation units. Interspecific differentiation between the two species was only slightly higher than that observed between LEPC DPSs, due largely to bidirectional introgression. The high resolution provided by our dataset identified a genomic continuum between the two species such that individuals sampled from the hybrid zone were imperfectly assigned to their presumptive species when considering only their physical characteristics. The admixture between the two species is reflected in the spectrum of individual ancestry coefficients, which has legal implications for the "take" of individuals under the Endangered Species Act. Overall, our data highlight the recurring dissonance between static policies and dynamic species boundaries that are increasingly obvious in the population genomic era.