A mathematical model for animal ecology with special reference to the ecology of the Tribolium beetle.
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Animals↗
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Results for “ecology”
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Ecological and sociological studies of gelada baboons. Feeding ecology.
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Animals↗
Activity shapes large herbivores' ecological influences.
The ecological effects of large herbivores are shaped by their spatial and temporal patterns of activity (i.e. where, when and how intensely they use specific locations). When large herbivores' ecological influences are perceived to be undesirable, the traditional approach has been to reduce their population size. This numbers-first logic assumes that ecological effects scale primarily with abundance. We argue that this framing provides an incomplete understanding of large herbivores' ecological impacts. Using African elephants (Loxodonta africana) as a well-documented case study, we show that ecological effects on plants, animals and ecosystem processes correlate more with spatio-temporal patterns of activity than with population size. In large, open systems characterized by strong gradients of water availability, forage quality, shade and risk, elephants concentrate into predictable hotspots while relaxing activity elsewhere, generating localized impacts and opportunities for recovery. By contrast, in small, fenced or fragmented landscapes, where movements are constrained, and gradients are weak, spatial self-regulation breaks down, producing homogenized use and widespread ecological effects. We contend that understanding where, when and under what constraints herbivores use space provides a more general and mechanistic basis for interpreting ecological influence than abundance alone, with implications that extend beyond elephants to large herbivores globally.
Animals↗
Re-emerging Marburg virus disease in Africa: spillover ecology, geographic expansion, and surveillance vulnerabilities.
Marburg virus disease (MVD) is re-emerging across Africa as a high-consequence zoonosis shaped by expanding ecological suitability, repeated spillover, and uneven surveillance capacity. This review synthesizes current evidence on the ecological, epidemiological, and operational determinants of contemporary Marburg virus (MARV) emergence. We conceptualize MVD as an ecological-emergence system produced by interactions among reservoir-host biology, environmental change, human exposure, health-system readiness, and mobility, rather than as a series of isolated outbreaks. Recent detections in multiple African regions indicate wider enzootic circulation than previously recognized and support repeated, reservoir-associated introductions from distributed ecological foci. Spillover risk is heightened where mining, land-use change, agricultural encroachment, settlement growth, climate-sensitive habitat disruption, and population movement increase contact with Egyptian rousette bats (Rousettus aegyptiacus) and contaminated roost environments. Following primary spillover, diagnostic delays, fragmented surveillance, limited laboratory decentralization, healthcare-associated transmission, and mobility-linked exposure can enable outbreak amplification and delayed recognition. Serological findings further suggest possible "shadow epidemiology," with unrecognized or mild MARV infections occurring outside confirmed outbreak chains. Critical preparedness gaps persist in ecological risk mapping, longitudinal reservoir surveillance, decentralized molecular diagnostics, genomic sequencing, data integration, and cross-border early warning. Future preparedness should move beyond reactive containment toward integrated One Health approach combining predictive ecological surveillance, rapid community-level detection, real-time genomics, infection prevention, risk communication, and regional coordination to identify spillover early and prevent human transmission.
Animals↗
Beyond Morphology: Reframing Lymph-Node Metastasis Prediction Through Clonal Ecology-Decades-Long Genomic Instability and Polyclonal-to-Monoclonal Transitions as the Missing Dimension in Cancer.
Recent whole-genome, lineage-tracing, single-cell, and spatial studies have reshaped our understanding of tumor evolution, revealing that cancers can arise from polyclonal populations, undergo decades-long genomic instability before clinical detection, and progress through dynamic changes in subclonal composition, cellular state, and ecological organization. These findings challenge the assumption underlying morphology-based prediction models that metastatic risk can be inferred from static histological features alone. Here, we revisit lymph-node metastasis prediction in colorectal cancer through clonal ecology, integrating computational pathology with evolutionary oncology. Drawing on the subclonal switchboard model proposed in 2012 and subsequent artificial intelligence (AI)-enabled approaches for tracking dominant and dormant subclones, we synthesize evidence that metastatic potential reflects clonal ancestry, evolutionary timing, spatial niche architecture, cellular plasticity, intercellular interactions, dormancy, and treatment-driven shifts in subclonal fitness. We define five complementary methodological pillars for operationalizing clonal ecology: single-cell transcriptomics for resolving rare subclones, evolutionary trajectories, and adaptive cell states; lineage tracing and phylogenetics for reconstructing clonal ancestry and divergence; spatial transcriptomics and genomics for mapping subclonal geography and tumor-stromal-immune interactions; longitudinal liquid biopsy surveillance for monitoring residual disease, clonal turnover, and emerging resistance; and AI-enabled multimodal integration for connecting histopathology, genomics, spatial biology, and longitudinal data into predictive ecological-state models. Multiple-instance learning and pathology foundation models provide scalable computational foundations for evolution-aware prediction. Translationally, dormant subclones represent actionable reservoirs of recurrence. A longitudinal clinical and experimental study of KMT2A-rearranged acute myeloid leukemia further supports central predictions of the subclonal switchboard framework by demonstrating treatment-associated shifts in subclonal dominance, persistence of cryptic adaptive programs, and ecological rewiring during resistance and relapse. We propose clonal ecology as a measurable dimension for extending morphology-driven prediction toward integrative models that anticipate evolutionary transitions, identify therapeutic windows, and proactively constrain adaptive tumor ecosystems before resistant or metastatic subclones achieve clinical dominance.
Humans↗
Characterizing the ecological niche of insertion sequences within prokaryotic genomes.
Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious mutations. However, they can also promote adaptive changes. These antagonistic properties make their overall impact on prokaryotic evolution difficult to grasp. Here, we address this challenge by leveraging the framework of transposon ecology to analyze IS occurrences across and within 30 499 prokaryotic genomes. Combining phylogenomics with multi-scale genomic analysis, quantitative ecology, and mathematical modeling, we provide evidence that although genomes generally provide sufficient resources for IS coexistence, universal mechanisms shape their occurrence and chromosomal distribution across genomes. These include (i) the preferential localization of ISs within highly variable and GC-heterogeneous chromosomal regions of genomic plasticity, which act as the primary reservoir of IS niches; (ii) a linear scaling between IS abundance and niche size, with an average of $5.4$ additional accessible insertion sites per IS; (iii) a dependence of IS occurrence on the presence of other ISs, suggesting a form of group behavior; (iv) the accumulation of AT-rich sequences in both coding and noncoding regions up to 100 kb around ISs, indicative of ecological isolation; and (v) the spatial partitioning of mobile genetic elements around ISs, reminiscent of ecological niche differentiation. Besides these general principles, we also uncover niche specificities associated with particular IS families, hinting at regulatory mechanisms that modulate IS activity. Altogether, this comprehensive transposon ecology approach offers new insights and avenues for understanding IS-host interactions and genome evolution, moving beyond traditional host-centric perspectives.
DNA Transposable Elements↗
Trichoderma specialized metabolites in biocontrol: gene-metabolite links, ecological functions, and translational bottlenecks.
Trichoderma spp. produce a diverse repertoire of metabolites with specific activities that contribute to biocontrol through direct antagonism, ecological signalling, and modulation of plant responses. However, current knowledge remains uneven: many metabolites are chemically described, whereas fewer are supported by robust gene-metabolite associations, experimentally validated ecological functions, and realistic translational evidence. Progress in this field will depend less on expanding compound catalogues than on integrating mechanistic, ecological, and translational evidence. This review examines the specialized metabolism of Trichoderma with emphasis on biosynthetic gene clusters, regulatory networks, ecological roles, and biosafety constraints relevant to biocontrol. Major metabolite classes, including polyketides, terpenoids, peptaibols, siderophores, diketopiperazines, and volatile organic compounds, are discussed together with representative case studies for which genetic and functional evidence is available. We further propose a translational framework to distinguish metabolites with mainly descriptive support from those approaching application readiness, based on four criteria: gene-level validation, demonstrated ecological role, manageable biosafety profile, and feasible delivery/stability. This perspective helps explain why metabolite inventories continue to expand faster than field translation. Recent advances in genomics, transcriptomics, metabolomics, genome editing, and formulation science are reshaping how Trichoderma metabolites are prioritized for future development.
Biosafety↗
The chemical landscape of plant surface metabolites: Acylsugars as models of ecological function and structural diversity.
Plants produce a multifunctional assortment of specialized metabolites that play important roles in defense, environmental adaptation, and ecological interactions. Among these compounds, acylsugars, nonvolatile metabolites produced primarily in glandular trichomes of Solanaceae species, have emerged as informative model systems for understanding plant surface chemistry. Differences in acyl chain length, branching pattern, saturation, and attachment position generate extensive chemical diversity that influences herbivore deterrence, pathogen resistance, and the physicochemical properties of leaf surfaces. Recent advances in analytical chemistry, particularly liquid chromatography-ion mobility-tandem mass spectrometry (LC-IM-MS/MS), have greatly improved the ability to separate structurally related acylsugar isomers and characterize metabolite complexity at high resolution. When integrated with genomics, transcriptomics, and emerging spatial metabolomics approaches, these analytical tools provide new insights into acylsugar biosynthesis, pathway regulation, evolutionary diversification, and ecological function across plant species. This review positions acylsugars, particularly those of Solanum species, as model systems for understanding how structural diversity, spatial localization, and specialized metabolism shape ecological and physiological function at plant surfaces. We examine acylsugar structural diversity, biosynthetic pathways, ecological and physiological functions, and interactions with environmental and atmospheric processes. Major challenges, including extensive isomeric complexity, incomplete pathway characterization, and difficulties linking chemical structure to biological function, are discussed alongside emerging opportunities in integrative omics, crop improvement, sustainable pest management, and environmental monitoring. Overall, acylsugars provide a powerful model for linking molecular structure, spatial localization, and ecological function, offering broader insight into how specialized metabolism shapes plant adaptation, defense, and environmental interactions.
Acylsugars↗
From sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leads.
Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.
Microbiota↗
Concurrent ecological and evolutionary processes contribute to mutualism breakdown between legumes and rhizobia.
Though they jointly shape community responses to environmental perturbations, ecology and evolution are often examined separately, even in microorganisms where both occur over short timescales. Here we examine ecological and evolutionary responses to 33 years of nitrogen fertilization using the legume-rhizobium mutualism. Pairing a manipulative inoculation study with full-length 16S rRNA gene amplicon sequencing and structural equation modeling allows us to synthesize across biological scales: whole bacterial community, genus Rhizobium, Rhizobium ASVs, and symbiosis plasmids. Clover's preferred partner decreases in N-addition soils, limiting host growth, while a diverse and largely uncharacterized Rhizobium community increases. This ecological change is compounded by a concurrent evolutionary degradation of symbiont partner quality via changing frequencies of symbiotic plasmids. Ecological (rarer symbionts) and evolutionary (inferior symbionts) processes each accounted for roughly half of this loss of host benefit, revealing that ecology and evolution jointly shape mutualism breakdown over the short timescales typical of microbial systems.
ecology↗
[Ecology and psychiatry].
Psychiatry, with a recent history as to a pragmatic discipline and a progressive development from the individual to the social, finds a holistic perspective of singular heuristic value in the ecological proposition. Ecopsychiatry is a general approach in which the diverse sources of psychiatric knowledge are grouped in order to get a view of macro-reality emerging from a methodological integration of behavior sciences and a unified theory orientating to a realistic praxis in the normative. This paper reviews the rationale, notion and historical development of the ecological principle in psychiatry. After a superficial analysis of the first contributions in this field, it is intented to outline the real of the actual psychiatric ecology mentioning their methods and contents. Following Bateson's postulation it is emphasized that ecological principles cannot be isolated from their own ideological contents--the ecological system necessarily involves science's ideas for their concepts need a constant evaluation.
Ecology↗
Genetic diversity and antifungal susceptibility among ecological niche populations of Aspergillus flavus in Yaoundé, Cameroon.
Aspergillus flavus is a ubiquitous fungus commonly found in a variety of ecological niches including soil, crops, the air, and humans. In humans, it is the second leading cause of invasive aspergillosis (IA) and is linked to other illnesses through contamination of agricultural products with aflatoxins. As such, A. flavus threatens food safety, economic wellbeing, and human health, particularly in less developed regions and countries such as Cameroon. To mitigate these effects, farmers and clinicians rely on triazoles to reduce aflatoxin contamination and treat IA. However, a consequence of increasing triazole use is the emergence and spread of triazole resistance in both agriculture and clinics. To identify the prevalence of triazole resistance and the potential genetic relationships among triazole resistant and susceptible strains, this study investigated antifungal susceptibility to both clinical and agricultural triazoles and analyzed genetic variation among various ecological niche populations of A. flavus in Cameroon. Strain genotypes were obtained through analysis of six polymorphic microsatellite markers. Our analyses revealed that 30.3% (17/56) of the strains were resistant to at least one of the four triazoles, with increased minimum inhibitory concentrations found among crop-isolated strains. A Permutational Multivariate Analysis of Variance suggested limited ecological niche-based clustering of genotypes, consistent with frequent gene flow and dispersal among ecological niches. A multilocus linkage disequilibrium analysis revealed evidence of non-random recombination in A. flavus. Overall, this study elucidates the interplay between ecological pressures, antifungal resistance, and genetic differentiation, and invites alternative methods to control aflatoxin contamination in foods without the use of agricultural fungicides.
Aspergillus flavus↗
Making sense of the virome in light of evolution and ecology.
Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.
Virome↗
Operationalizing Local Ecological Knowledge for Aquatic Biodiversity Conservation: A Systematic Review and Management Framework.
Effective conservation and management of aquatic biodiversity is severely constrained by the absence of long-term ecological data in small-scale, tropical, and data-poor fisheries, where roughly one-quarter to one-third of freshwater fish species and 37.5% of elasmobranchs are threatened with extinction once Data Deficient species are accounted for. Conventional monitoring and stock-assessment tools are often financially and technically inaccessible in these systems, leaving managers without the evidence needed to prioritize conservation action or implement precautionary governance. Local Ecological Knowledge (LEK) is a largely underutilized resource for natural resource management that can provide temporal depth, spatial resolution, and species-specific ecological insights unavailable from scientific records. We conducted a systematic review and bibliometric synthesis of 60 peer-reviewed studies (1997-2025) applying LEK to assess fish conservation status, examining how, where, and through what methods this knowledge has been used. Our analysis identifies four complementary pathways through which LEK informs conservation management: reconstructing multi-decadal population changes, documenting spatial contraction and habitat loss, detecting extreme rarity and local extirpation, and characterizing intrinsic sensitivity to exploitation based on life-history traits. Despite growing methodological rigor, freshwater systems and African fisheries remain critically underrepresented, and formal integration of LEK into fisheries governance and biodiversity assessment remains the exception rather than the rule. We propose a practical three-stage framework to operationalize LEK within existing management and conservation systems. Recognizing fishing communities as legitimate co-producers of ecological knowledge is both scientifically necessary and an equity imperative for achieving global biodiversity commitments under the Kunming-Montreal Global Biodiversity Framework.
Biodiversity↗
The reproductive ecology of the house mouse.
This paper attempts to integrate the physiological and ecological perspectives of the reproductive biology of the house mouse (Mus musculus). The endeavor is made within a larger context to provide a prototype for mammalian reproductive ecology in general. Specifically, the environmental regulation of the reproduction of Mus musculus is examined in relation to its ecological opportunism and, in particular, in relation to its history of global colonization. House mice can live as commensals of man or under totally feral conditions. Stable, high density, commensal populations are characterized by an insular division of the living space into demeterritories, each dominated by a single male. Feral populations typically are characterized by temporal, spatial, and social instability. Territoriality is improbable under such conditions, particularly given the necessity for large home ranges in most feral habitats. In both feral and commensal populations, however, male aggressiveness promotes the large-scale dispersal of young, all of which are potential colonizers. Of the ten or so environmental factors known to influence reproduction in house mice, seven probably are of routine importance in natural populations: diurnal modulation by daily light:dark cycles; caloric intake; nutrition; extreme temperature; agaonistic stimuli; socio-tactile cues; and priming pheronomes. The last two factors named operate directly on the secretion of luteinizing hormone or prolactin; the others act at many points in the reproductive system. Reproduction in the house mouse seems divorced from photoperiodically induced seasonality; indeed, this species breeds well even in constant darkness. Seasonal breeding may or may not then occur, depending upon dietary considerations, with or without a secondary interaction with variation in ambient temperature. There is no evidence for a dependence upon secondary plant compounds. Some of the effects of priming pheromones that have been observed previously in laboratory mice probably play no meaningful role in wild populations. The remaining pheromonal phenomena can be conceptualized as a single cueing system that has three components: (a) urinary cues of socially dominant males can accelerate ovulation in females, adult or prepubertal; (b) female urinary cues may elevate pheromonal potency in adult males, thereby forming a feedback loop by which the females elicit their own ovulation; and (c) the male's action on prepubertal females can be blocked by urinary cues emanating from other females. When all of the above is viewed in toto, the reproductive biology of the house mouse seems uniquely suited to support ecological opportunism. The relatively few environmental inhibitors of reproduction in this species should enhance the ability of dispersing young to colonize an exceptionally wide variety of habitats and climates...
Animals↗
The ecology and evolution of microbial immune systems: a look on the wild vibrio side.
Natural populations of vibrio beyond the well-studied pandemic strains of Vibrio cholerae, provide a powerful model for investigating the eco-evolutionary dynamics of microbial immune systems. Their genetic diversity, ecological versatility, ease of culturability and the availability of time-series data enable detailed studies of phage-host interactions in natural contexts. This review synthesizes recent advances in vibriophage research, highlighting key findings and emerging tools. High-throughput assays and genomic tools have offered new perspectives on phage specificity, host range and the evolutionary pressures shaping these interactions. Theoretical frameworks, such as arms race and fluctuating selection dynamics, are informed by empirical data from vibrio-phage systems, with time-series sampling providing crucial insights into their temporal and spatial dynamics. A major finding is the role of mobile genetic elements (MGEs) in encoding bacterial defence systems, which shape phage-host coevolution. Discoveries like the phage satellite PICMI illustrate how MGEs facilitate the transfer of antiviral systems, influencing ecological and evolutionary dynamics. The paradox of generalist vibriophages, rare despite their broad host ranges, is also explored. By integrating experimental approaches with field observations, vibriophage research advances microbial ecology and informs sustainable applications in aquaculture and phage therapy, reinforcing vibrios as a versatile model system.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.
Bacteriophages↗
Attitudinal versus ecological approaches to the characterization of institutional treatment environments.
The relational and discriminative properties of attitudinal and ecological measures of environments were examined within the context of a state hospital for mentally retarted clients. Three hypotheses were advanced, and the results gave substantial support for one of these and partial support for a second: (a) that the correlations between attitudinal and ecological measures should not differ significantly from zero, and (b) that differences among hospital treatment programs and living units should be reflected in ecological but not in attitudinal measures. However, the results did not provide clear confirmation for a third hypothesis: that differences among staff demographic characteristics and employment history should be reflected in attitudinal but not in ecological measures. It was suggested that these background variables may not be appropriate measures of personality-linked attributes.
Attitude of Health Personnel↗
3D tracking of marine megafauna to advance movement ecology.
Modern animal tracking devices reliably record movement in horizontal and vertical dimensions, positioning movement ecology to transition towards true three-dimensional (3D) analyses. True 3D tracking, in which horizontal and vertical positions are paired through time, is particularly valuable for marine megafauna, which traverse coastal, pelagic, and aerial environments, making them ideal for illustrating how 3D data can advance movement ecology. By synthesising early approaches to 3D tracking in these taxa, we show that these studies provide ecological perspectives unobtainable from two-dimensional data, identify key barriers limiting wider adoption, and highlight emerging solutions. Broader adoption of true 3D tracking is critical for addressing remaining knowledge gaps in marine megafauna ecology and for improving conservation frameworks to protect the 3D environments these species occupy.
animal-borne sensors↗