Journal of Theoretical Biology最新文献

Impact of evolutionary relatedness on species diversification and tree shape. 进化相关性对物种多样性和树形的影响

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-02-07 Epub Date: 2024-11-16 DOI: 10.1016/j.jtbi.2024.111992

Tianjian Qin, Luis Valente, Rampal S Etienne

{"title":"Impact of evolutionary relatedness on species diversification and tree shape.","authors":"Tianjian Qin, Luis Valente, Rampal S Etienne","doi":"10.1016/j.jtbi.2024.111992","DOIUrl":"10.1016/j.jtbi.2024.111992","url":null,"abstract":"Slowdowns in lineage accumulation are often observed in phylogenies of extant species. One explanation is the presence of ecological limits to diversity and hence to diversification. Previous research has examined whether and how species richness (SR) impacts diversification rates, but rarely considered the evolutionary relatedness (ER) between species, although ER can affect the degree of interaction between species, which likely sets these limits. To understand the influences of ER on species diversification and the interplay between SR and ER, we present a simple birth-death model in which the speciation rate depends on the ER. We use different metrics of ER that operate at different scales, ranging from branch/lineage-specific to clade-wide scales. We find that the scales at which an effect of ER operates yield distinct patterns in various tree statistics. When ER operates across the whole tree, we observe smaller and more balanced trees, with speciation rates distributed more evenly across the tips than in scenarios with lineage-specific ER effects. Importantly, we find that negative SR dependence of speciation masks the impact of ER on some of the tree statistics. Our model allows diverse evolutionary trajectories for producing imbalanced trees, which are commonly observed in empirical phylogenies but have been challenging to replicate with earlier models.","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"111992"},"PeriodicalIF":1.9,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142669395","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}

引用次数: 0

From Bayes to Darwin: Evolutionary search as an exaptation from sampling-based Bayesian inference.

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-12-19 DOI: 10.1016/j.jtbi.2024.112032

Márton Csillag, Hamza Giaffar, Eörs Szathmáry, Mauro Santos, Dániel Czégel

{"title":"From Bayes to Darwin: Evolutionary search as an exaptation from sampling-based Bayesian inference.","authors":"Márton Csillag, Hamza Giaffar, Eörs Szathmáry, Mauro Santos, Dániel Czégel","doi":"10.1016/j.jtbi.2024.112032","DOIUrl":"https://doi.org/10.1016/j.jtbi.2024.112032","url":null,"abstract":"Building on the algorithmic equivalence between finite population replicator dynamics and particle filtering based approximation of Bayesian inference, we design a computational model to demonstrate the emergence of Darwinian evolution over representational units when collectives of units are selected to infer statistics of high-dimensional combinatorial environments. The non-Darwinian starting point is two units undergoing a few cycles of noisy, selection-dependent information transmission, corresponding to a serial (one comparison per cycle), non-cumulative process without heredity. Selection for accurate Bayesian inference at the collective level induces an adaptive path to the emergence of Darwinian evolution within the collectives, capable of maintaining and iteratively improving upon complex combinatorial information. When collectives are themselves Darwinian, this mechanism amounts to a top-down (filial) transition in individuality. We suggest that such selection mechanism can explain the hypothesized emergence of fast timescale Darwinian dynamics over a population of neural representations within animal and human brains, endowing them with combinatorial planning capabilities. Further possible physical implementations include prebiotic collectives of non-replicating molecules and reinforcement learning agents with parallel policy search.","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112032"},"PeriodicalIF":1.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873144","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}

引用次数: 0

Bridging Wright-Fisher and Moran models.

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-12-19 DOI: 10.1016/j.jtbi.2024.112030

Arthur Alexandre, Alia Abbara, Cecilia Fruet, Claude Loverdo, Anne-Florence Bitbol

引用次数: 0

Beyond predation: Fish-coral interactions can tip the scales of coral disease.

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-12-19 DOI: 10.1016/j.jtbi.2024.112031

Buddhadev Ranjit, Arnab Chattopadhyay, Arindam Mandal, Santosh Biswas, Joydev Chattopadhyay

{"title":"Beyond predation: Fish-coral interactions can tip the scales of coral disease.","authors":"Buddhadev Ranjit, Arnab Chattopadhyay, Arindam Mandal, Santosh Biswas, Joydev Chattopadhyay","doi":"10.1016/j.jtbi.2024.112031","DOIUrl":"https://doi.org/10.1016/j.jtbi.2024.112031","url":null,"abstract":"Coral reefs are critical ecosystems, fostering biodiversity and sustaining the livelihoods of millions globally. Nonetheless, they confront escalating threats, with infectious diseases emerging as primary catalysts for extensive damage, surpassing the impacts of other human-induced stressors. Disease transmission via biotic factors, particularly during fish predation, is a crucial yet often overlooked pathway. While their feeding can spread infectious diseases through spores, it also controls the growth of macroalgae, a major competitor for space on the reef. Given this dual effect, the precise impact of fish on coral disease remains ambiguous and requires additional investigation. In this study, we addressed this gap for the first time by employing a mathematical model. Our analyses unveil intricate interactions between fish predation and coral health, revealing potential benefits and drawbacks for coral reef ecosystems. Coral survival hinges on a delicate balance of fish predation, with extremes (both low and high) offering some protection against disease outbreaks compared to moderate predation, which can cause sudden die-offs. More specifically, as fish predation intensifies, the ecosystem undergoes a tipping point, transitioning from a disease-dominated state to a healthier one. Moreover, the interplay between transmission rate and virulence in coral populations is significantly shaped by fish predation rates. Specifically, the threshold ratio of transmission to virulence, signalling a regime shift from a healthy to a disease-dominated state, exhibits a linear increase with fish predation rate. Overall, our findings emphasize the importance of considering biotic interactions in coral disease ecology and offer insights essential for effective reef conservation strategies.","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112031"},"PeriodicalIF":1.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872620","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}

引用次数: 0

Analysis of electrical activities in a functional neuron with dual memristors.

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-12-18 DOI: 10.1016/j.jtbi.2024.112034

Xinlin Song, Feifei Yang

{"title":"Analysis of electrical activities in a functional neuron with dual memristors.","authors":"Xinlin Song, Feifei Yang","doi":"10.1016/j.jtbi.2024.112034","DOIUrl":"https://doi.org/10.1016/j.jtbi.2024.112034","url":null,"abstract":"Neuron as a charged body, it is easily disturbed by the external electromagnetic field, which changes the electrical activities of the neurons. In fact, the interference of external electric or magnetic field is the process of energy injection of neurons, the injection of energy will redistribute the field energy inside the neurons, and the redistribution of energy will change the electrical activities of the neurons. Therefore, we design a neuron model with double memristors to explore the external electromagnetic field on the regulation of neural electrical activity. The dimensionless equations of the model with double memristors and its energy function are obtained based on the Kirchhoff's and the Helmholtz's theorems. The electrical activities of the neuron model under the external electromagnetic field distribution are researched by applying the nonlinear analysis methods, and the coherence resonance of the neuron is explored under the external noise electromagnetic field. The results indicate that the electrical activities of the model are controlled by the external electromagnetic field. This neuron model can be used to study the synchronization between magnetic field coupled or electric field coupled neurons.","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112034"},"PeriodicalIF":1.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871989","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}

引用次数: 0

Channel noise induced stochastic effect of Hodgkin-Huxley neurons in a real classification task.

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-12-16 DOI: 10.1016/j.jtbi.2024.112028

Yasemin Erkan, Erdem Erkan

{"title":"Channel noise induced stochastic effect of Hodgkin-Huxley neurons in a real classification task.","authors":"Yasemin Erkan, Erdem Erkan","doi":"10.1016/j.jtbi.2024.112028","DOIUrl":"10.1016/j.jtbi.2024.112028","url":null,"abstract":"Noise is generally considered to have negative effects on information processing performance. However, it has also been proven that adding random noise or a certain level of stochastic (random) variability to a nonlinear system can increase its performance or sensitivity to weak signals. Despite the studies on this concept, called stochastic resonance in computational neuroscience, this phenomenon is still among the topics that need detailed research, especially in machine learning. In this study, the effect of noise arising from the intrinsic dynamics of the neurons forming the network in a spiking neural network consisting of Hodgkin-Huxley neurons on the image classification success of the network is investigated. In the first part of this two-part study, a practical neural network model consisting of Hodgkin-Huxley neurons is proposed and the network is tested in a 4-class real classification task. It is observed that the network consisting of Hodgkin-Huxley neurons has a classification performance at least as successful as the artificial neural network. In the second part of the study, the neurons in the network are replaced with stochastic Hodgkin-Huxley neurons, which more realistically represent the biological neuron, and the classification performance of the network at different cell membrane sizes is examined. Findings reveal that a spiking network consisting of stochastic Hodgkin-Huxley neurons, in which intrinsic noise dynamics are incorporated into the system, shows maximum classification performance at an optimal intrinsic noise level. It is called this reflection observed in the classification performance of a spiking network, which is referred to as stochastic resonance in computational neuroscience, as stochastic classification resonance in this study. This study also highlights the importance of bridging the gap between biological neuroscience and artificial neural networks for a better understanding of neurological structure.","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112028"},"PeriodicalIF":1.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857059","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}

引用次数: 0

Deciphering circulating tumor cells binding in a microfluidic system thanks to a parameterized mathematical model.

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-12-16 DOI: 10.1016/j.jtbi.2024.112029

Giorgia Ciavolella, Julien Granet, Jacky G Goetz, Naël Osmani, Christèle Etchegaray, Annabelle Collin

{"title":"Deciphering circulating tumor cells binding in a microfluidic system thanks to a parameterized mathematical model.","authors":"Giorgia Ciavolella, Julien Granet, Jacky G Goetz, Naël Osmani, Christèle Etchegaray, Annabelle Collin","doi":"10.1016/j.jtbi.2024.112029","DOIUrl":"https://doi.org/10.1016/j.jtbi.2024.112029","url":null,"abstract":"The spread of metastases is a crucial process in which some questions remain unanswered. In this work, we focus on tumor cells circulating in the bloodstream, the so-called Circulating Tumor Cells (CTCs). Our aim is to characterize their trajectories under the influence of hemodynamic and adhesion forces. We focus on already available in vitro measurements performed with a microfluidic device corresponding to the trajectories of CTCs - without or with different protein depletions - interacting with an endothelial layer. A key difficulty is the weak knowledge of the fluid velocity that has to be reconstructed. Our strategy combines a differential equation model - a Poiseuille model for the fluid velocity and an ODE system for the cell adhesion model - and a robust and well-designed calibration procedure. The parameterized model quantifies the strong influence of fluid velocity on adhesion and confirms the expected role of several proteins in the deceleration of CTCs. Finally, it enables the generation of synthetic cells, even for unobserved experimental conditions, opening the way to a digital twin for flowing cells with adhesion.","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112029"},"PeriodicalIF":1.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857060","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}

引用次数: 0

Perceived risk induced multiscale model: Coupled within-host and between-host dynamics and behavioral dynamics.

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-12-10 DOI: 10.1016/j.jtbi.2024.111998

Xiaodan Sun, Weike Zhou, Yuhua Ruan, Guanghua Lan, Qiuying Zhu, Yanni Xiao

{"title":"Perceived risk induced multiscale model: Coupled within-host and between-host dynamics and behavioral dynamics.","authors":"Xiaodan Sun, Weike Zhou, Yuhua Ruan, Guanghua Lan, Qiuying Zhu, Yanni Xiao","doi":"10.1016/j.jtbi.2024.111998","DOIUrl":"10.1016/j.jtbi.2024.111998","url":null,"abstract":"A novel multiscale model is formulated to examine the co-evolution among behavioral dynamics, disease transmission dynamics and viral dynamics, in which perceived risk act as a bridge for realizing the bidirectional coupling of between-host dynamics and within-host dynamics. The model is validated by real data and exhibits rich dynamic behaviors including the periodic oscillations of the solutions, the discordance of transmission dynamics and viral dynamics. It is observed that new infections may increase with improving treatment efficacy, which may reveal the hidden mechanisms why it is hard to eliminate HIV/AIDS infection only with the strategy of treatment. If increasing treatment efficacy but without improving diagnosis rate, \"nearly elimination\" phenomenon may happen when the risk threshold for behavior changes is low, in which the number of new infections may drop to a relatively low level but increase again to a relatively high level after a period of time as people may hardly keep their awareness and increase their high risk behaviors. The findings indicate that the intervention measures should be implemented both at individual level and population level to realize \"ending the AIDS\".","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"111998"},"PeriodicalIF":1.9,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820331","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}

引用次数: 0

Learning to hunt: A data-driven stochastic feedback control model of predator-prey interactions.

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-12-09 DOI: 10.1016/j.jtbi.2024.112021

Deze Liu, Mohammad Tuqan, Daniel Burbano

{"title":"Learning to hunt: A data-driven stochastic feedback control model of predator-prey interactions.","authors":"Deze Liu, Mohammad Tuqan, Daniel Burbano","doi":"10.1016/j.jtbi.2024.112021","DOIUrl":"10.1016/j.jtbi.2024.112021","url":null,"abstract":"The dynamics unfolding during predator-prey interactions encapsulate a critical aspect of the natural world, dictating the survival and evolutionary trajectories of animal species. Underlying these complex dynamics, sensory-motor control strategies orchestrate the locomotory gates essential to guarantee survival or predation. While analytical models have been instrumental in understanding predator-prey interactions, dissecting sensory-motor control strategies remains a great challenge due to the adaptive and stochastic nature of animal behavior and the strong coupling of predator-prey interactions. Here, we propose a data-driven mathematical model describing the adaptive learning response of a dolphin while hunting a fish. Grounded in feedback control systems and stochastic differential equations theory, our model embraces the inherent unpredictability of animal behavior and sheds light on the adaptive learning strategies required to outmaneuver agile prey. The efficacy of our model was validated through numerical experiments mirroring crucial statistical properties of locomotor activity observed in empirical data. Finally, we explored the role of stochasticity in predator-prey dynamics. Interestingly, our findings indicate that varying noise levels can selectively favor either fish survival or dolphin hunting success.","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112021"},"PeriodicalIF":1.9,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815057","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}

引用次数: 0

Super-resolution ultrasound imaging of ischaemia flow: An in silico study. 缺血血流的超分辨率超声成像：模拟研究

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-12-06 DOI: 10.1016/j.jtbi.2024.112018

Lachlan Arthur, Vasiliki Voulgaridou, Georgios Papageorgiou, Weiping Lu, Steven R McDougall, Vassilis Sboros

{"title":"Super-resolution ultrasound imaging of ischaemia flow: An in silico study.","authors":"Lachlan Arthur, Vasiliki Voulgaridou, Georgios Papageorgiou, Weiping Lu, Steven R McDougall, Vassilis Sboros","doi":"10.1016/j.jtbi.2024.112018","DOIUrl":"10.1016/j.jtbi.2024.112018","url":null,"abstract":"Super-resolution ultrasound (SRU) is a new ultrasound imaging mode that promises to facilitate the detection of microvascular disease by providing new vascular bio-markers that are directly linked to microvascular pathophysiology, thereby augmenting current knowledge and potentially enabling new treatment. Such a capability can be developed through thorough understanding as articulated by means of mathematical models. In this study, a 2D numerical flow model is adopted for generating flow adaptation in response to ischaemia, in order to determine the ability of SRU to register the resulting flow perturbations. The flow model results demonstrate that variations in flow behaviour in response to locally induced ischaemia can be significant throughout the entire vascular bed. Measured velocities have variations that are dependent on the location of ischaemia, with median values ranging between 2-7 mms-1. Moreover, the distinction between healthy and ischaemic networks are recorded accurately in the SRU results showing excellent agreement between SRU maps and the model. Up to 7-fold spatial resolution improvement to conventional contrast ultrasound was achieved in microbubble localisation while the detection precision and recall was consistently above 98%. The microbubble tracking precision was of a similar accuracy, whereas the recall was reduced (77%) under varying ischaemic impacted flow. Further, regions with velocities up to 30 mms-1 are in excellent agreement with SRU maps, while at regions that include a proportion of higher velocities, the median velocity values are within 1.28%-3.32% of the ground-truth. In conclusion, SRU is a highly promising methodology for the direct measurement of microvascular flow dynamics and may provide a valuable tool for the understanding and subsequent modelling of behaviour in the vascular bed.","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112018"},"PeriodicalIF":1.9,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796455","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}

引用次数: 0