Theoretical Population Biology最新文献_第3页

Conditional gene genealogies given the population pedigree for a diploid Moran model with selfing 条件基因谱系给出了具有自交的二倍体莫兰模型的群体谱系。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-07-07 DOI: 10.1016/j.tpb.2025.05.003

Maximillian Newman , John Wakeley , Wai-Tong (Louis) Fan

We introduce a stochastic model of a population with overlapping generations and arbitrary levels of self-fertilization versus outcrossing. We study how the global graph of reproductive relationships, or population pedigree, influences the genealogical relationships of a sample of two gene copies at a genetic locus. Specifically, we consider a diploid Moran model with constant population size

N

over time, in which a proportion of offspring are produced by selfing. We show that the conditional distribution of the pairwise coalescence time at a single locus given the random pedigree converges to a limit law as

N

tends to infinity. The distribution of coalescence times obtained in this way predicts variation among unlinked loci in a sample of individuals. Traditional coalescent analyses implicitly average over pedigrees and generally make different predictions. We describe three different behaviors in the limit depending on the relative strengths, from large to small, of selfing versus outcrossing: partial selfing, limited outcrossing, and negligible outcrossing. In the case of partial selfing, coalescence times are related to the Kingman coalescent, similar to what is found in traditional analyses. In the case of limited outcrossing, the retained pedigree information forms a random graph, with coalescence times given by the meeting times of random walks on this graph. In the case of negligible outcrossing, which represents complete or nearly complete selfing, coalescence times are determined entirely by the fixed times to common ancestry of diploid individuals in the pedigree.

我们引入了一个具有重叠世代和任意水平的自交受精与异交的随机种群模型。我们研究生殖关系的全局图，或群体系谱，如何影响一个基因位点上两个基因拷贝样本的系谱关系。具体来说，我们考虑一个二倍体Moran模型，随着时间的推移，种群规模N恒定，其中有一部分后代是通过自交产生的。我们证明了当N趋于无穷时，给定随机系谱的单位点上成对合并时间的条件分布收敛于一个极限定律。以这种方式获得的聚结时间分布预测了个体样本中非连锁位点之间的变异。传统的聚结分析隐含地对谱系进行平均，并且通常做出不同的预测。根据自交与异交的相对优势，从大到小，我们描述了三种不同的极限行为：部分自交、有限异交和可忽略的异交。在部分自交的情况下，聚结时间与金曼聚结有关，与传统分析中发现的相似。在有限异交的情况下，保留的谱系信息形成一个随机图，合并时间由该图上随机游走的相遇次数给出。在可忽略的异交情况下，代表完全或几乎完全的自交，合并时间完全由谱系中二倍体个体共同祖先的固定时间决定。

{"title":"Conditional gene genealogies given the population pedigree for a diploid Moran model with selfing","authors":"Maximillian Newman , John Wakeley , Wai-Tong (Louis) Fan","doi":"10.1016/j.tpb.2025.05.003","DOIUrl":"10.1016/j.tpb.2025.05.003","url":null,"abstract":"<div><div>We introduce a stochastic model of a population with overlapping generations and arbitrary levels of self-fertilization versus outcrossing. We study how the global graph of reproductive relationships, or population pedigree, influences the genealogical relationships of a sample of two gene copies at a genetic locus. Specifically, we consider a diploid Moran model with constant population size <span><math><mi>N</mi></math></span> over time, in which a proportion of offspring are produced by selfing. We show that the conditional distribution of the pairwise coalescence time at a single locus given the random pedigree converges to a limit law as <span><math><mi>N</mi></math></span> tends to infinity. The distribution of coalescence times obtained in this way predicts variation among unlinked loci in a sample of individuals. Traditional coalescent analyses implicitly average over pedigrees and generally make different predictions. We describe three different behaviors in the limit depending on the relative strengths, from large to small, of selfing versus outcrossing: partial selfing, limited outcrossing, and negligible outcrossing. In the case of partial selfing, coalescence times are related to the Kingman coalescent, similar to what is found in traditional analyses. In the case of limited outcrossing, the retained pedigree information forms a random graph, with coalescence times given by the meeting times of random walks on this graph. In the case of negligible outcrossing, which represents complete or nearly complete selfing, coalescence times are determined entirely by the fixed times to common ancestry of diploid individuals in the pedigree.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"165 ","pages":"Pages 29-44"},"PeriodicalIF":1.2,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144602077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identity-by-descent segments in large samples 大样本中的血统识别片段。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-07-05 DOI: 10.1016/j.tpb.2025.06.003

Seth D. Temple , Elizabeth A. Thompson

If two haplotypes share the same alleles for an extended gene tract, these haplotypes are likely to be derived identical-by-descent from a recent common ancestor. Identity-by-descent segment lengths are correlated via unobserved ancestral tree and recombination processes, which commonly presents challenges to the derivation of theoretical results in population genetics. We show that the proportion of detectable identity-by-descent segments around a locus is normally distributed when the sample size and the scaled population size are large. We generalize this central limit theorem to cover flexible demographic scenarios, multi-way identity-by-descent segments, and multivariate identity-by-descent rates. The regularity conditions on sample size and scaled population size are unlikely to hold in genetic data from real populations, but provide intuition for when the Gaussian distribution may be a reasonable approximate model for the IBD rate. We use efficient simulations to study the distributional behavior of the detectable identity-by-descent rate. One consequence of non-normality in finite samples is that a genome-wide scan looking for excess identity-by-descent rates may be subject to anti-conservative control of family-wise error rates.

如果两个单倍型在一个扩展的基因束中具有相同的等位基因，那么这些单倍型很可能是由最近的共同祖先遗传而来的。血统身份片段长度通过未观察到的祖先树和重组过程相关联，这通常对群体遗传学理论结果的推导提出了挑战。我们表明，当样本大小和尺度总体大小较大时，基因座周围可检测的血统身份片段的比例呈正态分布。我们将这个中心极限定理推广到灵活的人口统计场景、多向血统分段和多变量血统率。样本大小和比例群体大小的规则条件不太可能在真实群体的遗传数据中成立，但为高斯分布何时可能是IBD率的合理近似模型提供了直觉。我们使用有效的模拟来研究可检测的下降身份率的分布行为。在有限样本中，非正态性的一个后果是，在全基因组扫描中寻找过多的血统识别率，可能会受到家庭误差率的反保守控制。

{"title":"Identity-by-descent segments in large samples","authors":"Seth D. Temple , Elizabeth A. Thompson","doi":"10.1016/j.tpb.2025.06.003","DOIUrl":"10.1016/j.tpb.2025.06.003","url":null,"abstract":"<div><div>If two haplotypes share the same alleles for an extended gene tract, these haplotypes are likely to be derived identical-by-descent from a recent common ancestor. Identity-by-descent segment lengths are correlated via unobserved ancestral tree and recombination processes, which commonly presents challenges to the derivation of theoretical results in population genetics. We show that the proportion of detectable identity-by-descent segments around a locus is normally distributed when the sample size and the scaled population size are large. We generalize this central limit theorem to cover flexible demographic scenarios, multi-way identity-by-descent segments, and multivariate identity-by-descent rates. The regularity conditions on sample size and scaled population size are unlikely to hold in genetic data from real populations, but provide intuition for when the Gaussian distribution may be a reasonable approximate model for the IBD rate. We use efficient simulations to study the distributional behavior of the detectable identity-by-descent rate. One consequence of non-normality in finite samples is that a genome-wide scan looking for excess identity-by-descent rates may be subject to anti-conservative control of family-wise error rates.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"165 ","pages":"Pages 10-21"},"PeriodicalIF":1.2,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144585410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The TMRCA of general genealogies in populations with deterministically varying size 具有决定性大小变化的人群中一般家谱的TMRCA。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-07-02 DOI: 10.1016/j.tpb.2025.06.002

Alejandro H. Wences , Lizbeth Peñaloza , Matthias Steinrücken , Arno Siri-Jégousse

We study the time to the most recent common ancestor (TMRCA) of a sample of finite size in a wide class of genealogical models for populations with deterministically varying size. This is made possible by recently developed results on inhomogeneous phase-type random variables, allowing us to obtain the density and the moments of the TMRCA of time-dependent coalescent processes in terms of matrix formulas. We also provide matrix simplifications permitting a more straightforward calculation. With these results, the TMRCA provides an explanatory variable to distinguish different evolutionary scenarios, and to infer model parameters.

我们研究了一个有限大小的样本的最近共同祖先（TMRCA）的时间在一个广泛的类家谱模型具有确定性的变化大小的群体。这可以通过最近发展的非均匀相位型随机变量的结果来实现，使我们能够根据矩阵公式获得时变凝聚过程的TMRCA的密度和矩。我们还提供了矩阵简化，允许更直接的计算。有了这些结果，TMRCA提供了一个解释变量来区分不同的进化情景，并推断模型参数。

引用次数: 0

Evolution of redirected help with stepping-stone dispersal 通过垫脚石分散的重定向帮助的进化。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-07-01 DOI: 10.1016/j.tpb.2025.06.001

Alan Flatrès, Geoff Wild

Individuals can be subject to brood failure for many reasons, e.g. egg predation. Some species have adopted a strategy to compensate for fitness loss due to brood failure. In some bird species, individuals that experience brood failure can help a related neighbor care for their offspring. This behavior is known as redirected helping and it compensates for the loss of fitness by improving inclusive fitness. However, inclusive fitness gains associated with redirected helping are counteracted in a ‘viscous’ population, where individuals remain close to their natal site, by increased competition among kin. In a previous model, we investigated how population viscosity affects the evolution of redirected help by building an infinite-island model that lacked explicit spatial structure and emphasized dispersal on a global scale. Here, we revisit the role of population viscosity in the evolution of redirected help with a spatially explicit stepping-stone dispersal model. The dispersal pattern in this new framework is much more constrained than in the infinite-island case, strengthening the population viscosity we are interested in. In contrast to previous work, we find that localized dispersal can prevent the evolution of redirected help and even lead to the evolution of spiteful behavior in some specific cases. Our predictions are sensitive to the scale of dispersal, survival rate and the benefits provided by helping. We discuss our findings with regard to the previous literature investigating the evolution of helping in a viscous population.

个体孵化失败的原因有很多，比如捕食蛋。一些物种采取了一种策略来补偿由于繁殖失败而造成的适应性损失。在一些鸟类物种中，经历孵卵失败的个体可以帮助有亲缘关系的邻居照顾它们的后代。这种行为被称为重定向帮助，它通过提高整体适应性来补偿适应性的损失。然而，与重定向帮助相关的包容性健康收益在“粘性”种群中被抵消，在“粘性”种群中，个体保持靠近其出生地，近亲之间的竞争加剧。在之前的模型中，我们通过建立一个缺乏明确空间结构并强调全球范围内分散的无限岛模型，研究了种群粘度如何影响重定向帮助的进化。在这里，我们用一个空间明确的踏脚石分散模型重新审视种群粘度在重定向帮助进化中的作用。这个新框架下的扩散模式比无限岛情况下的更受约束，加强了我们感兴趣的种群粘性。与之前的研究相反，我们发现局部分散可以阻止重定向帮助的进化，甚至在某些特定情况下导致恶意行为的进化。我们的预测对扩散的规模、存活率和帮助所带来的好处很敏感。我们讨论了我们的发现，关于以前的文献调查进化的帮助在粘性人口。

{"title":"Evolution of redirected help with stepping-stone dispersal","authors":"Alan Flatrès, Geoff Wild","doi":"10.1016/j.tpb.2025.06.001","DOIUrl":"10.1016/j.tpb.2025.06.001","url":null,"abstract":"<div><div>Individuals can be subject to brood failure for many reasons, e.g. egg predation. Some species have adopted a strategy to compensate for fitness loss due to brood failure. In some bird species, individuals that experience brood failure can help a related neighbor care for their offspring. This behavior is known as redirected helping and it compensates for the loss of fitness by improving inclusive fitness. However, inclusive fitness gains associated with redirected helping are counteracted in a ‘viscous’ population, where individuals remain close to their natal site, by increased competition among kin. In a previous model, we investigated how population viscosity affects the evolution of redirected help by building an infinite-island model that lacked explicit spatial structure and emphasized dispersal on a global scale. Here, we revisit the role of population viscosity in the evolution of redirected help with a spatially explicit stepping-stone dispersal model. The dispersal pattern in this new framework is much more constrained than in the infinite-island case, strengthening the population viscosity we are interested in. In contrast to previous work, we find that localized dispersal can prevent the evolution of redirected help and even lead to the evolution of spiteful behavior in some specific cases. Our predictions are sensitive to the scale of dispersal, survival rate and the benefits provided by helping. We discuss our findings with regard to the previous literature investigating the evolution of helping in a viscous population.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"165 ","pages":"Pages 22-28"},"PeriodicalIF":1.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144561735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Parthenogenesis, sexual conflict, and selection on fertilization rates in switching environments 孤雌生殖、性冲突和选择对转换环境中受精率的影响。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-05-27 DOI: 10.1016/j.tpb.2025.05.001

Xiaoyuan Liu , Jon W. Pitchford , George W.A. Constable

In the face of varying environments, organisms exhibit a variety of reproductive modes, from asexuality to obligate sexuality. Should reproduction be sexual, the morphology of the sex cells (gametes) produced by these organisms has important evolutionary implications; these cells can be the same size (isogamy), one larger and one smaller (anisogamy), and finally the larger cell can lose its capacity for motility (oogamy, the familiar sperm–egg system). Understanding the origin of the sexes, which lies in the types of gametes they produce, thus amounts to explaining these evolutionary transitions. Here we extend classic results in this area by exploring these transitions in a model in which organisms can reproduce both sexually and asexually. This reproductive mode is present in many algae and is accompanied by suppressed pheromone production in female populations of the brown alga Scytosiphon lomentaria. Our model investigates the co-evolution of gamete cell size with fertilization rate, which is a proxy for motility and pheromone production but is often held constant in anisogamy models. Using adaptive dynamics generalized to the case of switching environments, we find that isogamy can evolve to anisogamy through evolutionary branching, and that anisogamy can evolve to oogamy or suppressed pheromone production through a further branching driven by sexual conflict. We also derive analytic conditions on the model parameters required to arrest evolution on this isogamy–oogamy trajectory, with low fertilization rates and stochastically switching environments stabilizing isogamy under a bet-hedging strategy, and low fertilization costs stabilizing anisogamy and pheromone production.

面对变化的环境，生物表现出各种各样的生殖模式，从无性到专一性。如果生殖是有性的，这些生物产生的性细胞（配子）的形态具有重要的进化意义；这些细胞可以大小相同（同卵异体），一个大一个小（异卵异体），最后较大的细胞失去运动能力（卵异体，我们熟悉的精子-卵子系统）。了解性别的起源，这取决于它们产生的配子的类型，从而可以解释这些进化转变。在这里，我们通过探索生物可以有性繁殖和无性繁殖的模式中的这些转变，扩展了这一领域的经典结果。这种繁殖模式存在于许多藻类中，并伴随着雌性褐藻丝虹吸的信息素产生受到抑制。我们的模型研究了配子细胞大小与受精率的共同进化，受精率是运动和信息素产生的代理，但在异配模型中通常保持不变。将自适应动力学推广到切换环境的情况下，我们发现同种异体可以通过进化分支进化到异配异体，而异配异体可以通过性别冲突驱动的进一步分支进化到卵配异体或抑制信息素的产生。我们还推导出了在这条等配-卵配轨迹上停止进化所需的模型参数的解析条件，即在下注-对冲策略下，低受精率和随机切换环境稳定了等配，低受精成本稳定了异配和信息素的产生。

{"title":"Parthenogenesis, sexual conflict, and selection on fertilization rates in switching environments","authors":"Xiaoyuan Liu , Jon W. Pitchford , George W.A. Constable","doi":"10.1016/j.tpb.2025.05.001","DOIUrl":"10.1016/j.tpb.2025.05.001","url":null,"abstract":"<div><div>In the face of varying environments, organisms exhibit a variety of reproductive modes, from asexuality to obligate sexuality. Should reproduction be sexual, the morphology of the sex cells (gametes) produced by these organisms has important evolutionary implications; these cells can be the same size (isogamy), one larger and one smaller (anisogamy), and finally the larger cell can lose its capacity for motility (oogamy, the familiar sperm–egg system). Understanding the origin of the sexes, which lies in the types of gametes they produce, thus amounts to explaining these evolutionary transitions. Here we extend classic results in this area by exploring these transitions in a model in which organisms can reproduce both sexually and asexually. This reproductive mode is present in many algae and is accompanied by suppressed pheromone production in female populations of the brown alga <em>Scytosiphon lomentaria</em>. Our model investigates the co-evolution of gamete cell size with fertilization rate, which is a proxy for motility and pheromone production but is often held constant in anisogamy models. Using adaptive dynamics generalized to the case of switching environments, we find that isogamy can evolve to anisogamy through evolutionary branching, and that anisogamy can evolve to oogamy or suppressed pheromone production through a further branching driven by sexual conflict. We also derive analytic conditions on the model parameters required to arrest evolution on this isogamy–oogamy trajectory, with low fertilization rates and stochastically switching environments stabilizing isogamy under a bet-hedging strategy, and low fertilization costs stabilizing anisogamy and pheromone production.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"164 ","pages":"Pages 37-56"},"PeriodicalIF":1.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144183263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mathematical bounds on r2 and the effect size in case-control genome-wide association studies 病例对照全基因组关联研究中r2的数学界限和效应大小

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-05-15 DOI: 10.1016/j.tpb.2025.04.003

Sanjana M. Paye , Michael D. Edge

Case-control genome-wide association studies (GWAS) are often used to find associations between genetic variants and diseases. When case-control GWAS are conducted, researchers must make decisions regarding how many cases and how many controls to include in the study. Connections between variants and diseases are made using association statistics, including

χ^{2}

. Previous work in population genetics has shown that LD statistics, including

r^{2}

, are bounded by the allele frequencies in the population being studied. Since varying the case fraction changes sample allele frequencies, we use the known bounds on

r^{2}

to explore how the fraction of cases included in a study can affect statistical power to detect associations. We analyze a simple mathematical model and use simulations to study a quantity proportional to the

χ^{2}

noncentrality parameter, which is closely related to

r^{2}

, under various conditions. Varying the case fraction changes the

χ^{2}

noncentrality parameter, and by extension the statistical power, with effects depending on the dominance, penetrance, and frequency of the risk allele. Our framework explains previously observed results, such as asymmetries in power to detect risk vs. protective alleles, and the fact that a balanced sample of cases and controls does not always give the best power to detect associations, particularly for highly penetrant minor risk alleles that are either dominant or recessive. We show by simulation that our results can be used as a rough guide to statistical power for association tests other than

χ^{2}

tests of independence.

病例对照全基因组关联研究（GWAS）常用于发现遗传变异与疾病之间的关联。当进行病例对照GWAS时，研究人员必须决定在研究中纳入多少病例和多少对照。变异和疾病之间的联系使用关联统计，包括χ2。先前的群体遗传学研究表明，包括r2在内的LD统计数据受到被研究群体中等位基因频率的限制。由于改变病例比例会改变样本等位基因频率，因此我们使用r2上的已知界限来探索研究中包含的病例比例如何影响检测关联的统计能力。我们分析了一个简单的数学模型，并通过模拟研究了在各种条件下与χ2非中心性参数成正比的数量，而χ2非中心性参数与r2密切相关。改变病例比例会改变χ2非中心性参数，进而改变统计能力，其影响取决于风险等位基因的显性、外显率和频率。我们的框架解释了先前观察到的结果，例如检测风险与保护性等位基因的能力不对称，以及平衡的病例和对照样本并不总是提供检测关联的最佳能力，特别是对于显性或隐性高渗透的小风险等位基因。我们通过模拟表明，我们的结果可以作为关联检验的统计能力的粗略指南，而不是χ2独立性检验。

{"title":"Mathematical bounds on r2 and the effect size in case-control genome-wide association studies","authors":"Sanjana M. Paye , Michael D. Edge","doi":"10.1016/j.tpb.2025.04.003","DOIUrl":"10.1016/j.tpb.2025.04.003","url":null,"abstract":"<div><div>Case-control genome-wide association studies (GWAS) are often used to find associations between genetic variants and diseases. When case-control GWAS are conducted, researchers must make decisions regarding how many cases and how many controls to include in the study. Connections between variants and diseases are made using association statistics, including <span><math><msup><mrow><mi>χ</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span>. Previous work in population genetics has shown that LD statistics, including <span><math><msup><mrow><mi>r</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span>, are bounded by the allele frequencies in the population being studied. Since varying the case fraction changes sample allele frequencies, we use the known bounds on <span><math><msup><mrow><mi>r</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> to explore how the fraction of cases included in a study can affect statistical power to detect associations. We analyze a simple mathematical model and use simulations to study a quantity proportional to the <span><math><msup><mrow><mi>χ</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> noncentrality parameter, which is closely related to <span><math><msup><mrow><mi>r</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span>, under various conditions. Varying the case fraction changes the <span><math><msup><mrow><mi>χ</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> noncentrality parameter, and by extension the statistical power, with effects depending on the dominance, penetrance, and frequency of the risk allele. Our framework explains previously observed results, such as asymmetries in power to detect risk vs. protective alleles, and the fact that a balanced sample of cases and controls does not always give the best power to detect associations, particularly for highly penetrant minor risk alleles that are either dominant or recessive. We show by simulation that our results can be used as a rough guide to statistical power for association tests other than <span><math><msup><mrow><mi>χ</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> tests of independence.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"164 ","pages":"Pages 1-11"},"PeriodicalIF":1.2,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144089593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolution between two competing macrophyte populations along a resource gradient leads to collapse in a bistable lake ecosystem 两个相互竞争的大型植物种群沿着资源梯度的进化导致双稳态湖泊生态系统的崩溃。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-05-13 DOI: 10.1016/j.tpb.2025.04.001

Sirine Boucenna , Gael Raoul , Vasilis Dakos

While it is known that shallow lake ecosystems may experience abrupt shifts (ie tipping points) from a clear water state to a contrasting turbid alternative state as a result of eutrophication, the role of evolutionary processes and the impact of trait variation in this context remain largely unexplored. It is crucial to elucidate how eco-evolutionary feedbacks affect abrupt ecological transitions in shallow lakes and more in general in bistable ecosystems. These feedbacks can significantly alter the dynamics of aquatic plants competition, community structure, and species diversity, potentially affecting the existence of alternative states or either delay or expedite the thresholds at which these ecological shifts occur. In this paper, we explore the eco-evolutionary dynamics of submerged and floating macrophytes in a shallow lake ecosystem under asymmetric competition for nutrients and light along a gradient of nutrient diffusion. We use Adaptive Dynamics and a structured population model to analyze the evolution of the growth depth of the submerged and floating macrophytes populations, which influences their competitive ability for the two resources. We show how trait evolution can result in complex dynamics including evolutionary oscillations, extensive diversification and evolutionary suicide. Furthermore, we find that the co-evolution of the two competing populations plays a stabilizing role, but does not significantly alter the dynamics compared to when only one of the two populations is evolving. Overall, our study contributes to the understanding of the effects of evolution on the ecological dynamics of bistable ecosystems.

虽然众所周知，由于富营养化，浅湖生态系统可能会经历从清澈的水状态到对比浑浊的替代状态的突变（即引爆点），但在这种情况下，进化过程的作用和性状变异的影响在很大程度上仍未被探索。阐明生态进化反馈如何影响浅湖和双稳态生态系统的突然生态转变是至关重要的。这些反馈可以显著改变水生植物竞争、群落结构和物种多样性的动态，潜在地影响替代状态的存在，或延迟或加速这些生态转变发生的阈值。本文研究了浅湖生态系统中沉水植物和浮水植物在养分和光照不对称竞争下的生态进化动态。采用自适应动力学和结构种群模型，分析了沉水和浮水大型植物种群生长深度的演变及其对两种资源竞争能力的影响。我们展示了性状进化如何导致复杂的动力学，包括进化振荡、广泛多样化和进化自杀。此外，我们发现两个竞争种群的共同进化起着稳定作用，但与两个种群中只有一个进化时相比，这并没有显著改变动态。总的来说，我们的研究有助于理解进化对双稳态生态系统生态动力学的影响。

{"title":"Evolution between two competing macrophyte populations along a resource gradient leads to collapse in a bistable lake ecosystem","authors":"Sirine Boucenna , Gael Raoul , Vasilis Dakos","doi":"10.1016/j.tpb.2025.04.001","DOIUrl":"10.1016/j.tpb.2025.04.001","url":null,"abstract":"<div><div>While it is known that shallow lake ecosystems may experience abrupt shifts (ie tipping points) from a clear water state to a contrasting turbid alternative state as a result of eutrophication, the role of evolutionary processes and the impact of trait variation in this context remain largely unexplored. It is crucial to elucidate how eco-evolutionary feedbacks affect abrupt ecological transitions in shallow lakes and more in general in bistable ecosystems. These feedbacks can significantly alter the dynamics of aquatic plants competition, community structure, and species diversity, potentially affecting the existence of alternative states or either delay or expedite the thresholds at which these ecological shifts occur. In this paper, we explore the eco-evolutionary dynamics of submerged and floating macrophytes in a shallow lake ecosystem under asymmetric competition for nutrients and light along a gradient of nutrient diffusion. We use Adaptive Dynamics and a structured population model to analyze the evolution of the growth depth of the submerged and floating macrophytes populations, which influences their competitive ability for the two resources. We show how trait evolution can result in complex dynamics including evolutionary oscillations, extensive diversification and evolutionary suicide. Furthermore, we find that the co-evolution of the two competing populations plays a stabilizing role, but does not significantly alter the dynamics compared to when only one of the two populations is evolving. Overall, our study contributes to the understanding of the effects of evolution on the ecological dynamics of bistable ecosystems.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"164 ","pages":"Pages 23-36"},"PeriodicalIF":1.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Muller’s ratchet and gene duplication 穆勒棘轮和基因复制。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-05-13 DOI: 10.1016/j.tpb.2025.04.002

Fabian Freund , Johannes Wirtz , Yichen Zheng , Yannick Schäfer , Thomas Wiehe

Copy number of genes in gene families can be highly variable among individuals and may continue to change across generations. Here, we study a model of duplication–selection interaction, which is related to Haigh’s mutation–selection model of Muller’s ratchet. New gene copies are generated by duplication but fitness of individuals decreases as copy number increases. Our model comes in two flavors: duplicates are copied either from a single template or from any existing copy. A duplication–selection equilibrium exists in both cases for infinite size populations and is given by a shifted Poisson or a negative binomial distribution. Unless counteracted by synergistic epistasis, finite populations suffer from loss of low copy-number haplotypes by drift, forcing them into a regime called ‘run-away evolution’ in which new copies accumulate without bound nor equilibrium. We discuss a few empirical examples and interpret them in the light of our models. Generally, large gene families appear too over-dispersed to fit the single template model suggesting a dynamic, and potentially accelerating, duplication process.

基因家族中基因的拷贝数在个体之间变化很大，并可能在几代之间继续变化。本文研究了与Haigh的Muller棘轮突变选择模型相关的复制-选择相互作用模型。新的基因拷贝通过复制产生，但随着拷贝数的增加，个体的适应度降低。我们的模型有两种形式：从单个模板复制副本或从任何现有副本复制副本。对于无限大小的种群，在两种情况下都存在重复选择平衡，并由移位泊松分布或负二项分布给出。除非受到协同上位的抵消，否则有限种群会因漂移而失去低拷贝数的单倍型，迫使它们进入一种被称为“逃逸进化”的机制，在这种机制中，新的拷贝在没有约束和平衡的情况下积累。我们讨论了几个经验例子，并根据我们的模型对它们进行了解释。一般来说，大的基因家族似乎过于分散，不适合单一模板模型，这表明一个动态的、可能加速的复制过程。

{"title":"Muller’s ratchet and gene duplication","authors":"Fabian Freund , Johannes Wirtz , Yichen Zheng , Yannick Schäfer , Thomas Wiehe","doi":"10.1016/j.tpb.2025.04.002","DOIUrl":"10.1016/j.tpb.2025.04.002","url":null,"abstract":"<div><div>Copy number of genes in gene families can be highly variable among individuals and may continue to change across generations. Here, we study a model of duplication–selection interaction, which is related to Haigh’s mutation–selection model of Muller’s ratchet. New gene copies are generated by duplication but fitness of individuals decreases as copy number increases. Our model comes in two flavors: duplicates are copied either from a single template or from any existing copy. A duplication–selection equilibrium exists in both cases for infinite size populations and is given by a shifted Poisson or a negative binomial distribution. Unless counteracted by synergistic epistasis, finite populations suffer from loss of low copy-number haplotypes by drift, forcing them into a regime called ‘run-away evolution’ in which new copies accumulate without bound nor equilibrium. We discuss a few empirical examples and interpret them in the light of our models. Generally, large gene families appear too over-dispersed to fit the single template model suggesting a dynamic, and potentially accelerating, duplication process.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"164 ","pages":"Pages 12-22"},"PeriodicalIF":1.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Eco-evolutionary dynamics of anthelmintic resistance in soil-transmitted helminths 土壤传播蠕虫抗虫性的生态进化动态

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-04-12 DOI: 10.1016/j.tpb.2025.03.006

Swati Patel , Kelsey Lyberger , Carolin Vegvari , Hayriye Gulbudak

Anthelmintic resistance (AR) of soil-transmitted helminth parasites against the most widely available drugs is an ongoing concern for both human-infecting and livestock-infecting species. There has been substantial evidence of AR in livestock but less in humans, which may be due to a variety of reasons. In this paper, we develop an eco-evolutionary model that couples the life cycle of these parasites with their underlying evolution in a single biallelic genetic locus that confers resistance to treatment drugs. We determine the critical treatment frequency needed to effectively eliminate the population, for a fixed drug efficacy (without evolution) and use this to classify three qualitative distinct behaviors of the eco-evolutionary model. Then, we describe how aspects of the life cycle influence which qualitative outcome is achieved and the rate of spread of the resistance allele, comparing across parameterized models of human-infecting and livestock-infecting species. For all but one species, we find that lower fecundity rates and lower contact rates speed the spread of resistance, while lower larval death slows it down. The life cycle parameters of Ancylostoma duodenale and Ostertagia circumcincta are associated with the fastest and slowest spread of resistance, respectively. We discuss the mechanistic reason for these results.

土壤传播的蠕虫寄生虫对最广泛使用的药物的抗虫性（AR）是人类感染和牲畜感染物种持续关注的问题。有大量证据表明家畜中存在过敏性鼻炎，但人类较少，这可能是由于各种原因造成的。在本文中，我们开发了一个生态进化模型，将这些寄生虫的生命周期与它们在单个双等位基因遗传位点的潜在进化结合起来，从而赋予对治疗药物的抗性。我们确定了有效消除种群所需的临界治疗频率，对于固定的药物疗效（没有进化），并使用它来分类生态进化模型的三种定性不同行为。然后，我们描述了生命周期的各个方面如何影响定性结果的实现和抗性等位基因的传播速度，比较了人类感染和牲畜感染物种的参数化模型。除了一个物种外，我们发现较低的繁殖率和较低的接触率加速了抗药性的传播，而较低的幼虫死亡率则减缓了抗药性的传播。十二指肠钩虫和环切石尾虫的生命周期参数分别与耐药性传播最快和最慢有关。我们讨论了产生这些结果的机理原因。

{"title":"Eco-evolutionary dynamics of anthelmintic resistance in soil-transmitted helminths","authors":"Swati Patel , Kelsey Lyberger , Carolin Vegvari , Hayriye Gulbudak","doi":"10.1016/j.tpb.2025.03.006","DOIUrl":"10.1016/j.tpb.2025.03.006","url":null,"abstract":"<div><div>Anthelmintic resistance (AR) of soil-transmitted helminth parasites against the most widely available drugs is an ongoing concern for both human-infecting and livestock-infecting species. There has been substantial evidence of AR in livestock but less in humans, which may be due to a variety of reasons. In this paper, we develop an eco-evolutionary model that couples the life cycle of these parasites with their underlying evolution in a single biallelic genetic locus that confers resistance to treatment drugs. We determine the critical treatment frequency needed to effectively eliminate the population, for a fixed drug efficacy (without evolution) and use this to classify three qualitative distinct behaviors of the eco-evolutionary model. Then, we describe how aspects of the life cycle influence which qualitative outcome is achieved and the rate of spread of the resistance allele, comparing across parameterized models of human-infecting and livestock-infecting species. For all but one species, we find that lower fecundity rates and lower contact rates speed the spread of resistance, while lower larval death slows it down. The life cycle parameters of <em>Ancylostoma duodenale</em> and <em>Ostertagia circumcincta</em> are associated with the fastest and slowest spread of resistance, respectively. We discuss the mechanistic reason for these results.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"163 ","pages":"Pages 80-90"},"PeriodicalIF":1.2,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143844549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A matrix-analytical sampling formula for time-homogeneous coalescent processes under the infinite sites mutation model 无限位点突变模型下时间均匀聚结过程的矩阵解析抽样公式。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2025-04-01 DOI: 10.1016/j.tpb.2025.03.002

Asger Hobolth , Simon Boitard , Andreas Futschik , Raphael Leblois

In this paper we develop a general framework for calculating the probability of a genetic sample under a time-homogeneous coalescent process and the infinite sites mutation model. The evolutionary model that we consider can be characterized as a two-step procedure: A coalescent process that describes the ancestral relatedness of the samples and a sprinkling of mutations in separate sites on the ancestral tree according to a Poisson process. The coalescent process is defined using multivariate phase-type theory. The requirements are a rate matrix that determines the transition rates between the ancestral states, an initial state probability vector, and a reward matrix that informs about the characteristics of the ancestral states. For example, the reward matrix could contain information about the number of singleton, doubleton or higher-order lineages in the ancestral states. We analyze the probability generating function for the evolutionary model as a function of the initial state probability vector, the transition rate matrix, the reward matrix, and the mutation rate. The matrix-analytical expression of the probability generating function allows us to develop a general method for calculating the probability of a population genetic data set. We demonstrate that the method is computationally attractive for a small number of mutations and provide a simple and easy-to-implement algorithm for determining the probability of a sample from the evolutionary model. The method is computationally stable and only involves a single inverse matrix operation, matrix multiplications and matrix additions. We provide comprehensive understanding of the procedure by detailed calculations and discussions of several elementary examples. These examples include different sample representations (labeled samples and the site frequency spectrum) and different demographic and genetic models (the structured coalescent and the Beta-coalescent). We apply the sampling formula to calculate probabilities of spectra for the Kingman coalescent and the Beta-coalescent. Even for a small number of samples and mutations we find that the probabilities for spectra vary in huge orders of magnitudes. We compare the probabilities of the spectra to the values of Tajima’s

D

-statistics, and find that the

D

-statistic is a poor predictor for the probability of a spectrum. Finally, we investigate how the probabilities of the spectra vary with the parametrization of the Beta-coalescent.

在本文中，我们建立了计算一个遗传样本在时间均匀聚合过程和无限位点突变模型下的概率的一般框架。我们考虑的进化模型可以被描述为一个两步过程：一个描述样本祖先关系的凝聚过程和一个根据泊松过程在祖先树的不同位置上的零星突变。用多元相型理论定义了聚结过程。需求是决定祖先状态之间转换速率的速率矩阵，初始状态概率向量，以及告知祖先状态特征的奖励矩阵。例如，奖励矩阵可以包含关于祖先状态中单例、双例或高阶谱系的数量的信息。我们将进化模型的概率生成函数分析为初始状态概率向量、转移率矩阵、奖励矩阵和突变率的函数。概率生成函数的矩阵解析表达式使我们能够开发一种计算群体遗传数据集概率的一般方法。我们证明了该方法在计算上对少量突变具有吸引力，并提供了一种简单且易于实现的算法来确定进化模型中样本的概率。该方法计算稳定，只涉及单次矩阵逆运算、矩阵乘法和矩阵加法。我们通过详细的计算和几个基本例子的讨论，提供了对程序的全面理解。这些例子包括不同的样本表示（标记样本和位点频谱）和不同的人口统计学和遗传模型（结构聚结和β聚结）。我们应用抽样公式计算了Kingman聚结和beta聚结的光谱概率。即使对于少量的样本和突变，我们发现光谱的概率也会发生巨大的数量级变化。我们将光谱的概率与田岛的d统计量的值进行比较，发现d统计量对于光谱的概率是一个很差的预测器。最后，我们研究了β -聚结剂的参数化对光谱概率的影响。

{"title":"A matrix-analytical sampling formula for time-homogeneous coalescent processes under the infinite sites mutation model","authors":"Asger Hobolth , Simon Boitard , Andreas Futschik , Raphael Leblois","doi":"10.1016/j.tpb.2025.03.002","DOIUrl":"10.1016/j.tpb.2025.03.002","url":null,"abstract":"<div><div>In this paper we develop a general framework for calculating the probability of a genetic sample under a time-homogeneous coalescent process and the infinite sites mutation model. The evolutionary model that we consider can be characterized as a two-step procedure: A coalescent process that describes the ancestral relatedness of the samples and a sprinkling of mutations in separate sites on the ancestral tree according to a Poisson process. The coalescent process is defined using multivariate phase-type theory. The requirements are a rate matrix that determines the transition rates between the ancestral states, an initial state probability vector, and a reward matrix that informs about the characteristics of the ancestral states. For example, the reward matrix could contain information about the number of singleton, doubleton or higher-order lineages in the ancestral states. We analyze the probability generating function for the evolutionary model as a function of the initial state probability vector, the transition rate matrix, the reward matrix, and the mutation rate. The matrix-analytical expression of the probability generating function allows us to develop a general method for calculating the probability of a population genetic data set. We demonstrate that the method is computationally attractive for a small number of mutations and provide a simple and easy-to-implement algorithm for determining the probability of a sample from the evolutionary model. The method is computationally stable and only involves a single inverse matrix operation, matrix multiplications and matrix additions. We provide comprehensive understanding of the procedure by detailed calculations and discussions of several elementary examples. These examples include different sample representations (labeled samples and the site frequency spectrum) and different demographic and genetic models (the structured coalescent and the Beta-coalescent). We apply the sampling formula to calculate probabilities of spectra for the Kingman coalescent and the Beta-coalescent. Even for a small number of samples and mutations we find that the probabilities for spectra vary in huge orders of magnitudes. We compare the probabilities of the spectra to the values of Tajima’s <span><math><mi>D</mi></math></span>-statistics, and find that the <span><math><mi>D</mi></math></span>-statistic is a poor predictor for the probability of a spectrum. Finally, we investigate how the probabilities of the spectra vary with the parametrization of the Beta-coalescent.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"163 ","pages":"Pages 62-79"},"PeriodicalIF":1.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143781871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0