Cooperation is fundamental to human societies, and indirect reciprocity, where individuals cooperate to build a positive reputation for future benefits, plays a key role in promoting it. Previous theoretical and experimental studies have explored both the effectiveness and limitations of costly punishment in sustaining cooperation. While empirical observations show that costly punishment by third parties is common, some theoretical models suggest it may not be effective in the context of indirect reciprocity, raising doubts about its potential to enhance cooperation. In this study, we theoretically investigate the conditions under which costly punishment is effective. Building on a previous model, we introduce a new type of error in perceiving actions, where defection may be mistakenly perceived as cooperation. This extension models a realistic scenario where defectors have a strong incentive to disguise their defection as cooperation. Our analysis reveals that when defection is difficult to detect, norms involving costly punishment can emerge as the most efficient evolutionarily stable strategies. These findings demonstrate that costly punishment can play a crucial role in promoting cooperation within indirect reciprocity.
{"title":"Costly punishment sustains indirect reciprocity under low defection detectability","authors":"Yohsuke Murase","doi":"arxiv-2409.09701","DOIUrl":"https://doi.org/arxiv-2409.09701","url":null,"abstract":"Cooperation is fundamental to human societies, and indirect reciprocity,\u0000where individuals cooperate to build a positive reputation for future benefits,\u0000plays a key role in promoting it. Previous theoretical and experimental studies\u0000have explored both the effectiveness and limitations of costly punishment in\u0000sustaining cooperation. While empirical observations show that costly\u0000punishment by third parties is common, some theoretical models suggest it may\u0000not be effective in the context of indirect reciprocity, raising doubts about\u0000its potential to enhance cooperation. In this study, we theoretically\u0000investigate the conditions under which costly punishment is effective. Building\u0000on a previous model, we introduce a new type of error in perceiving actions,\u0000where defection may be mistakenly perceived as cooperation. This extension\u0000models a realistic scenario where defectors have a strong incentive to disguise\u0000their defection as cooperation. Our analysis reveals that when defection is\u0000difficult to detect, norms involving costly punishment can emerge as the most\u0000efficient evolutionarily stable strategies. These findings demonstrate that\u0000costly punishment can play a crucial role in promoting cooperation within\u0000indirect reciprocity.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247401","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}
Understanding how species interactions shape biodiversity is a core challenge in ecology. While much focus has been on long-term stability, there is rising interest in transient dynamics-the short-lived periods when ecosystems respond to disturbances and adjust toward stability. These transitions are crucial for predicting ecosystem reactions and guiding effective conservation. Our study introduces a model that blends pairwise and higher-order interactions, offering a more realistic view of natural ecosystems. We find pairwise interactions slow the journey to stability, while higher-order interactions speed it up. This model provides fresh insights into ecosystem resilience and recovery, helping improve strategies for managing species and ecological disruptions.
{"title":"How Combined Pairwise and Higher-Order Interactions Shape Transient Dynamics","authors":"Sourin Chatterjee, Sayantan Nag Chowdhury","doi":"arxiv-2409.09521","DOIUrl":"https://doi.org/arxiv-2409.09521","url":null,"abstract":"Understanding how species interactions shape biodiversity is a core challenge\u0000in ecology. While much focus has been on long-term stability, there is rising\u0000interest in transient dynamics-the short-lived periods when ecosystems respond\u0000to disturbances and adjust toward stability. These transitions are crucial for\u0000predicting ecosystem reactions and guiding effective conservation. Our study\u0000introduces a model that blends pairwise and higher-order interactions, offering\u0000a more realistic view of natural ecosystems. We find pairwise interactions slow\u0000the journey to stability, while higher-order interactions speed it up. This\u0000model provides fresh insights into ecosystem resilience and recovery, helping\u0000improve strategies for managing species and ecological disruptions.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"64 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247399","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}
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological information encoded in these non-standard nucleotides presents new challenges, as traditional sequencing technologies are unable to recognize or interpret novel base pairings. In this perspective, we explore the potential of nanopore sequencing, which is uniquely suited to decipher both standard and non-standard nucleotides by directly measuring the biophysical properties of nucleic acids. Nanopore technology offers real-time, long-read sequencing without the need for amplification or synthesis, making it particularly advantageous for expanded genetic systems like Artificially Expanded Genetic Information Systems (AEGIS). We discuss how the adaptability of nanopore sequencing and advancements in data processing can unlock the potential of these synthetic genomes and open new frontiers in understanding and utilizing expanded genetic codes.
{"title":"The Future of Decoding Non-Standard Nucleotides: Leveraging Nanopore Sequencing for Expanded Genetic Codes","authors":"Hyunjin Shim","doi":"arxiv-2409.09314","DOIUrl":"https://doi.org/arxiv-2409.09314","url":null,"abstract":"Expanding genetic codes from natural standard nucleotides to artificial\u0000non-standard nucleotides marks a significant advancement in synthetic biology,\u0000with profound implications for biotechnology and medicine. Decoding the\u0000biological information encoded in these non-standard nucleotides presents new\u0000challenges, as traditional sequencing technologies are unable to recognize or\u0000interpret novel base pairings. In this perspective, we explore the potential of\u0000nanopore sequencing, which is uniquely suited to decipher both standard and\u0000non-standard nucleotides by directly measuring the biophysical properties of\u0000nucleic acids. Nanopore technology offers real-time, long-read sequencing\u0000without the need for amplification or synthesis, making it particularly\u0000advantageous for expanded genetic systems like Artificially Expanded Genetic\u0000Information Systems (AEGIS). We discuss how the adaptability of nanopore\u0000sequencing and advancements in data processing can unlock the potential of\u0000these synthetic genomes and open new frontiers in understanding and utilizing\u0000expanded genetic codes.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"196 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247400","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}
Márcia Lemos-Silva, Sandra Vaz, Delfim F. M. Torres
We propose a nonstandard finite difference scheme for the Susceptible-Infected-Removed (SIR) continuous model. We prove that our discretized system is dynamically consistent with its continuous counterpart and we derive its exact solution. We end with the analysis of the long-term behavior of susceptible, infected and removed individuals, illustrating our results with examples. In contrast with the SIR discrete-time model available in the literature, our new model is simultaneously mathematically and biologically sound.
我们针对易感-感染-移除（SIR）连续模型提出了一种非标准有限差分方案。我们证明了我们的离散化系统与其连续对应系统在动态上是一致的，并推导出了其精确解。最后，我们分析了易感个体、受感染个体和被移除个体的长期行为，并用实例说明了我们的结果。与文献中的 SIR 离散时模型相比，我们的新模型在数学和生物学上都是合理的。
{"title":"Exact solution for a discrete-time SIR model","authors":"Márcia Lemos-Silva, Sandra Vaz, Delfim F. M. Torres","doi":"arxiv-2409.09157","DOIUrl":"https://doi.org/arxiv-2409.09157","url":null,"abstract":"We propose a nonstandard finite difference scheme for the\u0000Susceptible-Infected-Removed (SIR) continuous model. We prove that our\u0000discretized system is dynamically consistent with its continuous counterpart\u0000and we derive its exact solution. We end with the analysis of the long-term\u0000behavior of susceptible, infected and removed individuals, illustrating our\u0000results with examples. In contrast with the SIR discrete-time model available\u0000in the literature, our new model is simultaneously mathematically and\u0000biologically sound.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247405","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}
Jinyu Ye, Yuan Gao, Huan Gao, Qingqing Zhao, Minjie Zhou, Xiangdong Xue, Meng Shi
Global estuaries and coastal regions, acting as critical interfaces for mitigating nitrogen flux to marine, concurrently contend with contamination from tire wear particles (TWPs). However, the effects of pristine and photoaged TWP (P-TWP and A-TWP) and their leachates (P-TWPL and A-TWPL) on key nitrogen removal processes in estuarine sediments remain unclear. This study explored the responses of denitrification rate, anammox rate, and nitrous oxide (N2O) accumulation to P-TWP, A-TWP, P-TWPL, and A-TWPL exposures in estuarine sediments, and assessed the potential biotoxic substances in TWPL. Results indicate that P-TWP inhibited the denitrification rate and increased N2O accumulation without significantly impacting the anammox rate. A-TWP intensified the denitrification rate inhibition by further reducing narG gene abundance and NAR activity, and also decreased the hzo gene abundance, HZO activity, and Candidatus Kuenenia abundance, thereby slowing the anammox rate. N2O accumulation was lower after A-TWP exposure than P-TWP, with the NIR/NOS and NOR/NOS activity ratios closely associated with N2O accumulation. Batch experiments indicated that photoaging promoted Zn release from TWPL, significantly contributing to the inhibited denitrification rate and increased N2O accumulation by TWP. In addition, TWP drives changes in microbial community structure through released additives, with the abundance of DNB and AnAOB closely linked to the Zn, Mn, and As concentrations in TWPL. This study offers insights into assessing the environmental risks of TWPs in estuarine ecosystems.
{"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}
Emergence during mammalian evolution of concordant and divergent traits of genomic regulatory networks encompassing ubiquitous, qualitatively nearly identical yet quantitatively distinct arrays of sequences of transcription factor binding sites (TFBS) for 716 proteins is reported. A vast majority of TFs (770 of 716; 98%) comprising protein constituents of these networks appear to share common Gene Ontology (GO) features of sequence-specific double-stranded DNA binding (GO: 1990837). Genome-wide and individual chromosome-level analyses of 17,935 ATAC-seq-defined brain development regulatory regions (BDRRs) revealed nearly universal representations of TFBS for TF-constituents of these networks, TFBS densities of which appear consistently higher within thousands BDRRs of Modern Humans compare to Chimpanzee. Transposable elements (TE), including LTR/HERV, SINE/Alu, SVA, and LINE families, appear to harbor and spread genome-wide consensus regulatory nodes of identified herein highly conserved sequence-specific double-stranded DNA binding networks, selections of TFBS panels of which manifest individual chromosome-specific profiles and species-specific divergence patterns. Collectively, observations reported in this contribution highlight a previously unrecognized essential function of human genomic DNA sequences encoded by TE in providing genome-wide regulatory seed templates of highly conserved sequence-specific double-stranded DNA binding networks likely contributing to continuing divergent genomic evolution of human and chimpanzee brain development.
据报道，在哺乳动物的进化过程中，出现了基因组调控网络的一致性和差异性特征，这些网络包括 716 个蛋白质的转录因子结合位点（TFBS）序列阵列，它们无处不在，在质量上几乎相同，但在数量上却各不相同。构成这些网络蛋白质成分的绝大多数 TFs（716 个中的 770 个；98%）似乎具有基因本体（Gene Ontology，GO）的共同特征，即序列特异性双链 DNA 结合（GO：1990837）。对 17,935 个 ATAC-seq 定义的脑发育调控区（BDRRs）进行的全基因组和单个染色体水平的分析表明，这些网络中的 TF 成分的 TFBS 几乎具有普遍的代表性，与黑猩猩相比，现代人的数千个 BDRRs 中的 TFBS 密度似乎一直较高。包括LTR/HERV、SINE/Alu、SVA和LINE家族在内的可转座元件（TE）似乎包藏并传播着这里所发现的高度保守的序列特异性双链DNA结合网络的全基因组共识调控节点，其中的TFBS面板选择表现出个体染色体特异性特征和物种特异性分化模式。总之，本研究报告中的观察结果突显了由 TE 编码的人类基因组 DNA 序列在提供全基因组高度保守序列特异性双链 DNA 结合网络的调控种子模板方面具有以前未曾认识到的重要功能，这很可能有助于人类和黑猩猩大脑发育的持续差异基因组进化。
{"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}
Cecilia Fruet, Ella Linxia Müller, Claude Loverdo, Anne-Florence Bitbol
Bacterial populations often have complex spatial structures, which can impact their evolution. Here, we study how spatial structure affects the evolution of antibiotic resistance in a bacterial population. We consider a minimal model of spatially structured populations where all demes (i.e., subpopulations) are identical and connected to each other by identical migration rates. We show that spatial structure can facilitate the survival of a bacterial population to antibiotic treatment, starting from a sensitive inoculum. Indeed, the bacterial population can be rescued if antibiotic resistant mutants appear and are present when drug is added, and spatial structure can impact the fate of these mutants and the probability that they are present. Specifically, if the mutation that provides resistance is neutral or effectively neutral, its probability of fixation is increased in smaller populations. This promotes local fixation of resistant mutants in the structured population, which facilitates evolutionary rescue by cost-free drug resistance. Once the population is rescued by resistance, migrations allow resistant mutants to spread in all demes. Our main results extend to the case where there are resistant mutants in the inoculum, and to more complex spatial structures. They also extend to resistant mutants that carry a fitness cost, although the timescales involved are longer.
{"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}
Vladimir R. V. Assis, Nazareno G. F. Medeiros, Evandro N. Silva, Alexandre Colato, Ana T. C. Silva
We studied a mean-field predator-prey model with aging to simulate the mbox{interaction} between aphids (textit{Toxoptera aurantii}) and syrphid larvae in mbox{cacao} farms in Ilheus, Bahia. Based on the classical predator-prey model, we mbox{propose} a system of differential equations with three rate equations. mbox{Unlike} the original Lotka-Volterra model, our model includes two aphid population classes: juveniles (non-breeding) and adult females (asexually breeding). We obtained steady-state solutions for juvenile and adult populations by mbox{analyzing} the stability of the fixed points as a function of model mbox{parameters}. The results show that the absorbing state (zero prey population) is always possible, but not consistently stable. A nonzero stationary solution is achievable with appropriate parameter values. Using phase diagrams, we analyzed the mbox{stationary} solution, providing a comprehensive understanding of the dynamics involved. Simulations on complete graphs yielded results closely matching the differential equations. We also performed simulations on random networks to highlight the influence of network topology on system behavior.
{"title":"Why aphids are not pests in cacao? An approach based on a predator-prey model with aging","authors":"Vladimir R. V. Assis, Nazareno G. F. Medeiros, Evandro N. Silva, Alexandre Colato, Ana T. C. Silva","doi":"arxiv-2409.06861","DOIUrl":"https://doi.org/arxiv-2409.06861","url":null,"abstract":"We studied a mean-field predator-prey model with aging to simulate the\u0000mbox{interaction} between aphids (textit{Toxoptera aurantii}) and syrphid\u0000larvae in mbox{cacao} farms in Ilheus, Bahia. Based on the classical\u0000predator-prey model, we mbox{propose} a system of differential equations with\u0000three rate equations. mbox{Unlike} the original Lotka-Volterra model, our\u0000model includes two aphid population classes: juveniles (non-breeding) and adult\u0000females (asexually breeding). We obtained steady-state solutions for juvenile\u0000and adult populations by mbox{analyzing} the stability of the fixed points as\u0000a function of model mbox{parameters}. The results show that the absorbing\u0000state (zero prey population) is always possible, but not consistently stable. A\u0000nonzero stationary solution is achievable with appropriate parameter values.\u0000Using phase diagrams, we analyzed the mbox{stationary} solution, providing a\u0000comprehensive understanding of the dynamics involved. Simulations on complete\u0000graphs yielded results closely matching the differential equations. We also\u0000performed simulations on random networks to highlight the influence of network\u0000topology on system behavior.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204256","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}
Dynamics of species' abundances in ecological communities are often described using models that only account for a few species. It is not clear when and why this would be possible, as most species form part of diverse ecological communities, with many species that are not included in these few-variable descriptions. We study theoretically the circumstances under which the use of such models is justified, by considering the dynamics of a small set of focal species embedded within a diverse, sparsely-interacting community. We find that in some cases the focal species' dynamics are high-dimensional, making a few-variable description impossible. In other cases we show that such a description exists, even though the effect of the surrounding community on the focal species' dynamics is not small or simple. We give two different methods for approximating the dynamics, by using effective parameters that depend on the surrounding community, which are relevant under different assumptions on the relation between the explicitly modeled focal species and the rest of the species. Both methods work surprisingly well in many of the cases that we check, with effective dynamics that are often very similar and sometimes indistinguishable from the true dynamics, even when the effect of the community on the focal species is significant.
{"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}
Indirect reciprocity is a key explanation for the exceptional magnitude of cooperation among humans. This literature suggests that a large proportion of human cooperation is driven by social norms and individuals' incentives to maintain a good reputation. This intuition has been formalized with two types of models. In public assessment models, all community members are assumed to agree on each others' reputations; in private assessment models, people may have disagreements. Both types of models aim to understand the interplay of social norms and cooperation. Yet their results can be vastly different. Public assessment models argue that cooperation can evolve easily, and that the most effective norms tend to be stern. Private assessment models often find cooperation to be unstable, and successful norms show some leniency. Here, we propose a model that can organize these differing results within a single framework. We show that the stability of cooperation depends on a single quantity: the extent to which individual opinions turn out to be correlated. This correlation is determined by a group's norms and the structure of social interactions. In particular, we prove that no cooperative norm is evolutionarily stable when individual opinions are statistically independent. These results have important implications for our understanding of cooperation, conformity, and polarization.
{"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}
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