arXiv - QuanBio - Populations and Evolution最新文献

k-mer-based approaches to bridging pangenomics and population genetics 基于 k-聚合体的连接泛基因组学和群体遗传学的方法

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-18 DOI: arxiv-2409.11683

Miles D. Roberts, Olivia Davis, Emily B. Josephs, Robert J. Williamson

{"title":"k-mer-based approaches to bridging pangenomics and population genetics","authors":"Miles D. Roberts, Olivia Davis, Emily B. Josephs, Robert J. Williamson","doi":"arxiv-2409.11683","DOIUrl":"https://doi.org/arxiv-2409.11683","url":null,"abstract":"Many commonly studied species now have more than one chromosome-scale genome\u0000assembly, revealing a large amount of genetic diversity previously missed by\u0000approaches that map short reads to a single reference. However, many species\u0000still lack multiple reference genomes and correctly aligning references to\u0000build pangenomes is challenging, limiting our ability to study this missing\u0000genomic variation in population genetics. Here, we argue that $k$-mers are a\u0000crucial stepping stone to bridging the reference-focused paradigms of\u0000population genetics with the reference-free paradigms of pangenomics. We review\u0000current literature on the uses of $k$-mers for performing three core components\u0000of most population genetics analyses: identifying, measuring, and explaining\u0000patterns of genetic variation. We also demonstrate how different $k$-mer-based\u0000measures of genetic variation behave in population genetic simulations\u0000according to the choice of $k$, depth of sequencing coverage, and degree of\u0000data compression. Overall, we find that $k$-mer-based measures of genetic\u0000diversity scale consistently with pairwise nucleotide diversity ($pi$) up to\u0000values of about $pi = 0.025$ ($R^2 = 0.97$) for neutrally evolving\u0000populations. For populations with even more variation, using shorter $k$-mers\u0000will maintain the scalability up to at least $pi = 0.1$. Furthermore, in our\u0000simulated populations, $k$-mer dissimilarity values can be reliably\u0000approximated from counting bloom filters, highlighting a potential avenue to\u0000decreasing the memory burden of $k$-mer based genomic dissimilarity analyses.\u0000For future studies, there is a great opportunity to further develop methods to\u0000identifying selected loci using $k$-mers.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247365","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

Biological arrow of time: Emergence of tangled information hierarchies and self-modelling dynamics 生物时间之箭纠缠不清的信息层级和自我建模动态的出现

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-18 DOI: arxiv-2409.12029

Mikhail Prokopenko, Paul C. W. Davies, Michael Harré, Marcus Heisler, Zdenka Kuncic, Geraint F. Lewis, Ori Livson, Joseph T. Lizier, Fernando E. Rosas

{"title":"Biological arrow of time: Emergence of tangled information hierarchies and self-modelling dynamics","authors":"Mikhail Prokopenko, Paul C. W. Davies, Michael Harré, Marcus Heisler, Zdenka Kuncic, Geraint F. Lewis, Ori Livson, Joseph T. Lizier, Fernando E. Rosas","doi":"arxiv-2409.12029","DOIUrl":"https://doi.org/arxiv-2409.12029","url":null,"abstract":"We study open-ended evolution by focusing on computational and\u0000information-processing dynamics underlying major evolutionary transitions. In\u0000doing so, we consider biological organisms as hierarchical dynamical systems\u0000that generate regularities in their phase-spaces through interactions with\u0000their environment. These emergent information patterns can then be encoded\u0000within the organism's components, leading to self-modelling \"tangled\u0000hierarchies\". Our main conjecture is that when macro-scale patterns are encoded\u0000within micro-scale components, it creates fundamental tensions (computational\u0000inconsistencies) between what is encodable at a particular evolutionary stage\u0000and what is potentially realisable in the environment. A resolution of these\u0000tensions triggers an evolutionary transition which expands the problem-space,\u0000at the cost of generating new tensions in the expanded space, in a continual\u0000process. We argue that biological complexification can be interpreted\u0000computation-theoretically, within the G\"odel--Turing--Post recursion-theoretic\u0000framework, as open-ended generation of computational novelty. In general, this\u0000process can be viewed as a meta-simulation performed by higher-order systems\u0000that successively simulate the computation carried out by lower-order systems.\u0000This computation-theoretic argument provides a basis for hypothesising the\u0000biological arrow of time.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"190 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247364","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 weather-driven mathematical model of Culex population abundance and the impact of vector control interventions 库蚊种群数量和病媒控制干预措施影响的天气驱动数学模型

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-17 DOI: arxiv-2409.11550

Suman Bhowmick, Patrick Irwin, Kristina Lopez, Megan Lindsay Fritz, Rebecca Lee Smith

{"title":"A weather-driven mathematical model of Culex population abundance and the impact of vector control interventions","authors":"Suman Bhowmick, Patrick Irwin, Kristina Lopez, Megan Lindsay Fritz, Rebecca Lee Smith","doi":"arxiv-2409.11550","DOIUrl":"https://doi.org/arxiv-2409.11550","url":null,"abstract":"Even as the incidence of mosquito-borne diseases like West Nile Virus (WNV)\u0000in North America has risen over the past decade, effectively modelling mosquito\u0000population density or, the abundance has proven to be a persistent challenge.\u0000It is critical to capture the fluctuations in mosquito abundance across seasons\u0000in order to forecast the varying risk of disease transmission from one year to\u0000the next. We develop a process-based mechanistic weather-driven Ordinary\u0000Differential Equation (ODE) model to study the population biology of both\u0000aqueous and terrestrial stages of mosquito population. The progression of\u0000mosquito lifecycle through these stages is influenced by different factors,\u0000including temperature, daylight hours, intra-species competition and the\u0000availability of aquatic habitats. Weather-driven parameters are utilised in our\u0000work, are a combination of laboratory research and literature data. In our\u0000model, we include precipitation data as a substitute for evaluating additional\u0000mortality in the mosquito population. We compute the textit{Basic offspring\u0000number} of the associated model and perform sensitivity analysis. Finally, we\u0000employ our model to assess the effectiveness of various adulticides strategies\u0000to predict the reduction in mosquito population. This enhancement in modelling\u0000of mosquito abundance can be instrumental in guiding interventions aimed at\u0000reducing mosquito populations and mitigating mosquito-borne diseases such as\u0000the WNV.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247366","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

Dynamics of solutions to a multi-patch epidemic model with a saturation incidence mechanism 具有饱和发病机制的多斑块流行病模型的动态解

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-17 DOI: arxiv-2409.11443

Yawo Ezunkpe, Cynthia T. Nnolum, Rachidi B. Salako, Shuwen Xue

引用次数: 0

Higher-order interactions in random Lotka-Volterra communities 随机洛特卡-伏特拉群落中的高阶相互作用

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-17 DOI: arxiv-2409.10990

Laura Sidhom, Tobias Galla

引用次数: 0

Aggregation-diffusion in heterogeneous environments 异构环境中的聚合-扩散

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-16 DOI: arxiv-2409.10147

Jonathan R. Potts

{"title":"Aggregation-diffusion in heterogeneous environments","authors":"Jonathan R. Potts","doi":"arxiv-2409.10147","DOIUrl":"https://doi.org/arxiv-2409.10147","url":null,"abstract":"Aggregation-diffusion equations are foundational tools for modelling\u0000biological aggregations. Their principal use is to link the collective movement\u0000mechanisms of organisms to their emergent space use patterns in a rigorous,\u0000non-speculative way. However, most existing studies implicitly assume that\u0000organism movement is not affected by the underlying environment. In reality,\u0000the environment is a key determinant of emergent space use patterns, albeit in\u0000combination with collective aspects of motion. This work studies\u0000aggregation-diffusion equations in a heterogeneous environment in one spatial\u0000dimension. Under certain assumptions, it is possible to find exact analytic\u0000expressions for the steady-state solutions to the equation when diffusion is\u0000quadratic. Minimising the associated energy functional across these solutions\u0000provides a rapid way of determining the likely emergent space use pattern,\u0000which can be verified via numerics. This energy-minimisation procedure is\u0000applied to a simple test case, where the environment consists of a single clump\u0000of attractive resources. Here, self-attraction and resource-attraction combine\u0000to shape the emergent aggregation. Two counter-intuitive results emerge from\u0000the analytic results: (a) a non-monotonic dependence of clump width on the\u0000aggregation width, (b) a positive correlation between self-attraction strength\u0000and aggregation width when the resource attraction is strong. These are\u0000verified through numerical simulations. Overall, the study shows rigorously how\u0000environment and collective behaviour combine to shape organism space use,\u0000sometimes in counter-intuitive ways.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247402","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

Assortativity in sympatric speciation and species classification 同域物种变异和物种分类中的同源性

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-16 DOI: arxiv-2409.10466

Joao U. F. Lizarraga, Flavia M. D. Marquitti, Marcus A. M. de Aguiar

{"title":"Assortativity in sympatric speciation and species classification","authors":"Joao U. F. Lizarraga, Flavia M. D. Marquitti, Marcus A. M. de Aguiar","doi":"arxiv-2409.10466","DOIUrl":"https://doi.org/arxiv-2409.10466","url":null,"abstract":"We investigate the role of assortative mating in speciation using the\u0000sympatric model of Derrida and Higgs. The model explores the idea that genetic\u0000differences create incompatibilities between individuals, preventing mating if\u0000the number of such differences is too large. Speciation, however, only happens\u0000in this mating system if the number of genes is large. Here we show that\u0000speciation with small genome sizes can occur if assortative mating is\u0000introduced. In our model individuals are represented by three chromosomes: one\u0000responsible for reproductive compatibility, one for coding the trait on which\u0000assortativity will operate, and a neutral chromosome. Reproduction is possible\u0000if individuals are genetically similar with respect to the first chromosome,\u0000but among these compatible mating partners, the one with the most similar trait\u0000coded by the second chromosome is selected. We show that this type of\u0000assortativity facilitates speciation, which can happen with a small number of\u0000genes in the first chromosome. Species, classified according to reproductive\u0000isolation, dictated by the first chromosome, can display different traits\u0000values, as measured by the second and the third chromosomes. Therefore, species\u0000can also be identified based on similarity of the neutral trait, which works as\u0000a proxy for reproductive isolation.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247398","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

Substantial extension of the lifetime of the terrestrial biosphere 大幅延长陆地生物圈的寿命

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-16 DOI: arxiv-2409.10714

R. J. Graham, Itay Halevy, Dorian Abbot

{"title":"Substantial extension of the lifetime of the terrestrial biosphere","authors":"R. J. Graham, Itay Halevy, Dorian Abbot","doi":"arxiv-2409.10714","DOIUrl":"https://doi.org/arxiv-2409.10714","url":null,"abstract":"Approximately one billion years (Gyr) in the future, as the Sun brightens,\u0000Earth's carbonate-silicate cycle is expected to drive CO$_2$ below the minimum\u0000level required by vascular land plants, eliminating most macroscopic land life.\u0000Here, we couple global-mean models of temperature- and CO$_2$-dependent plant\u0000productivity for C$_3$ and C$_4$ plants, silicate weathering, and climate to\u0000re-examine the time remaining for terrestrial plants. If weathering is weakly\u0000temperature-dependent (as recent data suggest) and/or strongly\u0000CO$_2$-dependent, we find that the interplay between climate, productivity, and\u0000weathering causes the future luminosity-driven CO$_2$ decrease to slow and\u0000temporarily reverse, averting plant CO$_2$ starvation. This dramatically\u0000lengthens plant survival from 1 Gyr up to $sim$1.6-1.86 Gyr, until extreme\u0000temperatures halt photosynthesis, suggesting a revised kill mechanism for land\u0000plants and potential doubling of the future lifespan of Earth's land\u0000macrobiota. An increased future lifespan for the complex biosphere may imply\u0000that Earth life had to achieve a smaller number of ``hard steps'' (unlikely\u0000evolutionary transitions) to produce intelligent life than previously\u0000estimated. These results also suggest that complex photosynthetic land life on\u0000Earth and exoplanets may be able to persist until the onset of the moist\u0000greenhouse transition.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"29 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247397","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

Foundations of ecological and evolutionary change 生态和进化变化的基础

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-16 DOI: arxiv-2409.10766

A. Bradley Duthie, Victor J. Luque

引用次数: 0

Opponent Shaping for Antibody Development 为抗体开发塑造对手

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-16 DOI: arxiv-2409.10588

Sebastian Towers, Aleksandra Kalisz, Alicia Higueruelo, Francesca Vianello, Ming-Han Chloe Tsai, Harrison Steel, Jakob N. Foerster

{"title":"Opponent Shaping for Antibody Development","authors":"Sebastian Towers, Aleksandra Kalisz, Alicia Higueruelo, Francesca Vianello, Ming-Han Chloe Tsai, Harrison Steel, Jakob N. Foerster","doi":"arxiv-2409.10588","DOIUrl":"https://doi.org/arxiv-2409.10588","url":null,"abstract":"Anti-viral therapies are typically designed or evolved towards the current\u0000strains of a virus. In learning terms, this corresponds to a myopic best\u0000response, i.e., not considering the possible adaptive moves of the opponent.\u0000However, therapy-induced selective pressures act on viral antigens to drive the\u0000emergence of mutated strains, against which initial therapies have reduced\u0000efficacy. To motivate our work, we consider antibody designs that target not\u0000only the current viral strains but also the wide range of possible future\u0000variants that the virus might evolve into under the evolutionary pressure\u0000exerted by said antibodies. Building on a computational model of binding\u0000between antibodies and viral antigens (the Absolut! framework), we design and\u0000implement a genetic simulation of the viral evolutionary escape. Crucially,\u0000this allows our antibody optimisation algorithm to consider and influence the\u0000entire escape curve of the virus, i.e. to guide (or ''shape'') the viral\u0000evolution. This is inspired by opponent shaping which, in general-sum learning,\u0000accounts for the adaptation of the co-player rather than playing a myopic best\u0000response. Hence we call the optimised antibodies shapers. Within our\u0000simulations, we demonstrate that our shapers target both current and simulated\u0000future viral variants, outperforming the antibodies chosen in a myopic way.\u0000Furthermore, we show that shapers exert specific evolutionary pressure on the\u0000virus compared to myopic antibodies. Altogether, shapers modify the\u0000evolutionary trajectories of viral strains and minimise the viral escape\u0000compared to their myopic counterparts. While this is a simple model, we hope\u0000that our proposed paradigm will enable the discovery of better long-lived\u0000vaccines and antibody therapies in the future, enabled by rapid advancements in\u0000the capabilities of simulation tools.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247396","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