arXiv - QuanBio - Populations and Evolution最新文献_第3页

Determinism vs. stochasticity in competitive flour beetle communities 竞争性面粉甲虫群落的决定性与随机性

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-09 DOI: arxiv-2409.05317

Evan C. Johnson, Tad Dallas, Alan Hastings

{"title":"Determinism vs. stochasticity in competitive flour beetle communities","authors":"Evan C. Johnson, Tad Dallas, Alan Hastings","doi":"arxiv-2409.05317","DOIUrl":"https://doi.org/arxiv-2409.05317","url":null,"abstract":"As ecologists increasingly adopt stochastic models over deterministic ones,\u0000the question arises: when is this a positive development and when is this an\u0000unnecessary complication? While deterministic models -- like the Lotka-Volterra\u0000model -- provide straightforward predictions about competitive outcomes, they\u0000are often unrealistic. Stochastic models are more realistic, but their\u0000complexity can limit their usefulness in explaining coexistence. Here, we\u0000investigate the relative importance of deterministic and stochastic processes\u0000in competition between two flour beetle species, Tribolium castaneum and\u0000Tribolium confusum. Specifically, we use highly-replicated one-generation\u0000experiments (784 microcosms) to parameterize a mechanistic model. Both the full\u0000stochastic model and the underlying deterministic skeleton exhibit priority\u0000effects, where one species excludes the other, but the identity of the winning\u0000species depends on initial abundances. Stochasticity makes the identity of the\u0000winner less predictable, but deterministic dynamics still make reliable\u0000predictions (94% accuracy across a range of reasonable initial abundances). We\u0000conclude that deterministic population dynamics are sufficient to account for\u0000patterns of coexistence (or lack thereof), a potentially general finding that\u0000is supported by recent field studies. Additionally, we resolve longstanding\u0000issues in flour beetle research by identifying selective egg predation as the\u0000mechanism for priority effects, demonstrating the primacy of demographic\u0000stochasticity (compared to environmental stochasticity), and reinterpreting\u0000classic competition experiments to show that apparent coexistence often\u0000represents long-term transient dynamics.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reconstructing semi-directed level-1 networks using few quarnets 利用少量四元组重构半定向一级网络

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-09 DOI: arxiv-2409.06034

Martin Frohn, Niels Holtgrefe, Leo van Iersel, Mark Jones, Steven Kelk

引用次数: 0

Stratified dispersal explains mountain pine beetle's range expansion in Alberta 分层扩散解释了阿尔伯塔省山松甲虫分布范围扩大的原因

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-09 DOI: arxiv-2409.05320

Evan C. Johnson, Micah Brush, Mark A. Lewis

{"title":"Stratified dispersal explains mountain pine beetle's range expansion in Alberta","authors":"Evan C. Johnson, Micah Brush, Mark A. Lewis","doi":"arxiv-2409.05320","DOIUrl":"https://doi.org/arxiv-2409.05320","url":null,"abstract":"The mountain pine beetle (MPB), a destructive pest native to Western North\u0000America, has recently extended its range into Alberta, Canada. Predicting the\u0000dispersal of MPB is challenging due to their small size and complex dispersal\u0000behavior. Because of these challenges, estimates of MPB's typical dispersal\u0000distances have varied widely, ranging from 10 meters to 18 kilometers. Here, we\u0000use high-quality data from helicopter and field-crew surveys to parameterize a\u0000large number of dispersal kernels. We find that fat-tailed kernels -- those\u0000which allow for a small number of long-distance dispersal events --\u0000consistently provide the best fit to the data. Specifically, the\u0000radially-symmetric Student's t-distribution with parameters {nu} = 0.012 and\u0000{rho} = 1.45 stands out as parsimonious and user-friendly; this model predicts\u0000a median dispersal distance of 60 meters, but with the 95th percentile of\u0000dispersers travelling nearly 5 kilometers. The best-fitting mathematical models\u0000have biological interpretations. The Student's t-distribution, derivable as a\u0000mixture of diffusive processes with varying settling times, is consistent with\u0000observations that most beetles fly short distances while few travel far;\u0000early-emerging beetles fly farther; and larger beetles from larger trees\u0000exhibit greater variance in flight distance. Finally, we explain why other\u0000studies have found such a wide variation in the length scale in MPB dispersal,\u0000and we demonstrate that long-distance dispersal events are critical for\u0000modelling MPB range expansion.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mapping Evolution of Molecules Across Biochemistry with Assembly Theory 用组装理论绘制整个生物化学领域的分子演化图谱

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-09 DOI: arxiv-2409.05993

Sebastian Pagel, Abhishek Sharma, Leroy Cronin

{"title":"Mapping Evolution of Molecules Across Biochemistry with Assembly Theory","authors":"Sebastian Pagel, Abhishek Sharma, Leroy Cronin","doi":"arxiv-2409.05993","DOIUrl":"https://doi.org/arxiv-2409.05993","url":null,"abstract":"Evolution is often understood through genetic mutations driving changes in an\u0000organism's fitness, but there is potential to extend this understanding beyond\u0000the genetic code. We propose that natural products - complex molecules central\u0000to Earth's biochemistry can be used to uncover evolutionary mechanisms beyond\u0000genes. By applying Assembly Theory (AT), which views selection as a process not\u0000limited to biological systems, we can map and measure evolutionary forces in\u0000these molecules. AT enables the exploration of the assembly space of natural\u0000products, demonstrating how the principles of the selfish gene apply to these\u0000complex chemical structures, selecting vastly improbable and complex molecules\u0000from a vast space of possibilities. By comparing natural products with a\u0000broader molecular database, we can assess the degree of evolutionary\u0000contingency, providing insight into how molecular novelty emerges and persists.\u0000This approach not only quantifies evolutionary selection at the molecular level\u0000but also offers a new avenue for drug discovery by exploring the molecular\u0000assembly spaces of natural products. Our method provides a fresh perspective on\u0000measuring the evolutionary processes both, shaping and being read out, by the\u0000molecular imprint of selection.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Stochastic Gause predator-prey model: noise-induced extinctions and invariance 随机高斯捕食者-猎物模型：噪声引起的灭绝和不变性

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-08 DOI: arxiv-2409.05237

Leon Alexander Valencia, Ph. D, Jorge Mario Ramirez Osorio, Jorge Andres Sanchez

引用次数: 0

Evolutionary emergence of biological intelligence 生物智能的进化

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-07 DOI: arxiv-2409.04928

Takuya Isomura

{"title":"Evolutionary emergence of biological intelligence","authors":"Takuya Isomura","doi":"arxiv-2409.04928","DOIUrl":"https://doi.org/arxiv-2409.04928","url":null,"abstract":"Characterising the intelligence of biological organisms is challenging. This\u0000work considers intelligent algorithms developed evolutionarily within neural\u0000systems. Mathematical analyses unveil a natural equivalence between canonical\u0000neural networks, variational Bayesian inference under a class of partially\u0000observable Markov decision processes, and differentiable Turing machines, by\u0000showing that they minimise the shared Helmholtz energy. Consequently, canonical\u0000neural networks can biologically plausibly equip Turing machines and conduct\u0000variational Bayesian inferences of external Turing machines in the environment.\u0000Applying Helmholtz energy minimisation at the species level facilitates\u0000deriving active Bayesian model selection inherent in natural selection,\u0000resulting in the emergence of adaptive algorithms. In particular, canonical\u0000neural networks with two mental actions can separately learn transition\u0000mappings of multiple Turing machines. These propositions were corroborated by\u0000numerical simulations of algorithm implementation and neural network evolution.\u0000These notions offer a universal characterisation of biological intelligence\u0000emerging from evolution in terms of Bayesian model selection and belief\u0000updating.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"8 3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Shear and transport in a flow environment determine spatial patterns and population dynamics in a model of nonlocal ecological competition 流动环境中的剪切力和迁移决定了非局部生态竞争模型中的空间模式和种群动态

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-06 DOI: arxiv-2409.04268

Nathan O. Silvano, João Valeriano, Emilio Hernández-García, Cristóbal López, Ricardo Martinez-Garcia

{"title":"Shear and transport in a flow environment determine spatial patterns and population dynamics in a model of nonlocal ecological competition","authors":"Nathan O. Silvano, João Valeriano, Emilio Hernández-García, Cristóbal López, Ricardo Martinez-Garcia","doi":"arxiv-2409.04268","DOIUrl":"https://doi.org/arxiv-2409.04268","url":null,"abstract":"Populations very often self-organize into regular spatial patterns with\u0000important ecological and evolutionary consequences. Yet, most existing models\u0000neglect the effect that external biophysical drivers might have both on pattern\u0000formation and the spatiotemporal population dynamics once patterns form. Here,\u0000we investigate the effect of environmental flows on pattern formation and\u0000population dynamics using a spatially nonlocal logistic model (or\u0000Fisher-Kolmogorov equation) coupled to a simple shear and a Rankine vortex\u0000flow. We find that, whereas population abundance generally decreases with\u0000increasing flow intensity, the effect of the flow on the pattern instability\u0000depends on the spatial structure of the flow velocity field. This result shows\u0000that the velocity field interacts with the spatial feedbacks responsible for\u0000pattern formation in non-trivial ways, leading to a variety of spatiotemporal\u0000population dynamics regimes in which the total population abundance can exhibit\u0000either regular oscillations with a characteristic frequency or more erratic\u0000dynamics without a well-defined period. More generally, the diversity of\u0000spatiotemporal population dynamics caused by the interplay between\u0000self-organizing feedbacks and environmental flows highlights the importance of\u0000incorporating environmental and biophysical processes when studying both\u0000ecological pattern formation and its consequences.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Galled Perfect Transfer Networks 瘿完美传输网络

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-05 DOI: arxiv-2409.03935

Alitzel López Sánchez, Manuel Lafond

{"title":"Galled Perfect Transfer Networks","authors":"Alitzel López Sánchez, Manuel Lafond","doi":"arxiv-2409.03935","DOIUrl":"https://doi.org/arxiv-2409.03935","url":null,"abstract":"Predicting horizontal gene transfers often requires comparative sequence\u0000data, but recent work has shown that character-based approaches could also be\u0000useful for this task. Notably, perfect transfer networks (PTN) explain the\u0000character diversity of a set of taxa for traits that are gained once, rarely\u0000lost, but that can be transferred laterally. Characterizing the structure of\u0000such characters is an important step towards understanding more complex\u0000characters. Although efficient algorithms can infer such networks from\u0000character data, they can sometimes predict overly complicated transfer\u0000histories. With the goal of recovering the simplest possible scenarios in this\u0000model, we introduce galled perfect transfer networks, which are PTNs that are\u0000galled trees. Such networks are useful for characters that are incompatible in\u0000terms of tree-like evolution, but that do fit in an almost-tree scenario. We\u0000provide polynomial-time algorithms for two problems: deciding whether one can\u0000add transfer edges to a tree to transform it into a galled PTN, and deciding\u0000whether a set of characters are galled-compatible, that is, they can be\u0000explained by some galled PTN. We also analyze a real dataset comprising of a\u0000bacterial species trees and KEGG functions as characters, and derive several\u0000conclusions on the difficulty of explaining characters in a galled tree, which\u0000provide several directions for future research.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A graphical exploration of the relationship between parasite aggregation indices 寄生虫聚集指数之间关系的图解探索

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-05 DOI: arxiv-2409.03186

R. McVinish, R. J. G. Lester

引用次数: 0

Modelling the age distribution of longevity leaders 长寿领袖的年龄分布模型

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-05 DOI: arxiv-2409.03353

Csaba Kiss, László Németh, Bálint Vető

引用次数: 0