Journal of Theoretical Biology最新文献

{"title":"An individual-based simulation framework exploring the ecology and mechanistic underpinnings of larval crowding in laboratory populations of Drosophila","authors":"Srikant Venkitachalam ,&nbsp;Amitabh Joshi","doi":"10.1016/j.jtbi.2026.112378","DOIUrl":"10.1016/j.jtbi.2026.112378","url":null,"abstract":"<div><div>The study of larval competition in laboratory populations of <em>Drosophila</em>, implemented via the crowding of larval cultures, has contributed greatly to the understanding of the ecology of competition, the evolution of larval competitive ability, and formed the basis of rigorous testing of the theory of density-dependent selection. Earlier studies led to the view that the outcomes of larval competition, and resulting evolutionary consequences of crowding-adaptation, could largely be understood by varying the starting density of individuals in a crowded culture. However, recent studies have shown that the results of adaptation to larval crowding may not be well predicted by the overall larval density (i.e., total starting individuals/total volume of food). Cultures raised at the same overall density but at different egg number and food volume combinations were shown to have different underlying density-specific fitness functions, and crowding-adaptation in each of these cultures was attained through different evolutionary trajectories as well. A recent study showed that cultures with not just the same density, but the same egg and food volume combination, achieved through food columns of differing diameter and height, could also differ greatly in fitness-related trait outcomes. In that study, the density of larvae in the feeding band (volume of food close to the surface in contact with air, to which larval feeding is largely restricted) was a very important factor in predicting the outcomes of larval competition. Given these recent findings, it is important to understand the overall role of feeding band density, and how it influences density-specific fitness functions in different kinds of crowded cultures. As the older models of larval competition are now insufficient to capture current empirical data, we constructed an individual-based simulation framework informed in part by these more recent findings, in order to better understand the evolutionary ecology and mechanistic underpinnings of larval competition, and predict robust experiments for expanding our understanding of the process of larval competition in <em>Drosophila</em>.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"622 ","pages":"Article 112378"},"PeriodicalIF":2.0,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146004789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parameter-wise predictions and sensitivity analysis for random walk models in the life sciences","authors":"Yihan Liu ,&nbsp;David J. Warne ,&nbsp;Matthew J. Simpson","doi":"10.1016/j.jtbi.2025.112347","DOIUrl":"10.1016/j.jtbi.2025.112347","url":null,"abstract":"<div><div>Sensitivity analysis characterises input–output relationships for mathematical models, and has been widely applied to deterministic models across many applications in the life sciences. In contrast, sensitivity analysis for stochastic models has received less attention, with most previous work focusing on well-mixed, non-spatial problems. For explicit spatio-temporal stochastic models, such as random walk models (RWMs), sensitivity analysis has received far less attention. Here we present a new type of sensitivity analysis, called <em>parameter-wise prediction</em>, for two types of biologically-motivated and computationally expensive RWMs. To overcome the limitations of directly analysing stochastic simulations, we employ continuum-limit partial differential equation (PDE) descriptions as surrogate models, and we link these efficient surrogate descriptions to the RWMs using a range of biophysically-motivated <em>measurement error models</em>. Our approach is likelihood-based, which means that we also consider likelihood-based parameter estimation and identifiability analysis along with parameter sensitivity. The new approach is presented for two important classes of lattice-based RWM including a classical model where crowding effects are neglected, and an exclusion process model that explicitly incorporates crowding. Our workflow illustrates how different process models can be combined with different measurement error models to reveal how each parameter impacts the outcome of the expensive stochastic simulation. Open-access software to replicate all results is available on <span><span>GitHub</span><svg><path></path></svg></span> (Liu, 2025).</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"621 ","pages":"Article 112347"},"PeriodicalIF":2.0,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145859279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Habitat fragmentation promotes spatial scale separation under resource competition","authors":"James Austin Orgeron,&nbsp;Malbor Asllani","doi":"10.1016/j.jtbi.2025.112367","DOIUrl":"10.1016/j.jtbi.2025.112367","url":null,"abstract":"<div><div>Habitat fragmentation, often driven by human activities, alters ecological landscapes by disrupting connectivity and reshaping species interactions. In such fragmented environments, habitats can be modeled as networks, where individuals disperse across interconnected patches. We consider an intraspecific competition model, where individuals compete for space while dispersing according to a nonlinear random walk, capturing the heterogeneity of the network. The interplay between asymmetric competition, dispersal dynamics, and spatial heterogeneity leads to nonuniform species distribution: individuals with stronger competitive traits accumulate in central (hub) habitat patches, while those with weaker traits are displaced toward the periphery. We provide analytical insights into this mechanism, supported by numerical simulations, demonstrating how competition and spatial structure jointly influence species segregation. In the large-network limit, this effect becomes extreme, with dominant individuals disappearing from peripheral patches and subordinate ones from central regions, establishing spatial segregation. This pattern may act as a potential precursor to both speciation and diversity, as physical separation can reinforce divergence within the population over time and potentially support coexistence at the landscape scale.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"621 ","pages":"Article 112367"},"PeriodicalIF":2.0,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145890173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatial sucrose sink profiles shape phloem transport efficiency and xylem-phloem water exchange","authors":"Mazen Nakad ,&nbsp;Aaron Potkay ,&nbsp;Marc A. Hesse ,&nbsp;Maurizio Mencuccini ,&nbsp;Pierre Gentine ,&nbsp;Ensheng Weng","doi":"10.1016/j.jtbi.2025.112346","DOIUrl":"10.1016/j.jtbi.2025.112346","url":null,"abstract":"<div><div>The transport of photosynthates, particularly sucrose, is a key process in plant physiology, eco-hydrology, and earth system modeling. The phloem plays a central role in this transport, influencing processes ranging from plant survival during drought to ecosystem-scale carbon and water cycling. The core principle underlying our understanding of phloem transport is the pressure-flow hypothesis, in which sucrose is loaded into leaves, drawing water from the xylem through osmosis and generating pressure gradients for transport. Experimental challenges in measuring sugar fluxes and phloem turgor pressure have led to a reliance on theoretical models. However, discrepancies persist, particularly for long-distance transport, where past modeling assumptions have led to difficulties in maintaining sufficient pressure, a challenge that may be alleviated when considering unloading along the transport pathway. Criticisms of the pressure-flow hypothesis often overlook the role of local unloading along the phloem pathway, which can alleviate pressure demands by reducing sucrose concentration and viscosity. To account for their effects, this study examines the influence of local sucrose sinks on transport dynamics. Osmotically driven flows are investigated through the development of a new one-dimensional numerical model that incorporates sinks toward the stem and roots. Results show that different allocation schemes of sucrose sinks along the stem influence the speed of sucrose transport, with simulations that include local sucrose sink distributions aligning more closely with past observations than those without these sinks. Sink profiles with higher demand near the stem base are more consistent with the classical pressure-flow hypothesis, referred to as the passive Münch mechanism, promoting stable pressure gradients and efficient transport. These findings provide insight into how carbon allocation within the phloem may have evolved to optimize the efficiency of soluble compound transport.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"621 ","pages":"Article 112346"},"PeriodicalIF":2.0,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145844270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Can physical activity augment drug efficacy in PMO treatments - Insights from in-silico simulations of PTH and denosumab treatments","authors":"Rocío Ruiz-Lozano ,&nbsp;José Luis Calvo-Gallego ,&nbsp;Peter Pivonka ,&nbsp;Javier Martínez-Reina","doi":"10.1016/j.jtbi.2025.112353","DOIUrl":"10.1016/j.jtbi.2025.112353","url":null,"abstract":"<div><div>The aetiology of osteoporosis (OP) is diverse, with ageing and the oestrogen decline after menopause being the main causes of the most prevalent type, primary OP. The concurrence of other diseases (such as chronic kidney disease or hyperparathyroidism), the use of certain medications (glucocorticoids) or an inadequate diet or a sedentary lifestyle may also cause or accelerate the appearance of OP. To counteract the sedentary lifestyle, physical exercise is often recommended as a preventive therapy or even as a complement to pharmacological treatments. In this work, we use a mathematical model of bone remodelling based on cell populations that implements bone mechanical feedback as a function of the strain level and the number of cycles of daily activities. We coupled this bone remodelling model with PK-PD models of denosumab and teriparatide to study the joint effect of drug treatments and exercise on bone density of postmenopausal women. Our results show that low-intensity exercise alone could slow down bone loss and prevent OP, particularly if started at a young age, and it could improve the efficacy of drug treatments, increasing bone density and reducing fracture risk. The incremental benefit of physical activity is greater in denosumab treatments, where the anabolic effect of exercise complements the anticatabolic effect of denosumab. However, the bone density gain and the reduction in fracture risk is greater, in absolute terms, in teriparatide treatments. In any case, disuse and sedentary lifestyle are detrimental to bone density and compromises the efficacy of drug treatments.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"621 ","pages":"Article 112353"},"PeriodicalIF":2.0,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145821861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterisation of conserved and reacting moieties in chemical reaction networks","authors":"Hadjar Rahou ,&nbsp;Hulda S. Haraldsdóttir ,&nbsp;Filippo Martinelli ,&nbsp;Ines Thiele ,&nbsp;Ronan M.T. Fleming","doi":"10.1016/j.jtbi.2025.112348","DOIUrl":"10.1016/j.jtbi.2025.112348","url":null,"abstract":"<div><div>A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a structural description of biochemical networks by considering individual atoms and chemical bonds. To address combinatorial complexity, we introduce a well-established approach to group similar types of information within biochemical networks. A conserved moiety is a set of atoms whose association is invariant across all reactions in a network and arises from the decomposition of the reaction network. A reacting moiety is a set of bonds that are either broken, formed, or undergo a change in bond order in at least one reaction in the network and arises from the decomposition of the molecular network. By mathematically identifying these moieties, and by developing the link between these two decompositions, we establish the biological significance of conserved and reacting moieties according to the mathematical properties of the stoichiometric matrix. We also present a novel decomposition of the stoichiometric matrix based on conserved moieties. This approach establishes a clear connection between graph theory, linear algebra, and biological interpretation, thus offering new perspectives for the study of chemical reaction networks.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"621 ","pages":"Article 112348"},"PeriodicalIF":2.0,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145907268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Branch length statistics in phylogenetic trees under constant-rate birth-death dynamics","authors":"Tobias Dieselhorst,&nbsp;Johannes Berg","doi":"10.1016/j.jtbi.2025.112355","DOIUrl":"10.1016/j.jtbi.2025.112355","url":null,"abstract":"<div><div>Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in phylogenetic trees arising under a constant-rate birth-death model. We derive branch length distributions of phylogenetic branches with and without random sampling of individuals of the extant population under two distinct statistical scenarios: a fixed age of the birth-death process and a fixed number of individuals at the time of observation. We find that branches connected to the tree leaves (pendant branches) and branches in the interior of the tree behave very differently under sampling; pendant branches grow longer without limit as the sampling probability is decreased, whereas the interior branch lengths quickly reach an asymptotic distribution that does not depend on the sampling probability.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"621 ","pages":"Article 112355"},"PeriodicalIF":2.0,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145893478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the modulatory role of direct pedunculopontine nucleus-cortical circuitry in absence seizure dynamics: A computational study","authors":"Bing Hu,&nbsp;Jiaqin Peng,&nbsp;Wencan Li,&nbsp;Yuhan Xiao,&nbsp;Ningmin Zhu","doi":"10.1016/j.jtbi.2025.112366","DOIUrl":"10.1016/j.jtbi.2025.112366","url":null,"abstract":"<div><div>Pedunculopontine nucleus (PPN) has extensive projections with numerous brain tissues, and it has become an important target for clinical intervention in neurological diseases. In this study, we integrate the PPN into a typical corticothalamic-basal ganglia dynamical model to systematically investigate the mechanisms by which PPN-related projections regulate spike-and-wave discharges (SWDs) in absence seizures. We find that the glutamatergic (GLU) cortical-PPN projection can significantly control SWDs, through signal transmission via two GLU PPN-thalamic pathways. The coupling weights in PPN-thalamic pathways have a critical impact on the control pattern. We observe that bidirectional suppression of SWDs may be achieved by modulating the coupling strength in the GLU PPN-cortical projection. Furthermore, we analyze that, although from a computational perspective, the GLU PPN-substantia nigra pars reticulata (SNr) projection can potentially achieve control over SWDs through the SNr-thalamic pathways, this control method might be biologically challenging to implement. Finally, we observe that the reciprocal GLU projections between the PPN and the subthalamic nucleus (STN) play a regulatory role in the activity of basal ganglia, yet they do not exhibit a significant suppressive effect on SWDs. For the first time, we emphasize from a computational perspective that is the direct communication between the PPN and the cerebral cortex, rather than the communication between the PPN and the basal ganglia, might have a significant effect on the regulation of absence seizures. As a crucial component of the brainstem, the findings in this paper further elucidate the potential functions of the PPN in regulating brain activity.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"621 ","pages":"Article 112366"},"PeriodicalIF":2.0,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145879582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamics of integrated multi-trophic aquaculture (IMTA): A modeling approach incorporating zooplankton and scavenger","authors":"Honghui Gao ,&nbsp;Ming Chen ,&nbsp;Yuwei Liu","doi":"10.1016/j.jtbi.2025.112351","DOIUrl":"10.1016/j.jtbi.2025.112351","url":null,"abstract":"<div><div>A dynamic model is proposed to describe an integrated multi-trophic aquaculture (IMTA) system, including nutrients, detritus, phytoplankton, zooplankton and scavenger. The dynamic properties of the model are fully studied. Ecological reproductive indexes for the survival of phytoplankton, zooplankton, and scavenger play crucial roles in the construction of IMTA structure. Parameter values of the model are estimated based on experimental data. The study reveals that zooplankton in integrated aquaculture systems exhibit a dualistic function, potentially either enhancing or suppressing the growth of scavengers. This finding provides a mechanistic explanation for the paradoxical phenomenon observed in some marine ranching, where integrated aquaculture fails to enhance productivity, thereby challenging the conventional assumption of its universally positive effects. Furthermore, the study identifies key traits of zooplankton that promote scavengers production. Through bifurcation analysis of resource inputs, the research delineates the mechanistic basis for optimizing scavengers yield while maintaining ecosystem stability. These insights provide a theoretical foundation for enhancing the structure and sustainability of multi-trophic aquaculture systems.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"620 ","pages":"Article 112351"},"PeriodicalIF":2.0,"publicationDate":"2026-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145835351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Timing the initiation of sex: Delay mechanisms alter fitness outcomes in a rotifer population model","authors":"Bethany L.F. Stevens ,&nbsp;Silke F. van Daalen ,&nbsp;Tirzah J. Blomquist ,&nbsp;Kristin E. Gribble ,&nbsp;Michael G. Neubert","doi":"10.1016/j.jtbi.2025.112333","DOIUrl":"10.1016/j.jtbi.2025.112333","url":null,"abstract":"<div><div>Species that inhabit variable environments have complex mechanisms to precisely time their life-history transitions as conditions change. One such mechanism in rotifers is a block on sexual reproduction that extends across multiple asexual generations after emergence from diapause. It has been hypothesized that this delay is advantageous in competitive and stochastic environments. Here, we develop a model of cyclically parthenogenic rotifer populations with a novel formulation of a “mictic block” that prevents sexual reproduction by females that are not sufficiently distant, generationally, from a stem ancestor that was produced sexually. We find that mictic blocks are indeed adaptive but that the most successful phenotypes have shorter blocks than previously reported and that the success of different delay phenotypes is highly dependent on the duration of the growing season. For a fixed environmental regime, coexistence of distinct mixis phenotypes is possible, wherein a phenotype with a longer block performs better in years with an average-length growing season, and a phenotype with a shorter block and lower mixis ratio performs better in years with an “extreme” growing season, whether short or long. Our model provides an eco-evolutionary framework for the study of <em>Brachionus</em> rotifers, a model system for non-genetic maternal effects and the evolution of sex.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"620 ","pages":"Article 112333"},"PeriodicalIF":2.0,"publicationDate":"2026-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145806251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}