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Ecology, Spatial Structure, and Selection Pressure Induce Strong Signatures in Phylogenetic Structure

Artificial life 2025年第2期31卷 129-152页

作者： Moreno, Matthew Andres Rodriguez-Papa, Santiago Dolson, Emily University of Michigan Department of Ecology and Evolutionary Biology Center for the Study of Complex Systems Michigan Institute for Data and AI in Society Michigan State University Department of Computer Science and Engineering Michigan State University Department of Computer Science and Engineering Program in Ecology Evolution Behavior

evolutionary dynamics are shaped by a variety of fundamental, generic drivers, including spatial structure, ecology, and selection pressure. These drivers impact the trajectory of evolution and have been hypothesized to influence phylogenetic structure. For instance, they can help explain natural history, steer behavior of contemporary evolving populations, and influence the efficacy of application-oriented evolutionary optimization. Likewise, in inquiry-oriented Artificial Life systems, these drivers constitute key building blocks for open-ended evolution. Here we set out to assess (a) if spatial structure, ecology, and selection pressure leave detectable signatures in phylogenetic structure;(b) the extent, in particular, to which ecology can be detected and discerned in the presence of spatial structure;and (c) the extent to which these phylogenetic signatures generalize across evolutionary systems. To this end, we analyze phylogenies generated by manipulating spatial structure, ecology, and selection pressure within three computational models of varied scope and sophistication. We find that selection pressure, spatial structure, and ecology have characteristic effects on phylogenetic metrics, although these effects are complex and not always intuitive. Signatures have some consistency across systems when using equivalent taxonomic unit definitions (e.g., individual, genotype, species). Furthermore, we find that sufficiently strong ecology can be detected in the presence of spatial structure. We also find that, while low-resolution phylogenetic reconstructions can bias some phylogenetic metrics, high-resolution reconstructions recapitulate them faithfully. Although our results suggest a potential for evolutionary inference of spatial structure, ecology, and selection pressure through phylogenetic analysis, further methods development is needed to distinguish these drivers' phylometric signatures from each other and to appropriately normalize phylogenetic metrics.

关键词： agent-based simulation Artificial Life Ecology evolution evolutionary dynamics phylogenetic analysis phylogeny metrics

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Testing the Inference Accuracy of Accelerator-Friendly Approximate Phylogeny Tracking

Testing the Inference Accuracy of Accelerator-Friendly Appro...

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2025 IEEE Symposium on Computational Intelligence in Artificial Life and Cooperative Intelligent systems, ALIFE-CIS 2025

作者： Moreno, Matthew Andres Ranjan, Anika Dolson, Emily Zaman, Luis University of Michigan Department of Ecology and Evolutionary Biology Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and Ai in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Michigan State University Department of Computer Science and Engineering East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States

ISBN: (纸本)9798331508371

Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, agent-based approaches provide an opportunity to collect high-quality records of ancestry relationships. Such phylogenies can provide insight into evolutionary dynamics within these simulations. Previous work generally tracks lineages directly, yielding an exact phylogenetic record of evolutionary history. However, challenges exist in scaling direct ancestrytracking approaches to highly-distributed, many-processor evolution in silico. An alternative approach is to estimate phylogenetic history via noncoding annotations on digital genomes, akin to how bioinformaticians build phylogenies by assessing genetic similarities between organisms. Recent work has extended this 'hereditary stratigraphy' approach to support powerful hardware accelerator platforms, such as the Cerebras Wafer-Scale Engine. Although these second-generation 'surface'-based hereditary stratigraphy algorithms have demonstrated order-ofmagnitude speedups over first-generation 'column'-based algorithms, it remains unknown how they impact the accuracy of reconstructed phylogenies. To address this question, we assessed reconstruction accuracy under alternative configurations across a matrix of evolutionary conditions varying in selection pressure, spatial structure, and ecological dynamics. Encouragingly, we find that the second-generation approaches provide higher reconstruction quality across most surveyed conditions. © 2025 IEEE.

关键词： Biostratigraphy

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Testing the Inference Accuracy of Accelerator-Friendly Approximate Phylogeny Tracking

Testing the Inference Accuracy of Accelerator-Friendly Appro...

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Computational Intelligence in Artificial Life and Cooperative Intelligent systems (ALIFE-CIS), IEEE Symposium on

作者： Matthew Andres Moreno Anika Ranjan Emily Dolson Luis Zaman Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and AI in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States

ISBN: (数字)9798331508371

ISBN: (纸本)9798331508388

Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, agent-based approaches provide an opportunity to collect high-quality records of ancestry relationships. Such phylogenies can provide insight into evolutionary dynamics within these simulations. Previous work generally tracks lineages directly, yielding an exact phylogenetic record of evolutionary history. However, challenges exist in scaling direct ancestrytracking approaches to highly-distributed, many-processor evolution in silico. An alternative approach is to estimate phylogenetic history via noncoding annotations on digital genomes, akin to how bioinformaticians build phylogenies by assessing genetic similarities between organisms. Recent work has extended this “hereditary stratigraphy” approach to support powerful hardware accelerator platforms, such as the Cerebras Wafer-Scale Engine. Although these second-generation “surface”-based hereditary stratigraphy algorithms have demonstrated order-ofmagnitude speedups over first-generation “column”-based algorithms, it remains unknown how they impact the accuracy of reconstructed phylogenies. To address this question, we assessed reconstruction accuracy under alternative configurations across a matrix of evolutionary conditions varying in selection pressure, spatial structure, and ecological dynamics. Encouragingly, we find that the second-generation approaches provide higher reconstruction quality across most surveyed conditions.

关键词： Surface reconstruction Accuracy Annotations Heuristic algorithms Computational modeling Biological system modeling Stratigraphy Phylogeny History Bars

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Statistical methods for constructing disease comorbidity networks from longitudinal inpatient data

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Applied Network Science 2018年第1期3卷 46页

作者： Fotouhi, Babak Momeni, Naghmeh Riolo, Maria A. Buckeridge, David L. Program for Evolutionary Dynamics Harvard University Cambridge United States Sloan School of Management Massachusetts Institute of Technology Cambridge United States Center for the Study of Complex Systems University of Michigan Ann ArborMI United States Department of Epidemiology Biostatistics and Occupational Health McGill University Montreal Canada

Tools from network science can be utilized to study relations between diseases. Different studies focus on different types of inter-disease linkages. One of them is the comorbidity patterns derived from large-scale longitudinal data of hospital discharge records. Researchers seek to describe comorbidity relations as a network to characterize pathways of disease progressions and to predict future risks. The first step in such studies is the construction of the network itself, which subsequent analyses rest upon. There are different ways to build such a network. In this paper, we provide an overview of several existing statistical approaches in network science applicable to weighted directed networks. We discuss the differences between the null models that these models assume and their applications. We apply these methods to the inpatient data of approximately one million people, spanning approximately 17 years, pertaining to the Montreal Census Metropolitan Area. We discuss the differences in the structure of the networks built by different methods, and different features of the comorbidity relations that they extract. We also present several example applications of these methods. © 2018, The Author(s).

关键词： Epidemiology

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Interaction stochasticity supports cooperation in spatial Prisoner’s dilemma

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Physical Review E 2008年第5期78卷 051120-051120页

作者： Xiaojie Chen Feng Fu Long Wang State Key Laboratory for Turbulence and Complex Systems Center for Systems and Control College of Engineering Peking University Beijing 100871 China Program for Evolutionary Dynamics Harvard University Cambridge Massachusetts 02138 USA

Previous studies mostly assume deterministic interactions among neighboring individuals for games on graphs. In this paper, we relax this assumption by introducing stochastic interactions into the spatial Prisoner’s dilemma game, and study the effects of interaction stochasticity on the evolution of cooperation. Interestingly, simulation results show that there exists an optimal region of the intensity of interaction resulting in a maximum cooperation level. Moreover, we find good agreement between simulation results and theoretical predictions obtained from an extended pair-approximation method. We also show some typical snapshots of the system and investigate the mean payoffs for cooperators and defectors. Our results may provide some insight into understanding the emergence of cooperation in the real world where the interactions between individuals take place in an intermittent manner.

关键词： Game theory

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Expectation-driven migration promotes cooperation by group interactions

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Physical Review E 2012年第6期85卷 066104-066104页

作者： Te Wu Feng Fu Yanling Zhang Long Wang Center for Systems and Control State Key Laboratory for Turbulence and Complex Systems College of Engineering Peking University Beijing 100871 China Program for Evolutionary Dynamics Harvard University Cambridge Massachusetts 02138 USA

“Voting with feet” describes the prominent social phenomenon that people tend to move away from deteriorating neighborhoods and search for and join prosperous groups. To quantify the role this kind of expectation-driven migration plays in the evolution of cooperation, here we study a simple yet effective model of cooperation based on spatial public goods games. The population structure is characterized by a square lattice with some nodes being left empty. Individuals have expectations toward their current habitats. Dissatisfied players, whose expectation is not met after interacting with all directly connected neighbors, tend to abstain from the groups of low quality by moving away and explore the physical niches of avail. How fast interaction happens relatively to selection is regulated by the time-scale ratio of game interaction to natural selection. Under strong selection, simulation results show that cooperation is greatly improved for either low, moderate, or high expectations compared to whenever the expectation-driven migration is absent. Further explorations reveal that neither too high nor too low but rather a combination of moderate expectations and rapid interaction establishes cooperation for a moderate public goods enhancement factor. There exists an optimal interval of expectation level most favoring the evolution of cooperation as the required time-scale ratio is minimized.

关键词： GROUP theory PUBLIC goods MATHEMATICAL models NATURAL selection SIMULATION methods & models SPATIAL analysis (Statistics)

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Partner selections in public goods games with constant group size

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Physical Review E 2009年第2期80卷 026121-026121页

作者： Te Wu Feng Fu Long Wang Center for Systems and Control State Key Laboratory for Turbulence and Complex Systems College of Engineering Peking University Beijing 100871 China Program for Evolutionary Dynamics Harvard University Cambridge Massachusetts 02138 USA

Most of previous studies concerning the public goods game assume either participation is unconditional or the number of actual participants in a competitive group changes over time. How the fixed group size, prescribed by social institutions, affects the evolution of cooperation is still unclear. We propose a model where individuals with heterogeneous social ties might well engage in differing numbers of public goods games, yet with each public goods game being constant size during the course of evolution. To do this, we assume that each focal individual unidirectionally selects a constant number of interaction partners from his immediate neighbors with probabilities proportional to the degrees or the reputations of these neighbors, corresponding to degree-based partner selection or reputation-based partner selection, respectively. Because of the stochasticity the group formation is dynamical. In both selection regimes, monotonical dependence of the stationary density of cooperators on the group size was found, the latter over the whole range but the former over a restricted range of the renormalized enhancement factor. Moreover, the reputation-based regime can substantially improve cooperation. To interpret these differences, the microscopic characteristics of individuals are probed. We later extend the degree-based partner selection to general cases where focal individuals have preferences toward their neighbors of varying social ties to form groups. As a comparison, we as well investigate the situation where individuals locating on the degree regular graphs choose their coplayers at random. Our results may give some insights into better understanding the widespread teamwork and cooperation in the real world.

关键词： Condensed matter physics

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Inertia in strategy switching transforms the strategy evolution

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Physical Review E 2011年第6期84卷 066103-066103页

作者： Yanling Zhang Feng Fu Te Wu Guangming Xie Long Wang Center for Systems and Control State Key Laboratory for Turbulence and Complex Systems College of Engineering Peking University Beijing 100871 China Program for Evolutionary Dynamics Harvard University Cambridge Massachusetts 02138 USA

A recent experimental study [Traulsen et al., Proc. Natl. Acad. Sci. 107, 2962 (2010)] shows that human strategy updating involves both direct payoff comparison and the cost of switching strategy, which is equivalent to inertia. However, it remains largely unclear how such a predisposed inertia affects 2×2 games in a well-mixed population of finite size. To address this issue, the “inertia bonus” (strategy switching cost) is added to the learner payoff in the Fermi process. We find how inertia quantitatively shapes the stationary distribution and that stochastic stability under inertia exhibits three regimes, with each covering seven regions in the plane spanned by two inertia parameters. We also obtain the extended “1/3” rule with inertia and the speed criterion with inertia; these two findings hold for a population above two. We illustrate the above results in the framework of the Prisoner's Dilemma game. As inertia varies, two intriguing stationary distributions emerge: the probability of coexistence state is maximized, or those of two full states are simultaneously peaked. Our results may provide useful insights into how the inertia of changing status quo acts on the strategy evolution and, in particular, the evolution of cooperation.

关键词： INERTIA (Mechanics) PRISONER'S dilemma game PROBABILITY theory STOCHASTIC analysis PHYSICS research QUANTITATIVE research

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Partner switching stabilizes cooperation in coevolutionary prisoner’s dilemma

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Physical Review E 2009年第3期79卷 036101-036101页

作者： Feng Fu Te Wu Long Wang Program for Evolutionary Dynamics Harvard University Cambridge Massachusetts 02138 USA Center for Systems and Control State Key Laboratory for Turbulence and Complex Systems College of Engineering Peking University Beijing 100871 China

Previous studies suggest that cooperation prevails when individuals can switch their interaction partners quickly. However, it is still unclear how quickly individuals should switch adverse partners to maximize cooperation. To address this issue, we propose a simple model of coevolutionary prisoner’s dilemma in which individuals are allowed to either adjust their strategies or switch their defective partners. Interestingly, we find that, depending on the game parameter, there is an optimal tendency of switching adverse partnerships that maximizes the fraction of cooperators in the population. We confirm that the stabilization of cooperation by partner switching remains effective under some situations, where either normalized or accumulated payoff is used in strategy updating, and where either only cooperators or all individuals are privileged to sever disadvantageous partners. We also provide an extended pair approximation to study the coevolutionary dynamics. Our results may be helpful in understanding the role of partner switching in the stabilization of cooperation in the real world.

关键词： Stabilization

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Architecture of the Genotype-Phenotype Map and the Coevolution of complexity

Architecture of the Genotype-Phenotype Map and the Coevoluti...

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2021 Conference on Artificial Life, ALIFE 2021

作者： Kumawat, Bhaskar Zaman, Luis Undergraduate Program Indian Institute of Science Bangalore560012 India Department of Ecology and Evolutionary Biology University of Michigan Ann ArborMI48109 United States Center for the Study of Complex Systems University of Michigan Ann ArborMI48109 United States

The addition of parasites to a host population can drive an escalation in the host population’s phenotypic complexity – even in the absence of a direct fitness advantage for this increase. Parasites restrict certain regions of the genotype space, decreasing the fitness and the probability of survival of particular host phenotypes. While many artificial life frameworks model a direct correlation between genotype and fitness, the structure of genotype-phenotype maps can have important effects on evolutionary dynamics. Using a simple coarse-grained model for phenotypic transitions during evolution, we show that the escalation in phenotypic complexity under neutral co-evolution is dependent on the structure of the genotype-phenotype map. We discuss these results using the metaphor of evolutionary spandrels and highlight how these structural considerations might allow us to capture biological phenomena more accurately. © 2021 ALIFE. All Rights Reserved.

关键词： Biotic

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