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  1. Article ; Online: Correction: Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence.

    Pourhasanzade, Fateme / Iyer, Swami / Tjendra, Jesslyn / Landor, Lotta / Våge, Selina

    PLoS computational biology

    2023  Volume 19, Issue 10, Page(s) e1011600

    Abstract: This corrects the article DOI: 10.1371/journal.pcbi.1010228.]. ...

    Abstract [This corrects the article DOI: 10.1371/journal.pcbi.1010228.].
    Language English
    Publishing date 2023-10-27
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1011600
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  2. Article ; Online: Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence.

    Pourhasanzade, Fateme / Iyer, Swami / Tjendra, Jesslyn / Landor, Lotta / Våge, Selina

    PLoS computational biology

    2022  Volume 18, Issue 6, Page(s) e1010228

    Abstract: Viruses play diverse and important roles in ecosystems. In recent years, trade-offs between host and virus traits have gained increasing attention in viral ecology and evolution. However, microbial organism traits, and viral population parameters in ... ...

    Abstract Viruses play diverse and important roles in ecosystems. In recent years, trade-offs between host and virus traits have gained increasing attention in viral ecology and evolution. However, microbial organism traits, and viral population parameters in particular, are challenging to monitor. Mathematical and individual-based models are useful tools for predicting virus-host dynamics. We have developed an individual-based evolutionary model to study ecological interactions and evolution between bacteria and viruses, with emphasis on the impacts of trade-offs between competitive and defensive host traits on bacteria-phage population dynamics and trait diversification. Host dynamics are validated with lab results for different initial virus to host ratios (VHR). We show that trade-off based, as opposed to random bacteria-virus interactions, result in biologically plausible evolutionary outcomes, thus highlighting the importance of trade-offs in shaping biodiversity. The effects of nutrient concentration and other environmental and organismal parameters on the virus-host dynamics are also investigated. Despite its simplicity, our model serves as a powerful tool to study bacteria-phage interactions and mechanisms for evolutionary diversification under various environmental conditions.
    MeSH term(s) Bacteria ; Bacteriophages ; Biodiversity ; Biological Evolution ; Ecosystem ; Population Dynamics ; Viruses
    Language English
    Publishing date 2022-06-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1010228
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  3. Article ; Online: Evolution of cooperation in social dilemmas with assortative interactions

    Iyer, Swami / Killingback, Timothy

    2020  

    Abstract: Cooperation in social dilemmas plays a pivotal role in the formation of systems at all levels of complexity, from replicating molecules to multi-cellular organisms to human and animal societies. In spite of its ubiquity, the origin and stability of ... ...

    Abstract Cooperation in social dilemmas plays a pivotal role in the formation of systems at all levels of complexity, from replicating molecules to multi-cellular organisms to human and animal societies. In spite of its ubiquity, the origin and stability of cooperation pose an evolutionary conundrum, since cooperation, though beneficial to others, is costly to the individual cooperator. Thus natural selection would be expected to favor selfish behavior in which individuals reap the benefits of cooperation without bearing the costs of cooperating themselves. Many proximate mechanisms have been proposed to account for the origin and maintenance of cooperation, including kin selection, direct reciprocity, indirect reciprocity, and evolution in structured populations. Despite the apparent diversity of these approaches they all share a unified underlying logic: namely, each mechanism results in assortative interactions in which individuals using the same strategy interact with a higher probability than they would at random. Here we study the evolution of cooperation in both discrete strategy and continuous strategy social dilemmas with assortative interactions. For the sake of tractability, assortativity is modeled by an individual interacting with another of the same type with probability r and interacting with a random individual in the population with probability 1-r, where r is a parameter that characterizes the degree of assortativity in the system. For discrete strategy social dilemmas we use both a generalization of replicator dynamics and individual-based simulations to elucidate the donation, snowdrift, and sculling games with assortative interactions, and determine the analogs of Hamilton's rule, which govern the evolution of cooperation in these games. For continuous strategy social dilemmas we employ both a generalization of deterministic adaptive dynamics and individual-based simulations to study the donation, snowdrift, and tragedy of the commons games, and determine the effect of assortativity on the emergence ...
    Keywords ddc:330 ; adaptive dynamics ; coordination game ; evolutionary game theory ; hawk-dove game ; prisoners dilemma ; replicator dynamics ; tragedy of the commons
    Subject code 612
    Language English
    Publisher Basel: MDPI
    Publishing country de
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Testing for COVID-19 in patients with cancer.

    Alhalabi, Omar / Iyer, Swami / Subbiah, Vivek

    EClinicalMedicine

    2020  Volume 23, Page(s) 100374

    Keywords covid19
    Language English
    Publishing date 2020-05-03
    Publishing country England
    Document type Journal Article
    ISSN 2589-5370
    ISSN (online) 2589-5370
    DOI 10.1016/j.eclinm.2020.100374
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  5. Thesis ; Online: Evolutionary dynamics on complex networks

    Iyer, Swami

    2013  

    Abstract: Many complex systems such as the Internet can be represented as networks, with vertices denoting the constituent components of the systems and edges denoting the patterns of interactions among the components. In this thesis, we are interested in how the ... ...

    Abstract Many complex systems such as the Internet can be represented as networks, with vertices denoting the constituent components of the systems and edges denoting the patterns of interactions among the components. In this thesis, we are interested in how the structural properties of a network, such as its average degree, degree distribution, clustering, and homophily affect the processes that take place on it. In the first part of the thesis we focus on evolutionary game theory models for studying the evolution of cooperation in a population of predominantly selfish individuals. In the second part we turn our attention to an evolutionary model of disease dynamics and the impact of vaccination on the spread of infection. Throughout the thesis we use a network as an abstraction for a population, with vertices representing individuals in the population and edges specifying who can interact with whom. We analyze our models for a well-mixed population, i.e., an infinite population with random mixing, and compare the theoretical results with those obtained from computer simulations on model and empirical networks.
    Keywords Computer science
    Subject code 612
    Language ENG
    Publishing date 2013-01-01 00:00:01.0
    Publisher University of Massachusetts Boston
    Publishing country us
    Document type Thesis ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Evolution of Cooperation in Social Dilemmas on Complex Networks.

    Iyer, Swami / Killingback, Timothy

    PLoS computational biology

    2016  Volume 12, Issue 2, Page(s) e1004779

    Abstract: Cooperation in social dilemmas is essential for the functioning of systems at multiple levels of complexity, from the simplest biological organisms to the most sophisticated human societies. Cooperation, although widespread, is fundamentally challenging ... ...

    Abstract Cooperation in social dilemmas is essential for the functioning of systems at multiple levels of complexity, from the simplest biological organisms to the most sophisticated human societies. Cooperation, although widespread, is fundamentally challenging to explain evolutionarily, since natural selection typically favors selfish behavior which is not socially optimal. Here we study the evolution of cooperation in three exemplars of key social dilemmas, representing the prisoner's dilemma, hawk-dove and coordination classes of games, in structured populations defined by complex networks. Using individual-based simulations of the games on model and empirical networks, we give a detailed comparative study of the effects of the structural properties of a network, such as its average degree, variance in degree distribution, clustering coefficient, and assortativity coefficient, on the promotion of cooperative behavior in all three classes of games.
    MeSH term(s) Altruism ; Biological Evolution ; Computational Biology ; Computer Simulation ; Cooperative Behavior ; Games, Experimental ; Humans ; Models, Biological
    Language English
    Publishing date 2016-02-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1004779
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  7. Article ; Online: Evolutionary dynamics of a smoothed war of attrition game.

    Iyer, Swami / Killingback, Timothy

    Journal of theoretical biology

    2016  Volume 396, Page(s) 25–41

    Abstract: In evolutionary game theory the War of Attrition game is intended to model animal contests which are decided by non-aggressive behavior, such as the length of time that a participant will persist in the contest. The classical War of Attrition game ... ...

    Abstract In evolutionary game theory the War of Attrition game is intended to model animal contests which are decided by non-aggressive behavior, such as the length of time that a participant will persist in the contest. The classical War of Attrition game assumes that no errors are made in the implementation of an animal׳s strategy. However, it is inevitable in reality that such errors must sometimes occur. Here we introduce an extension of the classical War of Attrition game which includes the effect of errors in the implementation of an individual׳s strategy. This extension of the classical game has the important feature that the payoff is continuous, and as a consequence admits evolutionary behavior that is fundamentally different from that possible in the original game. We study the evolutionary dynamics of this new game in well-mixed populations both analytically using adaptive dynamics and through individual-based simulations, and show that there are a variety of possible outcomes, including simple monomorphic or dimorphic configurations which are evolutionarily stable and cannot occur in the classical War of Attrition game. In addition, we study the evolutionary dynamics of this extended game in a variety of spatially and socially structured populations, as represented by different complex network topologies, and show that similar outcomes can also occur in these situations.
    MeSH term(s) Biological Evolution ; Game Theory ; Models, Biological
    Language English
    Publishing date 2016-05-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2972-5
    ISSN 1095-8541 ; 0022-5193
    ISSN (online) 1095-8541
    ISSN 0022-5193
    DOI 10.1016/j.jtbi.2016.02.014
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  9. Article ; Online: Testing for COVID-19 in patients with cancer

    Alhalabi, Omar / Iyer, Swami / Subbiah, Vivek

    EClinicalMedicine

    2020  Volume 23, Page(s) 100374

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ISSN 2589-5370
    DOI 10.1016/j.eclinm.2020.100374
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Evolutionary dynamics of the traveler's dilemma and minimum-effort coordination games on complex networks.

    Iyer, Swami / Killingback, Timothy

    Physical review. E, Statistical, nonlinear, and soft matter physics

    2014  Volume 90, Issue 4, Page(s) 42134

    Abstract: The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games ...

    Abstract The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games are studied experimentally. Moreover, both the traveler's dilemma and the minimum-effort coordination games have potentially important applications in evolutionary biology. Interestingly, standard deterministic evolutionary game theory, as represented by the replicator dynamics in a well-mixed population, is also inadequate to account for the behavior observed in these games. Here we study the evolutionary dynamics of both these games in populations with interaction patterns described by a variety of complex network topologies. We investigate the evolutionary dynamics of these games through agent-based simulations on both model and empirical networks. In particular, we study the effects of network clustering and assortativity on the evolutionary dynamics of both games. In general, we show that the evolutionary behavior of the traveler's dilemma and minimum-effort coordination games on complex networks is in good agreement with that observed experimentally. Thus, formulating the traveler's dilemma and the minimum-effort coordination games on complex networks neatly resolves the paradoxical aspects of these games.
    MeSH term(s) Cluster Analysis ; Computer Simulation ; Game Theory ; Social Behavior ; Stochastic Processes
    Language English
    Publishing date 2014-10
    Publishing country United States
    Document type Journal Article
    ISSN 1550-2376
    ISSN (online) 1550-2376
    DOI 10.1103/PhysRevE.90.042134
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