Populations and Evolution

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Cross submissions (showing 4 of 4 entries )

[1] arXiv:2509.15338 (cross-list from q-bio.PE) [cn-pdf, pdf, html, other]

Title: Epidemic amplification by correlated superspreading Show Chinese title

Title: 由相关超级传播引起的疫情放大

Noah Silva de Leonardi, Benjamin D. Dalziel

Subjects: Populations and Evolution (q-bio.PE)

Infectious pathogens often propagate by superspreading, which focusses onward transmission on disproportionately few infected individuals. At the same time, infector-infectee pairs tend to have more similar transmission potentials than expected by chance, as risk factors assort among individuals who frequently interact. A key problem for infectious disease epidemiology, and in the dynamics of complex systems, is to understand how structured variation in individual transmission will scale to impact epidemic dynamics. Here we introduce a framework that reveals how population structure shapes epidemic thresholds, through autocorrelation of individual reproductive numbers along chains of transmission. We show that chains of superspreading can sustain epidemics even when the average transmission rate in the host population is below one, and derive a mathematical threshold beyond which correlated superspreading allows epidemics in otherwise subcritical systems. Empirical analysis of 47 transmission trees for 13 human pathogens indicate self-organizing bursts of superspreading are common and that many trees are near the critical boundary. Vaccination campaigns that proceed up assortative hierarchies of transmission are predicted to sustain the force of infection until herd immunity is reached, providing a mechanistic basis for threshold dynamics observed in real-world settings. Conversely, modulating correlations in transmission, rather than mean or variance, could enable cities and other complex systems to develop immune-like capacities that suppress contagion while preserving core functions. Show Chinese abstract

传染病病原体通常通过超级传播传播，这将后续传播集中在少数感染个体上。 同时，传染者与被传染者对往往比随机预期的具有更相似的传播潜力，因为风险因素在经常互动的个体中聚集。 传染病流行病学以及复杂系统动态学的一个关键问题是理解个体传播的结构化变异如何扩大以影响流行病动态。 在这里，我们引入了一个框架，揭示了种群结构如何通过传播链中个体繁殖数的自相关性来塑造流行病阈值。 我们表明，超级传播链即使在宿主种群的平均传播率低于1时也能维持流行病，并推导出一个数学阈值，超过该阈值时，相关的超级传播可以在原本亚临界系统中引发流行病。 对13种人类病原体的47个传播树进行实证分析表明，超级传播的自组织爆发是常见的，许多树接近临界边界。 预测按照传播的 assortative 层级进行的疫苗接种活动将持续感染力度，直到群体免疫达成，这为现实世界环境中观察到的阈值动态提供了机制基础。 相反，调节传播中的相关性，而不是均值或方差，可能使城市和其他复杂系统发展出类似免疫的能力，在保持核心功能的同时抑制传播。

[2] arXiv:2509.15787 (cross-list from q-bio.PE) [cn-pdf, pdf, html, other]

Title: A Visual Discrete Event-based Simulator for Protection of Plants against Herbivores Employed as Computational Optimization Game Show Chinese title

Title: 一种用于保护植物免受植食动物侵害的视觉离散事件模拟器，用作计算优化游戏

Lucas Dietrich, Benjamin Förster, Peter Langendörfer, Thomas Hinze

Subjects: Populations and Evolution (q-bio.PE)

Plants come with sophisticated strategies to survive within a highly competing environment. In addition, they need to resist frequent attacks from a variety of herbivores acting alone, in small groups, or in swarms. Since the amount of energy a plant might invest in defense and reproduction is limited, a complex optimization problem emerges. In a shared habitat, plants fight herbivores by shape and camouflage, by the release of specific toxins, or by attracting predators of herbivores. Furthermore, plants alert their surrounding field by signaling substances in the event of an assault. Transported by air or through a network of roots, signaling substances reach neighbors to trigger their defense. The offsprings of a plant commonly grow within a certain distance to benefit from symbiotic protection. We introduce a grid-based visual simulation software for detailed configuration and subsequent processing of the behavior of the resulting system in time and space. In terms of solution to a computational optimization problem inspired by nature, settings with low energy need and long life able to cope with different patterns of attack can be figured out and analyzed. Applications include novel techniques for efficient construction and secure operation of sensor networks. Show Chinese abstract

植物具有复杂的策略以在高度竞争的环境中生存。 此外，它们还需要抵御来自各种植食动物的频繁攻击，这些动物可能单独行动，或以小群体或大群形式活动。 由于植物可能在防御和繁殖上投入的能量是有限的，因此出现了一个复杂的优化问题。 在共享的栖息地中，植物通过形状和伪装、释放特定毒素，或吸引植食动物的捕食者来对抗植食动物。 此外，当遭受攻击时，植物会通过信号物质向周围环境发出警报。 这些信号物质通过空气或根系网络传播，到达邻近植物以触发它们的防御机制。 植物的后代通常生长在一定距离内，以受益于共生保护。 我们引入了一种基于网格的可视化模拟软件，用于详细配置并随后在时间和空间上处理系统的行为。 在解决受自然启发的计算优化问题方面，可以找出并分析那些能量需求低且寿命长、能够应对不同攻击模式的设置。 应用包括用于高效构建和安全运行传感器网络的新技术。

[3] arXiv:2509.15911 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: The evolution of asymmetrical regulation of physiology is central to aging Show Chinese title

Title: 生理的不对称调节的演变是衰老的核心

Mirre J P Simons, Marc Tatar

Comments: 22 pages, 5 figures

Subjects: Populations and Evolution (q-bio.PE)

The evolutionary biology of aging is fundamental to understanding the mechanisms of aging and how to develop anti-aging treatments. Thus far most evolutionary theory concerns the genetics of aging with limited physiological integration. Here we present an intuitive evolutionary framework built on how physiology is regulated and how this regulation itself is then predicted to age. Life has evolved to secure reproduction and avoid system failure in early life, and it is the physiological regulation that evolves in response to those early life selection pressures that leads to the emergence of aging. Importantly, asymmetrical regulation of physiology will evolve as the Darwinian fitness costs of loss of regulation will not be symmetrical. When asymmetrical regulatory systems break during aging, they cause physiological function to drift towards the physiological range where costs of dysregulation are lowest, rendering aging directional. Our model explains many puzzling aspects of the biology of aging. These include why aging appears (but is not) programmed, why aging is gradual yet heterogeneous, why cellular and hormonal signaling are closely related to aging, the compensation law of mortality, why trade-offs between reproduction and aging remain elusive, why longer-lived organisms show more signs of aging during their natural lifespans, and why longer-lived organisms can be less responsive to treatments of aging that work well in short-lived organisms. We provide predictions of our theory that are empirically testable. By incorporating physiological regulation into evolutionary models of aging, we provide a novel perspective to guide empirical research in this still growing field. Show Chinese abstract

衰老的进化生物学对于理解衰老的机制以及如何开发抗衰老治疗至关重要。迄今为止，大多数进化理论关注的是衰老的遗传学，而生理整合有限。在这里，我们提出一个直观的进化框架，该框架基于生理是如何被调节的，以及这种调节本身如何被预测为衰老。生命进化以确保早期生命的繁殖和避免系统故障，正是对这些早期生命选择压力做出反应的生理调节导致了衰老的出现。重要的是，生理的不对称调节将进化，因为失去调节的达尔文适应性成本不会是对称的。当不对称调节系统在衰老过程中崩溃时，它们会导致生理功能向失调成本最低的生理范围漂移，从而使衰老具有方向性。我们的模型解释了衰老生物学中的许多令人困惑的方面。这些包括为什么衰老似乎（但并非）是程序化的，为什么衰老是渐进的但又不均匀的，为什么细胞和激素信号传导与衰老密切相关，死亡补偿定律，为什么繁殖与衰老之间的权衡仍然难以捉摸，为什么寿命较长的生物在其自然寿命期间表现出更多的衰老迹象，以及为什么寿命较长的生物可能对在短寿生物中效果良好的衰老治疗不太敏感。我们提供了可进行实证检验的理论预测。通过将生理调节纳入衰老的进化模型，我们提供了一个新的视角，以指导这一仍在发展的领域中的实证研究。

[4] arXiv:2509.16133 (cross-list from q-bio.PE) [cn-pdf, pdf, html, other]

Title: A Unified and Predictive Measure of Functional Diversity Show Chinese title

Title: 一种统一且可预测的功能多样性度量

Adji Bousso Dieng, Amey Pasarkar

Comments: A single index to accurately measure functional diversity at different biological levels

Subjects: Populations and Evolution (q-bio.PE)

Despite the critical role of functional diversity (FD) in understanding ecological systems and processes, its robust quantification remains a significant challenge. A long-held view in the field is that it is not possible to capture its three facets -- functional richness, functional divergence, and functional evenness -- in a single index. This perspective has prompted recent proposals for FD measurement to use three separate indices, one for each aspect. Here, we challenge this paradigm by demonstrating that the probability-weighted Vendi Score (pVS), first introduced by Friedman and Dieng (2023), can serve as a powerful functional diversity index that can capture its three facets. We adapt pVS to functional ecology by defining it as the exponential of the R\'enyi entropy of the eigenvalues of the abundance-weighted trait similarity matrix. This formulation allows pVS to be applicable at any biological level. It can be defined at the species level, at which most existing FD metrics are defined, and at the individual level to naturally incorporate intraspecific trait variation (ITV) when detailed data are available. We theoretically and empirically demonstrate the robustness of pVS. We first mathematically prove it satisfies several essential desiderata for FD metrics, including invariance to functional redundancy, set monotonicity, distance monotonicity, and concavity. We then show that pVS consistently exhibits the expected ground-truth behavior on simulated ecosystem scenarios under which many FD metrics fail. By integrating abundances and trait similarities within a single, theoretically sound framework, pVS provides a generally applicable index for ecology. Show Chinese abstract

尽管功能多样性（FD）在理解生态系统和过程中的作用至关重要，但其稳健的量化仍然是一个重大挑战。 该领域长期以来的观点认为，无法在一个指数中捕捉其三个方面——功能丰富度、功能分化和功能均匀度。 这种观点促使最近提出的FD测量方法使用三个独立的指数，每个方面一个。 在此，我们通过证明概率加权Vendi评分（pVS），由Friedman和Dieng（2023）首次引入，可以作为一个强大的功能多样性指数，能够捕捉其三个方面，从而挑战这一范式。 我们通过将pVS定义为丰度加权性状相似矩阵特征值的Rényi熵的指数，将其适应到功能生态学中。 这种公式使得pVS可以在任何生物水平上应用。 它可以在物种水平上定义，大多数现有的FD指标都是在该水平上定义的，也可以在个体水平上定义，当有详细数据时自然地纳入种内性状变异（ITV）。 我们从理论上和经验上证明了pVS的稳健性。 我们首先数学上证明它满足FD指标的几个基本要求，包括对功能冗余的不变性、集合单调性、距离单调性和凹性。 然后我们展示，在许多FD指标失败的模拟生态系统场景下，pVS始终表现出预期的真实行为。 通过在一个理论严谨的框架内整合丰度和性状相似性，pVS为生态学提供了一个普遍适用的指数。

Replacement submissions (showing 1 of 1 entries )

[5] arXiv:2509.08578 (replaced) [cn-pdf, pdf, html, other]

Title: Multi-modal Adaptive Estimation for Temporal Respiratory Disease Outbreak Show Chinese title

Title: 多模态自适应估计用于时间呼吸系统疾病爆发

Hong Liu, Kerui Cen, Yanxing Chen, Zige Liu, Dong Chen, Zifeng Yang, Chitin Hon

Subjects: Machine Learning (cs.LG) ; Populations and Evolution (q-bio.PE) ; Quantitative Methods (q-bio.QM)

Timely and robust influenza incidence forecasting is critical for public health decision-making. This paper presents MAESTRO (Multi-modal Adaptive Estimation for Temporal Respiratory Disease Outbreak), a novel, unified framework that synergistically integrates advanced spectro-temporal modeling with multi-modal data fusion, including surveillance, web search trends, and meteorological data. By adaptively weighting heterogeneous data sources and decomposing complex time series patterns, the model achieves robust and accurate forecasts. Evaluated on over 11 years of Hong Kong influenza data (excluding the COVID-19 period), MAESTRO demonstrates state-of-the-art performance, achieving a superior model fit with an R-square of 0.956. Extensive ablations confirm the significant contributions of its multi-modal and spectro-temporal components. The modular and reproducible pipeline is made publicly available to facilitate deployment and extension to other regions and pathogens, presenting a powerful tool for epidemiological forecasting. Show Chinese abstract

及时且稳健的流感发病率预测对于公共卫生决策至关重要。 本文介绍了MAESTRO（多模态自适应时间呼吸系统疾病爆发估计），这是一种新颖的统一框架，通过将先进的时频建模与多模态数据融合相结合，包括监测数据、网络搜索趋势和气象数据。 通过自适应加权异构数据源并分解复杂的时间序列模式，该模型实现了稳健且准确的预测。 在超过11年的香港流感数据（不包括新冠疫情时期）上进行评估，MAESTRO表现出最先进的性能，达到了R平方值为0.956的优越模型拟合。 广泛的消融实验确认了其多模态和时频组件的重要贡献。 模块化和可重复的流程已公开提供，以促进部署和扩展到其他地区和病原体，为流行病学预测提供了一个强大的工具。