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PubMed1978

A semi-Markovian model for predator-prey interactions.

In the study of population dynamics, the predator-prey system is recognized as a vitally important aspect in natural population control. On aspect of predator-prey interactions is studied in this paper. The attack cycle of a predator is assumed to consist of four different activities, namely, search, pursuit, handle and eat, and digestion. A semi-Markovian model is proposed to obtain the number of prey devoured by a predator during the activity of a day. The advantages of a new semi-Markovian model to the queueing model developed by Curry and DeMichele (1977) is demonstrated, as the results from the semi-Markovian model are closer to Holling's (1966) experimental data than their results, which were based entirely on Poisson assumptions.

Animals↗
PubMed2025

Habitat Specialisation Impacts Clownfish Demographic Resilience to Pleistocene Sea-Level Fluctuations.

Habitat fragmentation and loss are key threats to biodiversity, yet their impacts on marine species remain poorly understood. Clownfishes, which rely on sea anemones for shelter and reproduction, provide an interesting model to explore how ecological specialisation mediates species responses to habitat perturbations. We used whole-genome data from 382 individuals across 10 species with varying host specialisations to reconstruct demographic histories and infer spatial genetic structure to assess the impact of Pleistocene sea-level fluctuations. Generalist species, associated with multiple hosts, maintained stable effective population sizes () and population connectivity during habitat fragmentation, reflecting resilience to environmental instability. In contrast, specialists experienced severedeclines and genetic structuring, driven by their dependence on specific hosts, without signs of population recovery following habitat reconnection. Spatial genomic analyses identified the Indonesian Through-Flow as a key dispersal corridor and the Coral Triangle as a critical hub of genetic diversity, while continental shelves and extensive open ocean regions appeared as barriers to gene flow. Our findings reveal how host specialisation shapes clownfish population dynamics, emphasising the importance of incorporating ecological dependencies into conservation assessments and deepening our understanding of species responses to ecological constraints and environmental changes over evolutionary timescales.

Animals↗
PubMed2025

Peruvian Population Genomics: Unraveling the Genetic Landscape and Admixture Dynamics of Urban Populations.

Latin American populations exhibit high genetic and phenotypic diversity shaped by complex admixture histories, yet remain underrepresented in genomic research. Here, we analyze genome-wide data from 432 urban individuals across 13 regions of Peru, including 346 newly genotyped from the Peruvian Genome Project. We revealed fine-scale population structure and demographic patterns shaped by both ancient and recent events. Indigenous American ancestries in urban individuals trace back to ancient north-south interactions consisted with archaeological records, while admixture events occurring within the last 8-10 generations involved sources already admixed between distinct ancestral lineages. Identity-by-descent analyses reveal sustained gene flow in southern Peru, while effective population size trends highlight demographic stability in Lima over the past 25 generations. Sex-biased admixture patterns suggest Indigenous ancestry contribution preferentially mediated by females. These findings offer a comprehensive view of Peru's genetic heritage, advancing our understanding of human genetic diversity and historical demographic processes in Latin America.

Admixture↗
PubMed2026

Single-cell RNA sequencing provides further insights into the immunostimulatory action of freeze-dried Lactiplantibacillus plantarum on Penaeus vannamei shrimp.

Immunostimulation through dietary interventions opened new avenues in developing disease control and prevention tools for shrimp aquaculture. We have previously shown that feeding with freeze-dried Lactiplantibacillus plantarum (LAB) increased disease resistance of Penaeus vannamei against both Vibrio parahaemolyticus and white spot syndrome virus (WSSV) based on bulk RNA sequencing of shrimp gills. This tissue participates in ion transport and serves as a first line of defense against environmental stressors and pathogenic infections. However, characterization of their cell composition and functions remains limited. Here, we implemented a single-cell RNA sequencing approach to further gather insights into how feeding with freeze-dried LAB modulates host immunity which may not be evident with bulk RNA sequencing approach. A total of five clusters with unique transcriptional signatures were identified, corresponding to pillar cells, septal cells, and sessile hemocytes. Pseudo-bulk analyses at global- and cluster-levels showed differential expression of genes related to host immunity and metabolism. We further revealed how overall transcriptomic changes are not exclusively caused by gene expression changes but may also be driven by cell population dynamics. This study highlighted how single-cell RNA sequencing approach may shed light on the mechanisms of action of immunostimulants which may be masked in bulk transcriptome analyses.

Animals↗
PubMed1978

Social group fission and the origin of intergroup genetic differentiation among the rhesus monkeys of Cayo Santiago.

The serum transferrin locus is used to investigate the roles of the lineal effect of fission, male migration effect of fission, and genetic drift in causing intergroup genetic differentiation among the rhesus macaques of Cayo Santiago. These three mechanisms prove sufficient to explain the degrees of differentiation between the newly formed social groups A, K, and L as of July 1, 1971. The lineal effect of fission provides a baseline of intergroup differentiation which is altered by forces leading to intragroup genetic change, the male migration effect and genetic drift. The importance of population dynamics for the distribution of alleles among subgroups of a population is recognized.

Animals↗
PubMed2025

Whole-genome sequencing, strain composition, and predicted antimicrobial resistance of Streptococcus pneumoniae causing invasive disease in England in 2017-20: a prospective national surveillance study.

BACKGROUND: Surveillance of the invasive disease burden caused by Streptococcus pneumoniae in England is performed by the UK Health Security Agency (UKHSA). In 2017, UKHSA switched from phenotypic methods to whole-genome sequencing (WGS) approaches for pneumococcal surveillance. Here, we present the first results of national WGS surveillance, up to the start of the COVID-19 pandemic, with the aim of describing the population genomics of this important pathogen. METHODS: We examined prospective national surveillance data from England, using bacterial isolates from cases of invasive pneumococcal disease (IPD) submitted to the national reference laboratory at UKHSA. A bioinformatic pipeline was developed to quality control WGS data and routinely report species and serotype. We assembled isolate data, assigned global pneumococcal sequencing clusters (GPSCs), and predicted antimicrobial resistance (AMR) profiles for isolates that passed further quality control. We collected additional data on patient outcomes and characteristics using enhanced surveillance questionnaires completed by patients' general practitioners. We used logistic regression analysis to assess the effects of various genomic and patient characteristics on the outcomes of IPD. FINDINGS: In England, between July 1, 2017, and Feb 29, 2020, there were 15 400 cases of IPD. From these cases, 13 749 (89·3%) isolates were sequenced, passed quality control, and were included in analyses. Serotype diversity was high during the study period, with 2751 (20%) isolates serotyped as 13-valent pneumococcal conjugate vaccine (PCV13) types, whereas serotype 8 was the most prevalent serotype (n=3074 [22·4%]) overall. There were 157 GPSCs within the collection, with GSPC3 the most common, encompassing 98·7% (3033 of 3074) of serotype 8 isolates. Most isolates (n=10 198 [74·2%]) did not contain AMR-associated genes. Resistance to co-trimoxazole was the most frequently predicted resistance (n=2331 [17%]), followed by resistance to tetracycline (n=1199 [8·7%]) and β-lactams (n=1149 [8·4%]). Logistic regression analysis found the presence of AMR-associated genes significantly increased the odds of patient death (odds ratio 1·18, 95% CI 1·01-1·38). Some GPSCs were also associated with a significant increase in the odds of patient death, such as GPSC12 (1·88, 1·48-2·38). Isolates from 2018 were associated with a significant increase in the odds of patient death (1·12, 1·00-1·25), whereas younger patient age was significantly associated with a reduction in the odds of patient death compared with being aged 85 years or older. INTERPRETATION: WGS-based surveillance has allowed us to interrogate country-wide population dynamics driving changes in pneumococcal serotype frequency. Here, we observe a stable but diverse population before the COVID-19 pandemic restrictions were enforced in England, with low rates of AMR. These findings will provide the baseline for pandemic and post-pandemic data, to collectively inform implementation and development of the vaccination programme within the country. FUNDING: None.

Streptococcus pneumoniae↗
PubMed2026

Fine-Scale Population Genomics Reveals Genetic Differentiation in the Brooding Amphipod Cheirimedon femoratus Across the South Shetland Islands, Antarctica.

Antarctic marine ecosystems are sensitive to environmental change, and impacts on processes such as population connectivity will play a fundamental role in future population dynamics and persistence, affecting short-term demography and long-term evolution. We investigated the population genomics of the common benthic brooding Antarctic amphipod Cheirimedon femoratus (Pfeffer, 1888), using 8837 high-quality single-nucleotide polymorphisms (SNPs) from 87 individuals collected at 4 sites in the South Shetland Islands, separated by up to 200 km: Deception Island, King George Island, Livingston Island, and Snow Island. While Admixture, F ST, principal component analysis (PCA), and demographic (Ne) analyses revealed a generally weak population genetic structure, Livingston Island emerged as a distinct population, especially compared to King George Island. All populations showed a heterozygote deficit with positive inbreeding coefficients (F IS), particularly high in the Snow Island population (~0.55). Tajima's D test suggested overall neutral evolution, although slight variation was observed among sites. Despite the limited dispersal potential of this brooding species, the observed connectivity may be maintained through passive dispersal, likely via floating macroalgae or ice-rafted debris, facilitated by prevailing regional ocean currents. This may enhance the population resilience of Antarctic benthic communities under environmental change, including regional warming and shifts in ocean circulation, compared to more isolated populations. Our findings underscore the complex interplay between passive connectivity and fine-scale differentiation in shaping Antarctic benthic invertebrate diversity.

Amphipoda↗
PubMed2026

Large language models in bioinformatics: a comprehensive survey.

The emergence of foundation models with trillion-level parameters has redefined the landscape of artificial intelligence. Various fields are developing their own large-scale models, which can solve many problems within the field and improve work efficiency. Biological large-scale models are a cross-disciplinary research field that combines mathematics, computer science, and biology, aiming to simulate and understand the structure, function, and dynamic changes of biological systems through the establishment of complex computational models. This field covers multiple levels such as biological pathways, population dynamics, protein folding, etc., providing us with tools for deep exploration of the mysteries of life and applications in medicine, ecology, and other fields. This article reviews the background and research status of biological large-scale models, and discusses future directions. Large language models (LLMs) and other large-scale foundation models have rapidly advanced in recent years, enabling powerful representation learning and generation across text, sequences, and multimodal data. In bioinformatics and biomedicine, these models are increasingly used to analyze genomic sequences, infer protein properties and structures, support drug discovery, and integrate heterogeneous biomedical evidence. This survey reviews the basic principles of LLMs and summarizes representative applications in (i) gene and genome sequence analysis, (ii) protein structure and function prediction, and (iii) drug design, including virtual screening and personalized medicine. We also discuss emerging multi-model modeling approaches, as well as key challenges such as data quality and privacy, interpretability, generalization to new organisms and tasks, and responsible deployment in health-related settings. Finally, we outline future directions for developing reliable, scalable, and explainable bioinformatics foundation models.

bioinformatics↗
PubMed1979

Ecological studies at Hofuf, Eastern Saudi Arabia, in relation to dermal leishmaniasis.

Field and laboratory investigations were carried out in connection with an epidemic of dermal leishmaniasis in Hofuf, Eastern Province of Saudi Arabia, during 1977. In this present note emphasis is laid on description of the population dynamics and species spectrum of the sandflies, the occurrence of the vector and the course of the epidemic of Leishmania tropica in correlation with the sandfly population and the natural reservoir and the rodent population.

Animals↗
PubMed2026

EV-B 3D polymerase remodels viral populations through 5'UTR recombination to subvert cardiac antiviral innate immunity.

Viral myocarditis, a leading cause of morbidity in young populations, is strongly linked to Coxsackievirus B (CV-B) infections harboring dominant 5'-terminally deleted (5'TD) and minor full-length (FL) CV-B RNA populations in cardiac tissues. Here, we demonstrate how viral RNA-dependent RNA polymerase (3Dpol)-driven recombination in the 5'UTR orchestrates viral RNA populations dynamics and subverts type I interferon responses. In primary human cardiomyocytes (HCMs), 3Dpol-mediated copy-choice recombination enhances 5'TD RNA replication while suppressing FL populations. Infection of immunocompetent mice with recombination-deficient CV-B3 (3Dpol Y276H) shifted 5'TD populations ratios toward immune-sensing viral RNAs, elevating cardiac IFN-β/ISG15 and accelerating viral clearance. Transfection experiments confirmed that 50-nt 5'TD RNAs (TD50) evade innate immunity, whereas shorter deletions (9-36-nt, TD15) restore type I interferon responses in HCMs. Our findings establish 3Dpol-driven recombination as a critical mechanism sustaining pathogenic 5'TD RNAs that subvert antiviral innate immunity, highlighting recombination inhibition as a promising therapeutic strategy against CV-B myocarditis.

Animals↗
PubMedDate not supplied

[An example of research on biological control: Entomophthora fungi pathogenic for aphids].

The results obtained in 15 years of research on the Entomophthorales pathogen of aphids showed the importance of the action of these fungi in the regulation of natural aphid populations and their possible use in agriculture as a biological control agent. Recent ecological studies on natural populations of aphids established the seasonal variation of the different fungal species and the diverse degrees of specificity between the species or groups of species of aphid and the various species of Entomophthora. The study of populations dynamics of an aphid species on a cultivated plant permitted the determination of the way a certain number of biotic and abiotic factors, such as temperature, humidity, thresholds of the insect population and of the infecting fungus lead to an epizootic development. If the air propagation of the disease by conidia is understood for a long time, the role of the soil as a reservoir for the infecting fungus has been demonstrated recently. Under favourable climatic conditions, the use of industrially produced resistant resting spores would allow the regulation of aphid populations in nature.

Animals↗
PubMed2026

Precision Engineering of Evolution-Resilient Rice against Bacterial Blight.

The persistent conflict between rice and Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight, exemplifies a dynamic genetic arms race in agriculture. The cyclical deployment and erosion of major resistance (R) genes highlight the high adaptive potential of Xoo and the need for strategies that are durable rather than absolute. This review synthesizes a paradigm shift from reactive, single R-gene deployment toward proactive engineering of evolution-resilient resistance. We explore the molecular-genetic basis of Xoo adaptability, including TAL effector diversification, non-TAL virulence functions, genome variation, and immune suppression mechanisms. In response, we propose a framework for durable disease management with three connected components: precision disarmament through editing of susceptibility-gene effector-binding elements and executor/decoy designs; smart induction through targeted delivery and immune priming; and ecological fortification through protective microbiomes. We also discuss the limits, trade-offs, and field-validation requirements of these approaches. Integrating frontier technologies with evolutionary genetics, predictive genomics, and pathogen population dynamics can help develop rice varieties and deployment systems that are more difficult for Xoo populations to overcome.

CRISPR↗
PubMed1978

Ecological studies in Madagascar of Biomphalaria pfeifferi, intermediate host of Schistosoma mansoni. 2. Biology and dynamics in the non-endemic area of Antananarivo.

The region of Antananarivo, where Schistosomiasis is not yet endemic, is compared to Ambositra, a well established focus of S. mansoni, with regard to climate, hydrology and snail habitats. Higher mean temperatures and a more pronounced dry season in Antananarivo contribute to sometimes less favourable hydrological conditions. Biomphalaria is found in very few and limited habitats. Population dynamics were followed up in selected habitats and showed ecological parameters comparable to those of the Ambositra-strain. Trematode infections were very scarce. Both strains of Biomphalaria are equally susceptible to infections with the malagasy strain of S. mansoni (up to 100 p. 100). Mortality rates, prepatency periods and the electrophoretic pattern of egg proteins are very similar. Foreign snail species like B. glabrata (albino strain) and B. pfeifferi (South African strain) are hardly susceptible to malagasy S. mansoni. Some cases of S. mansoni-infections are mentioned, which presumably had been contracted in non-endemic areas of the province of Antananarivo. The possibility and risk of implantation of schistosomiasis in this region and in the town is evaluated following the discussion of epidemiological details. The author concludes that in spite of some unfavourable conditions for S. mansoni the establishment of the cycle can locally not be excluded. Attention is all the more important, as control of endemic schistosomiasis would be particularly difficult under malagasy conditions of geography, climate, snail dynamics and human behaviour.

Adult↗
PubMed2025

Integrating multiscale mathematical modeling and multidimensional data reveals the effects of epigenetic instability on acquired drug resistance in cancer.

Biological and dynamic mechanisms by which Drug-tolerant persister (DTP) cells contribute to the development of acquired drug resistance have not been fully elucidated. Here, by integrating multidimensional data from drug-treated PC9 cells, we developed a novel multiscale mathematical model from an evolutionary perspective that encompasses epigenetic and cellular population dynamics. By coupling stochastic simulation with quantitative analysis, we identified epigenetic instability as the most prominent kinetic feature related to the emergence of DTP cell subpopulations and the effectiveness of intermittent treatment. Moreover, we revealed the optimal schedule for intermittent treatment, including the optimal area for therapeutic time and drug holidays. By leveraging single-cell RNA-seq data characterizing the drug tolerance of lung cancer, we validated the predictions made by our model and further revealed previously unrecognized biological features of DTP cells, such as cell autophagy and migration, as well as new biomarker genes of therapeutic tolerance. Our work not only provides a paradigm for the integration of multiscale mathematical models with newly emerging genomics data but also improves our understanding of the crucial roles of DTP cells and offers guidance for developing new intermittent treatment strategies against acquired drug resistance in cancer.

Drug Resistance, Neoplasm↗
PubMed2026

Persistent spread of carbapenemase-producing Klebsiella pneumoniae in acute care hospitals in 36 European countries (the CCRE survey): a prospective, multicentre, cross-sectional, epidemiological, microbiological, and genomic surveillance study.

BACKGROUND: Carbapenem-resistant Enterobacterales pose a substantial threat to patients and health-care systems. We conducted a survey of carbapenem-resistant and/or colistin-resistant Enterobacterales (CCRE survey) in 37 European countries to describe their occurrence, geographical distribution, and population dynamics and inform control policies. We report the results of Klebsiella pneumoniae species complex isolates in this study. METHODS: In this cross-sectional, epidemiological, microbiological, and genomic study conducted in all EU, European Economic Area and EU candidate countries as of 2019, hospital microbiology laboratories were selected on the basis of population coverage. Participating laboratories collected, from patient samples, the first ten successive isolates of carbapenem-resistant or carbapenem-susceptible increased exposure (carbapenem-R/I) K pneumoniae species complex or Escherichia coli, and carbapenem-susceptible (carbapenem-S) comparator isolates of the same species, accompanied by patient epidemiological and clinical information. Isolate collection started in 2019, with three possible starting dates-ie, March 1, April 1, or May 1, 2019, and ended after collection of ten carbapenem-R/I and carbapenem-S isolates or a maximum period of 6 months. Isolates were tested for phenotypic susceptibility to 16 antimicrobial agents of relevance to K pneumoniae species complex. Whole-genome sequencing was performed centrally using Illumina technology. Isolates from the CCRE survey were compared with those from the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) study. FINDINGS: 1566 carbapenem-R/I and 1407 carbapenem-S K pneumoniae species complex isolates collected from patients in 302 hospitals in 36 countries (one country did not send isolates) were analysed in this study. The high-risk lineages identified during a previous similar survey in 2013-14 (EuSCAPE) were found to continue to circulate across European hospitals in 2019 (ST11, ST15, ST101, and ST258/512). Moreover, concerning shifts in the pathogen population were observed. First, a higher proportion of carbapenem-R/I isolates was found to carry a carbapenemase gene in the CCRE survey (1398 [89·3%] of 1566) than in EuSCAPE (657 [69·6%] of 944), mainly related to increased acquisition of carbapenemase genes by high-risk lineages. Of note, among ST307 isolates from all hospitals, the proportion of carbapenem-R/I isolates carrying a carbapenemase gene increased from 14 (60·9%) of 23 in EuSCAPE to 164 (91·1%) of 180 in the CCRE survey. Second, an expansion of emerging multidrug-resistant lineages (ST147, ST307, and ST39) was also noted: Among 113 hospitals that contributed K pneumoniae species complex isolates to both EuSCAPE and the CCRE survey, the proportion of ST147 increased from 16 (3·4%) of 476 in EuSCAPE to 49 (7·4%) of 662 carbapenem-R/I isolates in the CCRE survey, that of ST307 increased from 15 (3·2%) of 476 to 88 (13·3%) of 662, and that of ST39 increased from 3 (0·6%) of 476 to 10 (1·5%) of 662. Third, there was an increased spread of isolates harbouring acquired virulence loci: isolates with the highest Kleborate virulence score of five increased from 7 (0·4%) of 1717 in EuSCAPE to 40 (1·3%) of 2973 in the CCRE survey. Notably, the increase was mainly observed in the carbapenem-S-group. INTERPRETATION: The survey findings portray an escalating epidemiological situation and suggest that control measures have not been able to interrupt transmission of high-risk lineages of carbapenemase-producing K pneumoniae in European hospitals. The heterogeneous and evolving situation with regards to circulating lineages and dominant carbapenemase genes requires strengthening and continuous adaptation of diagnostic, treatment, and control measures guided by genomic surveillance. FUNDING: European Centre for Disease Prevention and Control and Centre for Genomic Pathogen Surveillance.

Humans↗
PubMed2025

Multiomic Analyses Reveal the Molecular Mechanisms of Arid Adaptation in a Desert Rodent Species.

Organisms living in desert habitats face multiple simultaneous pressures, such as high temperatures and arid, and the population dynamics and community diversity of small rodents are strongly affected by climate extremes. However, the potential mechanisms by which desert rodents adapt to arid remain largely unexplored. Here, we assembled a 3.18 Gb genome, including 25,812 protein-encoding genes, for Orientallactaga sibirica, which is widely distributed across both arid and semihumid environments in Eurasia. Orientallactaga sibirica has longer ears and hind limbs to enhance heat dissipation, which may be related to the positively selected genes, such as Fgf10, Fgf11, Hoxc4, Hoxd1, and Bmp4. The renal transcriptome revealed increased fat and carbohydrate metabolism for metabolic water production in O. sibirica residing in arid habitats. Pathways such as material metabolism, oxidative stress response, osmoregulation, and water and salt reabsorption were enriched in candidate genes, such as Avp, Ang, and Ace, under positive selection in O. sibirica. Moreover, amino acid replacement was observed in the protein sequences of seven candidate genes, including Aldh7a1, Lnpep, Wnk4, C1qc, and Awat2, and these specific amino acid replacements of genes such as Umod and Scnn1a were related to unique osmoregulation, osmotic protection, and water retention compensation mechanisms. Water deprivation under laboratory conditions induced the upregulation of Umod and Aldh7a1 expression, further supporting the results observed in the wild population. These findings demonstrate that the positively selected genes related to limb development and specific amino acid replacements in the genes Umod and Scnn1a for unique osmoregulation in the renal vascular system may contribute to arid adaptation in the desert rodent species O. sibirica. This study provides novel insights into the adaptive evolution of desert small mammals and can serve as a reference for future research on renal damage-related diseases, such as human kidney stones and salt-sensitive hypertension.

Animals↗