arXiv - QuanBio - Populations and Evolution最新文献_第2页

Exact solution for a discrete-time SIR model 离散时间 SIR 模型的精确解

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-13 DOI: arxiv-2409.09157

Márcia Lemos-Silva, Sandra Vaz, Delfim F. M. Torres

引用次数: 0

Effects of pristine and photoaged tire wear particles and their leachable additives on key nitrogen removal processes and nitrous oxide accumulation in estuarine sediments 原始和光老化轮胎磨损颗粒及其可浸出添加剂对河口沉积物关键脱氮过程和氧化亚氮积累的影响

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-13 DOI: arxiv-2409.08739

Jinyu Ye, Yuan Gao, Huan Gao, Qingqing Zhao, Minjie Zhou, Xiangdong Xue, Meng Shi

{"title":"Effects of pristine and photoaged tire wear particles and their leachable additives on key nitrogen removal processes and nitrous oxide accumulation in estuarine sediments","authors":"Jinyu Ye, Yuan Gao, Huan Gao, Qingqing Zhao, Minjie Zhou, Xiangdong Xue, Meng Shi","doi":"arxiv-2409.08739","DOIUrl":"https://doi.org/arxiv-2409.08739","url":null,"abstract":"Global estuaries and coastal regions, acting as critical interfaces for\u0000mitigating nitrogen flux to marine, concurrently contend with contamination\u0000from tire wear particles (TWPs). However, the effects of pristine and photoaged\u0000TWP (P-TWP and A-TWP) and their leachates (P-TWPL and A-TWPL) on key nitrogen\u0000removal processes in estuarine sediments remain unclear. This study explored\u0000the responses of denitrification rate, anammox rate, and nitrous oxide (N2O)\u0000accumulation to P-TWP, A-TWP, P-TWPL, and A-TWPL exposures in estuarine\u0000sediments, and assessed the potential biotoxic substances in TWPL. Results\u0000indicate that P-TWP inhibited the denitrification rate and increased N2O\u0000accumulation without significantly impacting the anammox rate. A-TWP\u0000intensified the denitrification rate inhibition by further reducing narG gene\u0000abundance and NAR activity, and also decreased the hzo gene abundance, HZO\u0000activity, and Candidatus Kuenenia abundance, thereby slowing the anammox rate.\u0000N2O accumulation was lower after A-TWP exposure than P-TWP, with the NIR/NOS\u0000and NOR/NOS activity ratios closely associated with N2O accumulation. Batch\u0000experiments indicated that photoaging promoted Zn release from TWPL,\u0000significantly contributing to the inhibited denitrification rate and increased\u0000N2O accumulation by TWP. In addition, TWP drives changes in microbial community\u0000structure through released additives, with the abundance of DNB and AnAOB\u0000closely linked to the Zn, Mn, and As concentrations in TWPL. This study offers\u0000insights into assessing the environmental risks of TWPs in estuarine\u0000ecosystems.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247403","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

Highly conserved sequence-specific double-stranded DNA binding networks contributing to divergent genomic evolution of human and chimpanzee brain development 高度保守的序列特异性双链 DNA 结合网络促成了人类和黑猩猩大脑发育的基因组进化差异

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-12 DOI: arxiv-2409.07812

Gennadi Glinsky

{"title":"Highly conserved sequence-specific double-stranded DNA binding networks contributing to divergent genomic evolution of human and chimpanzee brain development","authors":"Gennadi Glinsky","doi":"arxiv-2409.07812","DOIUrl":"https://doi.org/arxiv-2409.07812","url":null,"abstract":"Emergence during mammalian evolution of concordant and divergent traits of\u0000genomic regulatory networks encompassing ubiquitous, qualitatively nearly\u0000identical yet quantitatively distinct arrays of sequences of transcription\u0000factor binding sites (TFBS) for 716 proteins is reported. A vast majority of\u0000TFs (770 of 716; 98%) comprising protein constituents of these networks appear\u0000to share common Gene Ontology (GO) features of sequence-specific\u0000double-stranded DNA binding (GO: 1990837). Genome-wide and individual\u0000chromosome-level analyses of 17,935 ATAC-seq-defined brain development\u0000regulatory regions (BDRRs) revealed nearly universal representations of TFBS\u0000for TF-constituents of these networks, TFBS densities of which appear\u0000consistently higher within thousands BDRRs of Modern Humans compare to\u0000Chimpanzee. Transposable elements (TE), including LTR/HERV, SINE/Alu, SVA, and\u0000LINE families, appear to harbor and spread genome-wide consensus regulatory\u0000nodes of identified herein highly conserved sequence-specific double-stranded\u0000DNA binding networks, selections of TFBS panels of which manifest individual\u0000chromosome-specific profiles and species-specific divergence patterns.\u0000Collectively, observations reported in this contribution highlight a previously\u0000unrecognized essential function of human genomic DNA sequences encoded by TE in\u0000providing genome-wide regulatory seed templates of highly conserved\u0000sequence-specific double-stranded DNA binding networks likely contributing to\u0000continuing divergent genomic evolution of human and chimpanzee brain\u0000development.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204255","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

Spatial structure facilitates evolutionary rescue by cost-free drug resistance 空间结构有利于无成本抗药性的进化救援

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-11 DOI: arxiv-2409.07377

Cecilia Fruet, Ella Linxia Müller, Claude Loverdo, Anne-Florence Bitbol

{"title":"Spatial structure facilitates evolutionary rescue by cost-free drug resistance","authors":"Cecilia Fruet, Ella Linxia Müller, Claude Loverdo, Anne-Florence Bitbol","doi":"arxiv-2409.07377","DOIUrl":"https://doi.org/arxiv-2409.07377","url":null,"abstract":"Bacterial populations often have complex spatial structures, which can impact\u0000their evolution. Here, we study how spatial structure affects the evolution of\u0000antibiotic resistance in a bacterial population. We consider a minimal model of\u0000spatially structured populations where all demes (i.e., subpopulations) are\u0000identical and connected to each other by identical migration rates. We show\u0000that spatial structure can facilitate the survival of a bacterial population to\u0000antibiotic treatment, starting from a sensitive inoculum. Indeed, the bacterial\u0000population can be rescued if antibiotic resistant mutants appear and are\u0000present when drug is added, and spatial structure can impact the fate of these\u0000mutants and the probability that they are present. Specifically, if the\u0000mutation that provides resistance is neutral or effectively neutral, its\u0000probability of fixation is increased in smaller populations. This promotes\u0000local fixation of resistant mutants in the structured population, which\u0000facilitates evolutionary rescue by cost-free drug resistance. Once the\u0000population is rescued by resistance, migrations allow resistant mutants to\u0000spread in all demes. Our main results extend to the case where there are\u0000resistant mutants in the inoculum, and to more complex spatial structures. They\u0000also extend to resistant mutants that carry a fitness cost, although the\u0000timescales involved are longer.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204259","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

When can few-species models describe dynamics within a complex community? 少物种模型何时能描述复杂群落的动态？

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-10 DOI: arxiv-2409.06379

Stav Marcus, Guy Bunin

{"title":"When can few-species models describe dynamics within a complex community?","authors":"Stav Marcus, Guy Bunin","doi":"arxiv-2409.06379","DOIUrl":"https://doi.org/arxiv-2409.06379","url":null,"abstract":"Dynamics of species' abundances in ecological communities are often described\u0000using models that only account for a few species. It is not clear when and why\u0000this would be possible, as most species form part of diverse ecological\u0000communities, with many species that are not included in these few-variable\u0000descriptions. We study theoretically the circumstances under which the use of\u0000such models is justified, by considering the dynamics of a small set of focal\u0000species embedded within a diverse, sparsely-interacting community. We find that\u0000in some cases the focal species' dynamics are high-dimensional, making a\u0000few-variable description impossible. In other cases we show that such a\u0000description exists, even though the effect of the surrounding community on the\u0000focal species' dynamics is not small or simple. We give two different methods\u0000for approximating the dynamics, by using effective parameters that depend on\u0000the surrounding community, which are relevant under different assumptions on\u0000the relation between the explicitly modeled focal species and the rest of the\u0000species. Both methods work surprisingly well in many of the cases that we\u0000check, with effective dynamics that are often very similar and sometimes\u0000indistinguishable from the true dynamics, even when the effect of the community\u0000on the focal species is significant.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204257","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

Indirect reciprocity under opinion synchronization 意见同步下的间接互惠

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-09-09 DOI: arxiv-2409.05551

Yohsuke Murase, Christian Hilbe

{"title":"Indirect reciprocity under opinion synchronization","authors":"Yohsuke Murase, Christian Hilbe","doi":"arxiv-2409.05551","DOIUrl":"https://doi.org/arxiv-2409.05551","url":null,"abstract":"Indirect reciprocity is a key explanation for the exceptional magnitude of\u0000cooperation among humans. This literature suggests that a large proportion of\u0000human cooperation is driven by social norms and individuals' incentives to\u0000maintain a good reputation. This intuition has been formalized with two types\u0000of models. In public assessment models, all community members are assumed to\u0000agree on each others' reputations; in private assessment models, people may\u0000have disagreements. Both types of models aim to understand the interplay of\u0000social norms and cooperation. Yet their results can be vastly different. Public\u0000assessment models argue that cooperation can evolve easily, and that the most\u0000effective norms tend to be stern. Private assessment models often find\u0000cooperation to be unstable, and successful norms show some leniency. Here, we\u0000propose a model that can organize these differing results within a single\u0000framework. We show that the stability of cooperation depends on a single\u0000quantity: the extent to which individual opinions turn out to be correlated.\u0000This correlation is determined by a group's norms and the structure of social\u0000interactions. In particular, we prove that no cooperative norm is\u0000evolutionarily stable when individual opinions are statistically independent.\u0000These results have important implications for our understanding of cooperation,\u0000conformity, and polarization.","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":"142204262","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

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