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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 Q2 BIOLOGY Pub Date : 2025-02-07 DOI: 10.1016/j.jtbi.2024.111992
Tianjian Qin , Luis Valente , Rampal S. Etienne
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.
在现存物种的系统发育过程中,经常可以观察到世系积累速度减慢的现象。一种解释是多样性存在生态限制,因此多样化也存在生态限制。以往的研究探讨了物种丰富度(SR)是否以及如何影响物种多样化率,但很少考虑物种之间的进化亲缘关系(ER),尽管ER会影响物种之间的相互作用程度,而物种之间的相互作用程度很可能设定了这些限制。为了了解ER对物种多样化的影响以及SR和ER之间的相互作用,我们提出了一个简单的出生-死亡模型,在这个模型中,物种的演化率取决于ER。我们使用了不同的ER指标,这些指标在不同的尺度上起作用,从特定的分支/系到整个类群的尺度。我们发现,ER效应在不同尺度上的作用会产生不同的树统计模式。当ER作用于整棵树时,我们观察到的树更小、更平衡,与特定世系的ER效应相比,树尖上的物种变异率分布更均匀。重要的是,我们发现物种演化的负SR依赖性掩盖了ER对某些树统计数据的影响。我们的模型允许不同的进化轨迹产生不平衡的树,这是在经验系统发生中经常观察到的现象,但在早期的模型中却很难复制。
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引用次数: 0
A mathematical model of microglia glucose metabolism and lactylation with positive feedback.
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2025-01-30 DOI: 10.1016/j.jtbi.2025.112049
Kamila Larripa, Anca Rǎdulescu

In this paper, we present and analyze a model for metabolism and lactylation in a single microglia. The model includes positive feedback from lactylation in the glycolotyic pathway, and links metabolism and inflammation. Specific pathways include the transition of glucose to pyruvate to lactate in a microglia, as well as the gradient transport of glucose and lactate into and out of the cell. Additionally, the upregulation of certain pathways by either epigenetic modification or the inflammatory response are included. Bifurcation and sensitivity analyses demonstrate the importance of key parameters and pathways in the model, specifically the role of lactylation. Our model is validated by qualitatively reproducing recent in vitro experiments in which exogenous glucose and lactate are modified.

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引用次数: 0
Tradeoffs in the energetic value of neuromodulation in a closed-loop neuromechanical system.
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2025-01-29 DOI: 10.1016/j.jtbi.2025.112050
Zhuojun Yu, Yangyang Wang, Peter J Thomas, Hillel J Chiel

Rhythmic motor behaviors controlled by neuromechanical systems, consisting of central neural circuitry, biomechanics, and sensory feedback, show efficiency in energy expenditure. The biomechanical elements (e.g., muscles) are modulated by peripheral neuromodulation which may improve their strength and speed properties. However, there are relatively few studies on neuromodulatory control of muscle function and metabolic mechanical efficiency in neuromechanical systems. To investigate the role of neuromodulation on the system's mechanical efficiency, we consider a neuromuscular model of motor patterns for feeding in the marine mollusk Aplysia californica. By incorporating muscle energetics and neuromodulatory effects into the model, we demonstrate tradeoffs in the energy efficiency of Aplysia's rhythmic swallowing behavior as a function of the level of neuromodulation. A robust efficiency optimum arises from an intermediate level of neuromodulation, and excessive neuromodulation may be inefficient and disadvantageous to an animal's metabolism. This optimum emerges from physiological constraints imposed upon serotonergic modulation trajectories on the energy efficiency landscape. Our results may lead to experimentally testable hypotheses of the role of neuromodulation in rhythmic motor control.

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引用次数: 0
White lies for coral reefs: Dynamics of two-patch coral reefs model with asymmetric dispersal
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2025-01-27 DOI: 10.1016/j.jtbi.2025.112046
Xin Zhao , Shiyang Yu , Meng Fan
Coral reef ecosystem is a crucial component of marine ecosystems and is undergoing severe degradation due to the combined dural impact of environmental changes and human activities. Soundscape technology is an innovative coral reef restoration approach that attracts fish to degraded reefs. Inspired by such technique, a five-dimensional mathematical dynamical model incorporating the asymmetric dispersal of parrotfish is formulated to characterize the dynamic interaction among macroalgae, coral, algal turf, and parrotfish in coral reef ecosystem. Theoretical analyses are conducted and the impact of dispersal on the stability of coral reef ecosystems is systematically studied. The global sensitivity analysis is presented by using PRCC method and the impact of dispersal coefficients on the dynamic behavior of the model is explored through numerical simulations, which provide deeper insights into the influence of key parameters on the stability of the model. The main findings indicate that, adopting soundscape technology facilitates the recovery of coral reefs, make it easier to maintain a coral-dominated state, and reduce the possibility of phase shifts, thereby enhance the stability, biodiversity, and recovery of coral reef ecosystem.
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引用次数: 0
Discovering the climate dependent disease transmission mechanism through learning-explaining framework
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2025-01-25 DOI: 10.1016/j.jtbi.2025.112047
Jintao Wang, Yanni Xiao, Pengfei Song
There are evidence showing that meteorological factors, such as temperature and humidity, have critical effects on transmission of some infectious diseases, while quantifying the influence is challenging. In this study we develop a learning-explaining framework to discover the particular dependence of transmission mechanisms on meteorological factors based on multiple source data. The incidence rate based on the epidemic data and epidemic model is theoretically identified, and meanwhile the practical discovery of particular formula is feasible through deep neural networks (DNN), symbolic regression (SR) and sparse identification of nonlinear dynamics (SINDy). In particular, we initially learn the incidence rate in an SIRS model based on epidemic data, then use mechanism discovery methods to explore the possible explicit forms of the incidence rate, and consequently explore the possible relationship between transmission rate and meteorological factors. We finally use information criteria and a definition of evaluation score to make model selection, and hence suggest the optimal explicit formula. We illustrate the idea by derive the incidence rate and transmission rate of respiratory infectious diseases based on the case data on influenza-like illness (ILI) in Xi’an, Shaanxi Province of China and meteorological data from 1st January 2010 to 10th November 2016. The finding reveals that the influence of meteorological factors on transmission exhibits very strong nonlinearity, and modeling the effect should be of great care.
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引用次数: 0
Revisiting the exclusion principle in epidemiology at the limit of a large competitive advantage
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2025-01-21 DOI: 10.1016/j.jtbi.2025.112045
Nir Gavish
The competitive exclusion principle in epidemiology implies that when competing strains of a pathogen provide complete protection for each other, the strain with the largest reproduction number outcompetes the other strains and drives them to extinction. The introduction of various trade-off mechanisms may facilitate the coexistence of competing strains, especially when their respective basic reproduction numbers are close so that the competition between the strains is weak. Yet, one may expect that a substantial competitive advantage of one of the strains will eventually outbalance trade-off mechanisms driving less competitive strains to extinction. The literature, however, lacks a rigorous validation of this statement.
In this work, we challenge the validity of the exclusion principle at a limit in which one strain has a vast competitive advantage over the other strains. We show that when one strain is significantly more transmissible than the others, and under broad conditions, an epidemic system with two strains has a stable endemic equilibrium in which both strains coexist with comparable prevalence. Thus, the competitive exclusion principle does not unconditionally hold beyond the established case of complete immunity.
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引用次数: 0
Costly punishment sustains indirect reciprocity under low defection detectability 在低背叛可探测性条件下,代价高昂的惩罚维持间接互惠。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2025-01-11 DOI: 10.1016/j.jtbi.2025.112043
Yohsuke Murase
Cooperation is fundamental to human societies, and indirect reciprocity, where individuals cooperate to build a positive reputation for future benefits, plays a key role in promoting it. Previous theoretical and experimental studies have explored both the effectiveness and limitations of costly punishment in sustaining cooperation. While empirical observations show that costly punishment by third parties is common, some theoretical models suggest it may not be effective in the context of indirect reciprocity, raising doubts about its potential to enhance cooperation. In this study, we theoretically investigate the conditions under which costly punishment is effective. Building on a previous model, we introduce a new type of error in perceiving actions, where defection may be mistakenly perceived as cooperation. This extension models a realistic scenario where defectors have a strong incentive to disguise their defection as cooperation. Our analysis reveals that when defection is difficult to detect, norms involving costly punishment can emerge as the most efficient evolutionarily stable strategies. These findings demonstrate that costly punishment can play a crucial role in promoting cooperation within indirect reciprocity.
合作是人类社会的基础,而间接互惠,即个人合作为未来的利益建立积极的声誉,在促进合作方面发挥着关键作用。以往的理论和实验研究都探讨了代价高昂的惩罚在维持合作中的有效性和局限性。虽然经验观察表明,第三方的代价高昂的惩罚很常见,但一些理论模型表明,在间接互惠的背景下,这种惩罚可能并不有效,这使人们对其加强合作的潜力产生了怀疑。在本研究中,我们从理论上考察了代价惩罚有效的条件。在之前的模型的基础上,我们引入了一种感知行为的新类型的错误,其中背叛可能被错误地视为合作。这个扩展模型模拟了一个现实的场景,即叛逃者有强烈的动机将他们的叛逃伪装成合作。我们的分析表明,当背叛难以察觉时,包含代价高昂的惩罚的规范可能成为最有效的进化稳定策略。这些发现表明,代价高昂的惩罚可以在间接互惠中促进合作发挥关键作用。
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引用次数: 0
Compartment model of strategy-dependent time delays in replicator dynamics 复制因子动力学中策略依赖时滞的隔室模型。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2025-01-10 DOI: 10.1016/j.jtbi.2025.112044
Małgorzata Fic , Frank Bastian , Jacek Miȩkisz , Chaitanya S. Gokhale
Real-world processes often exhibit temporal separation between actions and reactions - a characteristic frequently ignored in many modelling frameworks. Adding temporal aspects, like time delays, introduces a higher complexity of problems and leads to models that are challenging to analyse and computationally expensive to solve. In this work, we propose an intermediate solution to resolve the issue in the framework of evolutionary game theory. Our compartment-based model includes time delays while remaining relatively simple and straightforward to analyse. We show that this model yields qualitatively comparable results with models incorporating explicit delays. Particularly, we focus on the case of delays between parents’ interaction and an offspring joining the population, with the magnitude of the delay depending on the parents’ strategy. We analyse Stag-Hunt, Snowdrift, and the Prisoner’s Dilemma game and show that strategy-dependent delays are detrimental to affected strategies. Additionally, we present how including delays may change the effective games played in the population, subsequently emphasising the importance of considering the studied systems’ temporal aspects to model them accurately.
现实世界的过程经常表现出动作和反应之间的时间分离——这是许多建模框架经常忽略的一个特征。添加时间方面,如时间延迟,会引入更高的问题复杂性,并导致分析具有挑战性的模型和计算成本高昂的模型。在这项工作中,我们提出了一个在进化博弈论框架下解决这个问题的中间解决方案。我们基于隔间的模型包括了时间延迟,但分析起来相对简单直接。我们表明,该模型与包含显式延迟的模型在质量上可比较。特别地,我们关注父母的互动和后代加入群体之间的延迟的情况,延迟的大小取决于父母的策略。我们分析了猎鹿游戏、雪堆游戏和囚徒困境游戏,并表明依赖于策略的延迟对受影响的策略是有害的。此外,我们介绍了包括延迟如何改变人群中有效的博弈,随后强调了考虑所研究系统的时间方面以准确建模的重要性。
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引用次数: 0
Design, optimization, and inference of biphasic decay of infectious virus particles 感染性病毒颗粒双相衰变的设计、优化和推断。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2025-01-10 DOI: 10.1016/j.jtbi.2025.112042
Jérémy Seurat , Krista R. Gerbino , Justin R. Meyer , Joshua M. Borin , Joshua S. Weitz
Virus population dynamics are driven by counter-balancing forces of production and loss. Whereas viral production arises from complex interactions with susceptible hosts, the loss of infectious virus particles is often approximated as a first-order kinetic process. As such, experimental protocols to measure infectious virus loss are not typically designed to identify non-exponential decay processes. Here, we propose methods to evaluate if an experimental design is adequate to identify multiphasic virus particle decay and to optimize the sampling times of decay experiments, accounting for uncertainties in viral kinetics. First, we evaluate synthetic scenarios of biphasic decays, with varying decay rates and initial proportions of subpopulations. We show that robust inference of multiphasic decay is more likely when the faster decaying subpopulation predominates insofar as early samples are taken to resolve the faster decay rate. Moreover, design optimization involving non-equal spacing between observations increases the precision of estimation while reducing the number of samples. We then apply these methods to infer multiple decay rates associated with the decay of bacteriophage (‘phage’) ΦD9, an evolved isolate derived from phage Φ21. A pilot experiment confirmed that ΦD9 decay is multiphasic, but was unable to resolve the rate or proportion of the fast decaying subpopulation(s). We then applied a Fisher information matrix-based design optimization method to propose non-equally spaced sampling times. Using this strategy, we were able to robustly estimate multiple decay rates and the size of the respective subpopulations. Notably, we conclude that the vast majority (94%) of the phage ΦD9 population decays at a rate 16-fold higher than the slow decaying population. Altogether, these results provide both a rationale and a practical approach to quantitatively estimate heterogeneity in viral decay.
病毒种群动态是由生产和损失的平衡力量驱动的。鉴于病毒的产生源于与易感宿主的复杂相互作用,传染性病毒颗粒的损失通常近似为一级动力学过程。因此,测量传染性病毒损失的实验方案通常不用于确定非指数衰减过程。在这里,我们提出了一些方法来评估实验设计是否足以识别多相病毒颗粒衰变,并优化衰变实验的采样时间,考虑到病毒动力学的不确定性。首先,我们评估了具有不同衰变速率和亚种群初始比例的双相衰变的综合情景。我们表明,只要采取早期样本来解决更快的衰变速率,当更快的衰变亚群占主导地位时,多相衰变的稳健推断更有可能。此外,设计优化涉及非等间距的观测值提高了估计的精度,同时减少了样本数量。然后,我们应用这些方法来推断与噬菌体(“噬菌体”)ΦD9(从噬菌体Φ21衍生的进化分离物)的衰变相关的多种衰变速率。初步实验证实ΦD9衰变是多相的,但无法确定快速衰变亚群的速率或比例。然后,我们应用基于Fisher信息矩阵的设计优化方法来提出非等间隔采样时间。使用这种策略,我们能够可靠地估计多个衰减率和各自亚种群的大小。值得注意的是,我们得出结论,绝大多数(94%)噬菌体ΦD9种群的衰减速度比缓慢衰减的种群高16倍。总之,这些结果提供了定量估计病毒衰变异质性的基本原理和实用方法。
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引用次数: 0
Quantifying the impact of metronomic chemotherapy chemo-switch regimen and the sequencing of chemotherapy and radiotherapy on pancreatic ductal adenocarcinoma treatment 量化节奏化疗化疗切换方案和化疗放疗顺序对胰管腺癌治疗的影响。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-12-24 DOI: 10.1016/j.jtbi.2024.112033
Xu Wang , Xi Chen , Jinhui Zhu , Sheng Li
Metronomic chemotherapy (MCT) is a novel chemotherapy approach characterized by a high-frequency, low-dose administration strategy. The “chemo-switch” regimen involves the sequential use of two dosing strategies: maximum tolerated dose (MTD) chemotherapy and MCT. For patients with pancreatic ductal adenocarcinoma (PDAC), selecting novel chemotherapy regimens appropriately according to their physical conditions may help address the challenges associated with MTD chemotherapy, such as excessive toxicity, prolonged tumor recovery, and suboptimal efficacy. There is currently limited research on mathematical models related to novel chemotherapy regimens and PDAC, as well as on the impact of different drug administration strategies and the sequence of chemoradiotherapy in combined treatment. To address these gaps, we propose a two-dimensional multiscale mathematical model. Initially, we model the individual effects of MTD chemotherapy, antiangiogenic therapy, and radiotherapy. Subsequently, we analyze the anti-tumor effects of various chemotherapy regimens and their underlying mechanisms. Furthermore, we assess how different drug administration regimens and the sequencing of chemotherapy and radiotherapy affect treatment outcomes. Simulation results indicate that, compared to standard MTD chemotherapy, using the MCT regimen or introducing MCT during MTD chemotherapy (chemo-switch regimen) demonstrates better anti-tumor efficacy and sustained tumor perfusion, enhancing drug accumulation within tumor regions. Combined therapy exhibits superior efficacy compared to monotherapy. Placing radiotherapy after anti-angiogenic therapy and chemotherapy suggests more effective in suppressing tumor growth and sustaining tumor perfusion. It is noteworthy that while this study focuses on PDAC treatment, its findings can be extrapolated to other fibrotic tumors, thereby facilitating similar analyses across different tumor types.
节拍化疗(MCT)是一种以高频率、低剂量给药为特点的新型化疗方法。“化疗转换”方案包括顺序使用两种给药策略:最大耐受剂量(MTD)化疗和MCT。对于胰腺导管腺癌(pancreatic ductal adencarcinoma, PDAC)患者,根据自身的身体状况选择合适的化疗方案,可能有助于解决MTD化疗带来的毒性过大、肿瘤恢复时间过长、疗效不佳等挑战。目前,关于新型化疗方案和PDAC的数学模型,以及不同给药策略和放化疗顺序对联合治疗的影响的研究有限。为了解决这些差距,我们提出了一个二维多尺度数学模型。首先,我们模拟了MTD化疗、抗血管生成治疗和放疗的个体效应。随后,我们分析了各种化疗方案的抗肿瘤作用及其潜在机制。此外,我们评估了不同的药物给药方案和化疗和放疗的顺序如何影响治疗结果。模拟结果表明,与标准MTD化疗相比,使用MCT方案或在MTD化疗期间引入MCT(化疗切换方案)具有更好的抗肿瘤效果和持续的肿瘤灌注,增强了肿瘤区域内的药物积累。联合治疗的疗效优于单一治疗。在抗血管生成治疗和化疗后进行放疗可以更有效地抑制肿瘤生长和维持肿瘤灌注。值得注意的是,虽然本研究的重点是PDAC治疗,但其发现可以外推到其他纤维化肿瘤,从而促进了不同肿瘤类型的类似分析。
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Journal of Theoretical Biology
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