Theoretical Population Biology最新文献_第4页

Connectivity, conservation and catch: Understanding the effects of dispersal between harvested and protected patches 连通性、保护和捕捞：了解收获区和保护区之间扩散的影响。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-03-24 DOI: 10.1016/j.tpb.2025.03.005

Femke N. Reurik , Juan Segura , Frank M. Hilker

Overharvesting is a pressing global problem, and spatial management, such as protecting designated areas, is one proposed solution. This study examines how connectivity (in terms of dispersal rate) between protected and harvested areas affects the asymptotic total population size and the asymptotic yield, which are key questions for conservation management and the design of protected areas. We utilise a two-patch model with heterogeneous habitat qualities, symmetric dispersal and density-dependent growth functions in both discrete and continuous time. One patch is subject to proportional harvesting, while the other one is protected.

Our results show that increased dispersal does not always increase the asymptotic total population size or the asymptotic yield. Depending on the circumstances, dispersal enables the protected patch to rescue the harvested patch from overexploitation, potentially increasing both total population size and yield. However, high levels of dispersal can also lead to a lower total population size or even cause extinction of both patches if harvesting pressure is strong. The population in the protected patch needs to have high reproductive potential and the protected patch needs to be the effectively larger patch in order to benefit monotonically from increased dispersal. These findings provide a fundamental understanding of how dispersal influences dynamics in fragmented landscapes under harvesting pressure.

过度采伐是一个紧迫的全球问题，而空间管理，如保护指定区域，是一个被提议的解决方案。本研究探讨了保护区和采伐区之间的连通性（以分散率为依据）如何影响渐近种群总数和渐近产量，这是保护管理和保护区设计的关键问题。我们使用了一个双斑块模型，该模型在离散和连续时间内具有异质性栖息地质量，对称扩散和密度依赖的生长函数。一块土地按比例收割，而另一块则受到保护。我们的结果表明，增加的分散并不总是增加渐近总种群大小或渐近产量。根据环境的不同，分散可以使受保护的斑块免于过度开发，从而潜在地增加种群总数和产量。然而，如果收获压力很大，高水平的分散也会导致种群总数减少，甚至导致两个斑块的灭绝。保护斑块中的种群需要具有较高的繁殖潜力，保护斑块需要是有效的较大的斑块，才能单调地从增加的分散中获益。这些发现提供了在收获压力下分散如何影响破碎景观动态的基本理解。

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引用次数: 0

Spatial evolutionary public goods game theory applied to optimal resource allocation and defense strategies in herbaceous plants 空间演化公共物品博弈论在草本植物资源配置与防御策略中的应用。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-03-22 DOI: 10.1016/j.tpb.2025.02.003

Molly Creagar , Richard Rebarber , Brigitte Tenhumberg

Empirical evidence suggests that the attractiveness of a plant to herbivores can be affected by the investment in defense by neighboring plants, as well as investment in defense by the focal plant. Thus, the payoff for allocating to defense may not only be influenced by the frequency and intensity of herbivory but also by defense strategies employed by other plants in the environment. We use a combination of spatial evolutionary game theory and stochastic dynamic programming to predict the proportion of plants in the population investing in defense (cooperators) and the proportion of plants that do not (defectors). Our model accounts for metabolic costs of maintenance of stored resources when predicting optimal resource allocation to growth, reproduction, and storage; this cost is not commonly accounted for in previous models. For both annual and perennial plants, our model predicts an evolutionarily stable proportion of cooperators and defectors (mixed stable strategy), but the proportion of cooperators is higher in a population of perennial plants than in a population of annual plants. We also show that including a metabolic cost of maintaining stored resources does not change the proportion of cooperators but does decrease plant fitness and allocation to overwinter storage.

经验证据表明，植物对食草动物的吸引力会受到邻近植物的防御投资以及重点植物的防御投资的影响。因此，分配给防御的报酬可能不仅受到食草动物的频率和强度的影响，还受到环境中其他植物所采用的防御策略的影响。我们将空间进化博弈理论与随机动态程序设计相结合，预测种群中投资防御的植物（合作者）的比例和不投资防御的植物（叛逃者）的比例。在预测生长、繁殖和储存的最佳资源分配时，我们的模型考虑了维持储存资源的新陈代谢成本。对于一年生和多年生植物，我们的模型都预测了合作者和叛逃者在进化过程中的稳定比例（混合稳定策略），但合作者的比例在多年生植物种群中高于一年生植物种群。我们还证明，加入维持储存资源的代谢成本不会改变合作者的比例，但会降低植物的适应性和越冬储存的分配。

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引用次数: 0

Exact calculation of the expected SFS in structured populations 结构种群中预期SFS的精确计算。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-03-21 DOI: 10.1016/j.tpb.2025.03.003

Armando Arredondo , Josué Corujo , Camille Noûs , Simon Boitard , Lounès Chikhi , Olivier Mazet

The Site Frequency Spectrum (SFS), summary statistic of the distribution of derived allele frequencies in a sample of DNA sequences, provides information about genetic variation and can be used to make population inferences. The exact calculation of the expected SFS in a panmictic population under the infinite-site model of mutation has been known in the Markovian coalescent theory for decades, but its generalization to the structured coalescent is hampered by the almost exponential growth of the states space. We show here how to obtain this expected SFS as the solution of a linear system. More precisely, we propose a complete algorithmic procedure, from how to build a suitable state space and sort it, to how to take advantage of the sparsity of the rate matrix and to solve numerically the linear system using an iterative method. We then build a specialization for the simplest case of the symmetrical

n

-island model to arrive at a ready-to-use software called SISiFS from which a demographic parameters inference framework could easily be developed.

位点频率谱（Site Frequency Spectrum， SFS）是对DNA序列样本中衍生等位基因频率分布的汇总统计，它提供了遗传变异的信息，可用于群体推断。在马尔可夫聚结理论中，对于无限位点突变模型下的泛生种群期望SFS的精确计算已经有几十年的历史了，但由于状态空间几乎呈指数增长，阻碍了它向结构聚结的推广。我们在这里展示如何获得这个期望的SFS作为线性系统的解。更准确地说，我们提出了一个完整的算法过程，从如何建立一个合适的状态空间并对其进行排序，到如何利用率矩阵的稀疏性，并使用迭代方法对线性系统进行数值求解。然后，我们为对称n岛模型的最简单情况建立专业化，以获得一个称为SISiFS的即用型软件，从中可以轻松开发人口统计参数推断框架。

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引用次数: 0

Importance of environmental productivity and diet quality in intraguild predation 环境生产力和饲料质量在野生捕食中的重要性。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-03-12 DOI: 10.1016/j.tpb.2025.03.004

Toshiyuki Namba , Yasuhiro Takeuchi , Malay Banerjee

In the intricate network of ecological interactions, intraguild predation emerges as a fundamental community module incorporating omnivory. Classical equilibrium theory predicts the exclusion of the intraguild predator and prey at low and high environmental productivity, respectively, with the coexistence of both species occurring only at intermediate productivity levels. However, empirical studies challenge this theoretical prediction, particularly concerning the extinction of intraguild prey in highly productive environments. To address this enigmatic issue, Diehl (2003), Abrams and Fung (2010a) explore the impact of food quality and propose that low nutritional quality of the basal resource stabilizes omnivorous systems. Yet, the influence of intermediate consumer quality remains inadequately explored. This study employs analytical and numerical bifurcation studies to investigate the effects of the quality of two diet types. Various bifurcations, including supercritical and subcritical Hopf bifurcations, saddle-node bifurcations of periodic solutions, and transcritical bifurcations of periodic solutions are observed. These bifurcations are directly linked to the destinies of intraguild prey and predators. The results reveal that, in highly productive environments, it may not be the intermediate consumer but the omnivore that faces extinction. This discovery holds significant implications for the conservation and management of omnivorous systems.

在错综复杂的生态相互作用网络中，野生动物捕食作为一个基本的融合杂食的群落模块出现。经典平衡理论预测，在低环境生产力和高环境生产力条件下，捕食者和被捕食者将分别被排除在外，而两种物种仅在中等环境生产力水平下共存。然而，实证研究对这一理论预测提出了挑战，特别是关于高产环境中野生猎物的灭绝。为了解决这个谜一样的问题，Diehl（2003）和Abrams and Fung （2010a）探讨了食物质量的影响，并提出基础资源的低营养质量可以稳定杂食性系统。然而，中间消费者素质的影响仍未得到充分探讨。本研究采用分析分岔法和数值分岔法研究了两种日粮对肉鸡品质的影响。观察到各种分岔，包括超临界和亚临界Hopf分岔、周期解的鞍节点分岔和周期解的跨临界分岔。这些分化直接关系到野生猎物和捕食者的命运。研究结果表明，在高产的环境中，面临灭绝的可能不是中间消费者，而是杂食动物。这一发现对杂食性系统的保护和管理具有重要意义。

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引用次数: 0

The Patterson-Price-Reich's rule of population structure analysis from genetic marker data 基于遗传标记数据的群体结构分析的Patterson-Price-Reich规则。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-03-08 DOI: 10.1016/j.tpb.2025.03.001

Jinliang Wang

Delineating population structure from the marker genotypes of a sample of individuals is now routinely conducted in the fields of molecular ecology, evolution and conservation biology. Various Bayesian and likelihood methods as well as more general statistical methods (e.g. PCA) have been proposed to detect population structure, to assign sampled individuals to discrete clusters (subpopulations), and to estimate the admixture proportions of each sampled individual. Regardless of the methods, the power of a structure analysis depends on the strength of population structure (measured by F_ST) relative to the amount of marker information (measured by NL, where N and L are the numbers of sampled individuals and loci respectively). Patterson, Price and Reich (2006) proposed that population structure is unidentifiable when data size D = NL is smaller than

1 / F_{S T}^{2}

and quickly becomes identifiable easily with an increasing D or F_ST when

D > 1 / F_{S T}^{2}

. In this study, I investigated this phase change PPR rule by analysing both simulated genomic data and empirical data by four likelihood admixture analysis methods. The results show that the PPR rule is largely valid, but the accuracy of a structure analysis is also affected by the number of subpopulations K. A more complicated population structure with a larger K requires a larger

N L F_{S T}^{2}

to resolve accurately. For a given

N L F_{S T}^{2}

above the PPR threshold value of 1, increasing L and decreasing N is advantageous over increasing N and decreasing L in improving admixture estimation accuracy.

从个体样本的标记基因型描绘种群结构现在在分子生态学、进化和保护生物学等领域经常进行。已经提出了各种贝叶斯和似然方法以及更一般的统计方法（例如PCA）来检测种群结构，将采样个体分配到离散集群（亚种群），并估计每个采样个体的混合比例。无论采用何种方法，结构分析的能力取决于群体结构的强度（通过FST测量）相对于标记信息的数量（通过NL测量，其中N和L分别是采样个体和位点的数量）。Patterson， Price和Reich（2006）提出，当数据量D = NL小于1/FST2时，群体结构是无法识别的，当D bbbb1 /FST2时，随着D或FST的增加，群体结构很快就容易识别了。在本研究中，我通过四种似然混合分析方法对模拟基因组数据和经验数据进行分析，研究了小反刍兽疫的相变规律。结果表明，PPR规则在很大程度上是有效的，但结构分析的准确性也受到K亚群数量的影响。K越大，越复杂的群体结构需要更大的NLFST2才能准确解析。当NLFST2大于PPR阈值1时，增加L和减少N比增加N和减少L更有利于提高外加剂估计精度。

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引用次数: 0

A mathematical framework for time-variant multi-state kinship modelling 时变多态亲属关系建模的数学框架。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-03-05 DOI: 10.1016/j.tpb.2025.02.002

Joe W.B. Butterick, Peter W.F. Smith, Jakub Bijak, Jason Hilton

Recent research on kinship modelling in demography has extended age-structured models (i) to include additional characteristics, or “stages” (multi-state kinship), and (ii) to time-variant situations. A wide variety of population structures can affect kinship networks. However, only one prior model has comprehensively considered such effects, and under specific assumptions relating to the nature of individuals’ stages. As such, the leading multi-state framework for kin is theoretically limited in scope, and moreover, has yet to be implemented under time-variant demographic rates. Generalising kinship models to encompass arbitrary population characteristics and extending them to time-dependent processes remain open challenges in demography.

This research proposes a methodology to extend multi-state kinship. We present a model which theoretically accounts for any stage, both in time-variant and time-invariant environments. Drawing from Markov processes, a concise mathematical alternative to existing theory is developed.

The benefits of our model are illustrated by an application where we define stages as spatial locations, exemplified by clusters of local authority districts (LADs) in England and Wales. Our results elucidate how spatial distribution – a demographic characteristic ubiquitous across (and between) societies – can affect an individual’s network of relatives.

最近对人口统计学中亲属关系模型的研究扩展了年龄结构模型(i)，以包括额外的特征或“阶段”（多状态亲属关系），以及（ii）到时变情况。各种各样的人口结构可以影响亲属网络。然而，只有一个先前的模型在与个体所处阶段的性质有关的特定假设下全面考虑了这种影响。因此，领先的多国家亲属框架在理论上是有限的，而且，在时变人口比率下尚未实施。推广亲属关系模型以涵盖任意人口特征并将其扩展到依赖时间的过程仍然是人口学中的开放挑战。本研究提出了一种扩展多国家亲属关系的方法。我们提出了一个模型，理论上可以解释任何阶段，无论是时变环境还是时变环境。从马尔可夫过程，一个简洁的数学替代现有的理论发展。我们的模型的好处通过一个应用程序来说明，我们将阶段定义为空间位置，以英格兰和威尔士的地方当局区（LADs）集群为例。我们的研究结果阐明了空间分布——一种跨社会（或跨社会）普遍存在的人口特征——如何影响个人的亲属网络。

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引用次数: 0

The central limit theorem for the number of mutations in the genealogy of a sample from a large population 一个大群体中样本家谱突变数的中心极限定理。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-02-11 DOI: 10.1016/j.tpb.2025.02.001

Yun-Xin Fu

The number

K

of mutations identifiable in a sample of

n

sequences from a large population is one of the most important summary statistics in population genetics and is ubiquitous in the analysis of DNA sequence data.

K

can be expressed as the sum of

n - 1

independent geometric random variables. Consequently, its probability generating function was established long ago, yielding its well-known expectation and variance. However, the statistical properties of

K

is much less understood than those of the number of distinct alleles in a sample. This paper demonstrates that the central limit theorem holds for

K

, implying that

K

follows approximately a normal distribution when a large sample is drawn from a population evolving according to the Wright-Fisher model with a constant effective size, or according to the constant-in-state model, which allows population sizes to vary independently but bounded uniformly across different states of the coalescent process. Additionally, the skewness and kurtosis of

K

are derived, confirming that

K

has asymptotically the same skewness and kurtosis as a normal distribution. Furthermore, skewness converges at speed

1 / \sqrt{ln (n)}

and while kurtosis at speed

1 / ln (n)

. Despite the overall convergence speed to normality is relatively slow, the distribution of

K

for a modest sample size is already not too far from normality, therefore the asymptotic normality may be sufficient for certain applications when the sample size is large enough.

在一个大群体的n个序列样本中可识别的K个突变数是群体遗传学中最重要的汇总统计之一，在DNA序列数据分析中普遍存在。K可以表示为n-1个独立几何随机变量的和。因此，它的概率生成函数很早就建立起来了，从而产生了众所周知的期望和方差。然而，与样本中不同等位基因的数量相比，对K的统计特性的了解要少得多。本文证明了K的中心极限定理是成立的，这意味着当从根据Wright-Fisher模型（有效大小恒定）或根据恒态模型（允许总体大小独立变化，但在凝聚过程的不同状态之间有统一界限）进化的总体中抽取一个大样本时，K近似服从正态分布。此外，导出了K的偏度和峰度，证实了K具有与正态分布渐近相同的偏度和峰度。此外，偏度以1/ln(n)速度收敛，而峰度以1/ln(n)速度收敛。尽管总体收敛到正态的速度相对较慢，但适度样本量下K的分布已经离正态不远了，因此当样本量足够大时，对于某些应用来说，渐近正态可能是足够的。

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引用次数: 0

A stochastic field theory for the evolution of quantitative traits in finite populations 有限种群数量性状演化的随机场理论。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-02-01 DOI: 10.1016/j.tpb.2024.10.003

Ananda Shikhara Bhat

Infinitely many distinct trait values may arise in populations bearing quantitative traits, and modeling their population dynamics is thus a formidable task. While classical models assume fixed or infinite population size, models in which the total population size fluctuates due to demographic noise in births and deaths can behave qualitatively differently from constant or infinite population models due to density-dependent dynamics. In this paper, I present a stochastic field theory for the eco-evolutionary dynamics of finite populations bearing one-dimensional quantitative traits. I derive stochastic field equations that describe the evolution of population densities, trait frequencies, and the mean value of any trait in the population. These equations recover well-known results such as the replicator-mutator equation, Price equation, and gradient dynamics in the infinite population limit. For finite populations, the equations describe the intricate interplay between natural selection, noise-induced selection, eco-evolutionary feedback, and neutral genetic drift in determining evolutionary trajectories. My work uses ideas from statistical physics, calculus of variations, and SPDEs, providing alternative methods that complement the measure-theoretic martingale approach that is more common in the literature.

在具有数量性状的种群中可能出现无限多不同的性状值，因此对其种群动态建模是一项艰巨的任务。虽然经典模型假设人口规模固定或无限，但由于出生和死亡中的人口噪声而导致总人口规模波动的模型，由于密度依赖的动态，其行为在质量上可能与恒定或无限人口模型不同。本文提出了具有一维数量特征的有限种群的生态演化动力学的随机场理论。我推导了随机场方程，描述了种群密度、性状频率和种群中任何性状的平均值的演变。这些方程恢复了众所周知的结果，如复制-突变方程、Price方程和无限种群极限下的梯度动力学。对于有限种群，这些方程描述了自然选择、噪声诱导选择、生态进化反馈和中性遗传漂变之间复杂的相互作用，以确定进化轨迹。我的方法使用了统计物理、变分演算和spde的思想，提供了补充文献中更常见的度量理论鞅方法的替代方法。

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引用次数: 0

Stochastic offspring distributions amplify selection bias in mutation accumulation experiments 随机子代分布放大了突变积累实验中的选择偏倚。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-02-01 DOI: 10.1016/j.tpb.2024.11.002

Mojgan Ezadian, Lindi M. Wahl

Mutation accumulation (MA) experiments play an important role in understanding evolution. For microbial populations, such experiments often involve periods of population growth, such that a single individual can make a visible colony, followed by severe bottlenecks. Previous work has quantified the effect of positive and negative selection on MA experiments, demonstrating for example that with 20 generations of growth between bottlenecks, big-benefit mutations can be over-represented by a factor of five or more (Wahl and Agashe, 2022). This previous work assumed a deterministic model for population growth. We now develop a fully stochastic model, including realistic offspring distributions that incorporate genetic drift and allow for the loss of rare lineages. We demonstrate that when stochastic offspring distributions are considered, selection bias is even stronger than previously predicted. We describe several analytical and numerical methods that offer an accurate correction for the effects of selection on the observed distribution of fitness effects, describe the practical considerations in implementing each method, and demonstrate the use of this correction on simulated MA data.

突变累积（MA）实验在了解进化方面发挥着重要作用。对于微生物种群来说，此类实验通常涉及种群增长期，例如单个个体就能形成一个可见的菌落，随后是严重的瓶颈期。之前的研究已经量化了正向和负向选择对 MA 实验的影响，例如，在瓶颈期之间的 20 代增长中，大收益突变的比例可能会超过 5 倍或更多（Wahl 和 Agashe，2022 年）。之前的研究假设了一个确定性的种群增长模型。我们现在建立了一个完全随机的模型，包括现实的后代分布，其中包含遗传漂变并允许稀有品系的消失。我们证明，当考虑到随机后代分布时，选择偏差甚至比以前预测的更强。我们介绍了几种分析和数值方法，这些方法可以准确校正选择对观察到的适性效应分布的影响，描述了实施每种方法时的实际考虑因素，并在模拟 MA 数据上演示了这种校正方法的使用。

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引用次数: 0

Effect of competition on emergent phases and phase transitions in competitive systems 竞争对竞争系统中涌现阶段和相变的影响。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-02-01 DOI: 10.1016/j.tpb.2024.12.003

Shikun Wang , Yuanshi Wang , Hong Wu

This paper considers Lotka–Volterra competitive systems characterizing laboratory experiment by Hu et al. (Science, 378:85-89, 2022). Using dynamical systems theory and projection method, we give theoretical analysis and numerical simulation on the model with four species by demonstrating equilibrium stability, periodic oscillation and chaotic fluctuation in the systems. It is shown that varying one competition strength could lead to emergent phases and phase transitions between stable full coexistence, stable partial coexistence, stable persistence of a unique species, persistent periodic oscillation, and persistent chaotic fluctuation in a smooth fashion. Here, the stronger the competition is, the less the number of stable coexisting species, or the higher the amplitude of periodic oscillation, or the more irregular the fluctuation. Our results are consistent with experimental observation and provide new insight. This work is important in understanding effect of competition on emergent phases and phase transitions in competitive systems.

本文考虑了Lotka-Volterra竞争系统特征的实验室实验，由Hu等人（科学，378:85- 89,2022）。利用动力系统理论和投影方法，对该模型进行了理论分析和数值模拟，证明了系统的平衡稳定性、周期振荡和混沌涨落。研究表明，改变一种竞争强度可以导致出现相和稳定的完全共存、稳定的部分共存、一个独特物种的稳定持续、持续的周期振荡和持续的混沌波动之间的平稳相变。在这里，竞争越强，稳定共存物种的数量越少，或者周期振荡的幅度越大，或者波动越不规则。我们的结果与实验观察一致，并提供了新的见解。这项工作对于理解竞争系统中竞争对涌现阶段和相变的影响具有重要意义。

引用次数: 0