Publications by authors named "Simon A Levin"

177 Publications

Governance in the Face of Extreme Events: Lessons from Evolutionary Processes for Structuring Interventions, and the Need to Go Beyond.

Ecosystems 2021 Sep 7:1-15. Epub 2021 Sep 7.

Department of Agricultural and Resource Economics, University of California, Davis, California 95616 USA.

The increasing frequency of extreme events, exogenous and endogenous, poses challenges for our societies. The current pandemic is a case in point; but "once-in-a-century" weather events are also becoming more common, leading to erosion, wildfire and even volcanic events that change ecosystems and disturbance regimes, threaten the sustainability of our life-support systems, and challenge the robustness and resilience of societies. Dealing with extremes will require new approaches and large-scale collective action. Preemptive measures can increase general resilience, a first line of protection, while more specific reactive responses are developed. Preemptive measures also can minimize the negative effects of events that cannot be avoided. In this paper, we first explore approaches to prevention, mitigation and adaptation, drawing inspiration from how evolutionary challenges have made biological systems robust and resilient, and from the general theory of complex adaptive systems. We argue further that proactive steps that go beyond will be necessary to reduce unacceptable consequences.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10021-021-00680-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8422834PMC
September 2021

Vaccine nationalism and the dynamics and control of SARS-CoV-2.

Science 2021 Sep 24;373(6562):eabj7364. Epub 2021 Sep 24.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA.

[Figure: see text].
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.abj7364DOI Listing
September 2021

Irrigated areas drive irrigation water withdrawals.

Nat Commun 2021 07 26;12(1):4525. Epub 2021 Jul 26.

Open Evidence Research, Universitat Oberta de Catalunya (UOC), Barcelona, Spain.

A sustainable management of global freshwater resources requires reliable estimates of the water demanded by irrigated agriculture. This has been attempted by the Food and Agriculture Organization (FAO) through country surveys and censuses, or through Global Models, which compute irrigation water withdrawals with sub-models on crop types and calendars, evapotranspiration, irrigation efficiencies, weather data and irrigated areas, among others. Here we demonstrate that these strategies err on the side of excess complexity, as the values reported by FAO and outputted by Global Models are largely conditioned by irrigated areas and their uncertainty. Modelling irrigation water withdrawals as a function of irrigated areas yields almost the same results in a much parsimonious way, while permitting the exploration of all model uncertainties. Our work offers a robust and more transparent approach to estimate one of the most important indicators guiding our policies on water security worldwide.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-021-24508-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8313559PMC
July 2021

Introduction to PNAS special issue on evolutionary models of financial markets.

Proc Natl Acad Sci U S A 2021 Jun;118(26)

Sloan School of Management, Massachusetts Institute of Technology, Cambridge, MA 02142.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.2104800118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8255779PMC
June 2021

Sunsetting as an adaptive strategy.

Proc Natl Acad Sci U S A 2021 Jun;118(26)

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-1003.

Major financial legislation is invariably enacted in the wake of a financial crisis. However, legislating following a crisis is hazardous because information is scarce regarding causes of the crisis, let alone what would be an appropriate response. Compounding the lack of information, crisis-driven legislation is sticky, but financial markets are dynamically innovative, which can undermine the efficacy of regulation. As a result, it is foreseeable that such legislation will contain at least some provisions that are inapt or inadequate or, more often, have consequences that are not well understood or even knowable. This article advocates the use of sunsetting as a mechanism for mitigating the potentially adverse consequences of crisis-driven financial legislation. With sunsetting, after a fixed time span, legislation and its implementing regulation must be reenacted to remain in force. This approach has parallels in evolutionary biology, in which a central issue is the ability to adapt to changing environments. Sunsetting does not mean simply discarding (or reenacting) existing regulations, but revisiting them and improving them, much as mutation and recombination do in the evolutionary process.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.2015258118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8256028PMC
June 2021

Evolution of an asymptomatic first stage of infection in a heterogeneous population.

J R Soc Interface 2021 06 16;18(179):20210175. Epub 2021 Jun 16.

Department of Molecular Biology, Princeton University, Princeton, NJ, USA.

Pathogens evolve different life-history strategies, which depend in part on differences in their host populations. A central feature of hosts is their population structure (e.g. spatial). Additionally, hosts themselves can exhibit different degrees of symptoms when newly infected; this latency is a key life-history property of pathogens. With an evolutionary-epidemiological model, we examine the role of population structure on the evolutionary dynamics of latency. We focus on specific power-law-like formulations for transmission and progression from the first infectious stage as a function of latency, assuming that the across-group to within-group transmission ratio increases if hosts are less symptomatic. We find that simple population heterogeneity can lead to local evolutionarily stable strategies (ESSs) at zero and infinite latency in situations where a unique ESS exists in the corresponding homogeneous case. Furthermore, there can exist more than one interior evolutionarily singular strategy. We find that this diversity of outcomes is due to the (possibly slight) advantage of across-group transmission for pathogens that produce fewer symptoms in a first infectious stage. Thus, our work reveals that allowing individuals without symptoms to travel can have important unintended evolutionary effects and is thus fundamentally problematic in view of the evolutionary dynamics of latency.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1098/rsif.2021.0175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8205539PMC
June 2021

Generalized Stoichiometry and Biogeochemistry for Astrobiological Applications.

Bull Math Biol 2021 May 18;83(7):73. Epub 2021 May 18.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.

A central need in the field of astrobiology is generalized perspectives on life that make it possible to differentiate abiotic and biotic chemical systems McKay (2008). A key component of many past and future astrobiological measurements is the elemental ratio of various samples. Classic work on Earth's oceans has shown that life displays a striking regularity in the ratio of elements as originally characterized by Redfield (Redfield 1958; Geider and La Roche 2002; Eighty years of Redfield 2014). The body of work since the original observations has connected this ratio with basic ecological dynamics and cell physiology, while also documenting the range of elemental ratios found in a variety of environments. Several key questions remain in considering how to best apply this knowledge to astrobiological contexts: How can the observed variation of the elemental ratios be more formally systematized using basic biological physiology and ecological or environmental dynamics? How can these elemental ratios be generalized beyond the life that we have observed on our own planet? Here, we expand recently developed generalized physiological models (Kempes et al. 2012, 2016, 2017, 2019) to create a simple framework for predicting the variation of elemental ratios found in various environments. We then discuss further generalizing the physiology for astrobiological applications. Much of our theoretical treatment is designed for in situ measurements applicable to future planetary missions. We imagine scenarios where three measurements can be made-particle/cell sizes, particle/cell stoichiometry, and fluid or environmental stoichiometry-and develop our theory in connection with these often deployed measurements.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11538-021-00877-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131296PMC
May 2021

A well-timed shift from local to global agreements accelerates climate change mitigation.

Nat Commun 2021 05 18;12(1):2908. Epub 2021 May 18.

School of Environmental Sciences, University of Guelph, Guelph, ON, Canada.

Recent attempts at cooperating on climate change mitigation highlight the limited efficacy of large-scale negotiations, when commitment to mitigation is costly and initially rare. Deepening existing voluntary mitigation pledges could require more stringent, legally-binding agreements that currently remain untenable at the global scale. Building-blocks approaches promise greater success by localizing agreements to regions or few-nation summits, but risk slowing mitigation adoption globally. Here, we show that a well-timed policy shift from local to global legally-binding agreements can dramatically accelerate mitigation compared to using only local, only global, or both agreement types simultaneously. This highlights the scale-specific roles of mitigation incentives: local agreements promote and sustain mitigation commitments in early-adopting groups, after which global agreements rapidly draw in late-adopting groups. We conclude that focusing negotiations on local legally-binding agreements and, as these become common, a renewed pursuit of stringent, legally-binding world-wide agreements could best overcome many current challenges facing climate mitigation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-021-23056-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131631PMC
May 2021

Biased perceptions explain collective action deadlocks and suggest new mechanisms to prompt cooperation.

iScience 2021 Apr 29;24(4):102375. Epub 2021 Mar 29.

Center for BioComplexity, High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA.

When individuals face collective action problems, their expectations about others' willingness to contribute affect their motivation to cooperate. Individuals, however, often misperceive the cooperation levels in a population. In the context of climate action, people underestimate the pro-climate positions of others. Designing incentives to enable cooperation and a sustainable future must thereby consider how social perception biases affect collective action. We propose a theoretical model and investigate the effect of social perception bias in non-linear public goods games. We show that different types of bias play a distinct role in cooperation dynamics. False uniqueness (underestimating own views) and false consensus (overestimating own views) both explain why communities get locked in suboptimal states. Such dynamics also impact the effectiveness of typical monetary incentives, such as fees. Our work contributes to understanding how targeting biases, e.g., by changing the information available to individuals, can comprise a fundamental mechanism to prompt collective action.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.isci.2021.102375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8080528PMC
April 2021

Analysis of the potential impact of durability, timing, and transmission blocking of COVID-19 vaccine on morbidity and mortality.

EClinicalMedicine 2021 May 26;35:100863. Epub 2021 Apr 26.

Center for Disease Dynamics, Economics & Policy, Washington, D.C., USA.

Background: COVID-19 vaccines have been approved and made available. While questions of vaccine allocation strategies have received significant attention, important questions remain regarding the potential impact of the vaccine given uncertainties regarding efficacy against transmission, availability, timing, and durability.

Methods: We adapted a susceptible-exposed-infectious-recovered (SEIR) model to examine the potential impact on hospitalization and mortality assuming increasing rates of vaccine efficacy, coverage, and administration. We also evaluated the uncertainty of the vaccine to prevent infectiousness as well as the impact on outcomes based on the timing of distribution and the potential effects of waning immunity.

Findings: Increased vaccine efficacy against disease reduces hospitalizations and deaths from COVID-19; however, the relative benefit of transmission blocking varied depending on the timing of vaccine distribution. Early in an outbreak, a vaccine that reduces transmission will be relatively more effective than one introduced later in the outbreak. In addition, earlier and accelerated implementation of a less effective vaccine is more impactful than later implementation of a more effective vaccine. These findings are magnified when considering the durability of the vaccine. Vaccination in the spring will be less impactful when immunity is less durable.

Interpretation: Policy choices regarding non-pharmaceutical interventions, such as social distancing and face mask use, will need to remain in place longer if the vaccine is less effective at reducing transmission or distributed slower. In addition, the stage of the local outbreak greatly impacts the overall effectiveness of the vaccine in a region and should be considered when allocating vaccines.

Funding: Centers for Disease Control and Prevention (CDC) MInD-Healthcare Program (U01CK000589, 1U01CK000536), James S. McDonnell Foundation 21st Century Science Initiative Collaborative Award in Understanding Dynamic and Multiscale Systems, National Science Foundation (CNS-2027908), National Science Foundation Expeditions (CCF1917819), C3.ai Digital Transformation Institute (AWD1006615), and Google, LLC.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.eclinm.2021.100863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8072137PMC
May 2021

Emergent Field-Driven Robot Swarm States.

Phys Rev Lett 2021 Mar;126(10):108002

Chongqing Key Laboratory of Soft Condensed Matter Physics and Smart Materials, College of Physics, Chongqing University, Chongqing, 400044 China.

We present an ecology-inspired form of active matter consisting of a robot swarm. Each robot moves over a planar dynamic resource environment represented by a large light-emitting diode array in search of maximum light intensity; the robots deplete (dim) locally by their presence the local light intensity and seek maximum light intensity. Their movement is directed along the steepest local light intensity gradient; we call this emergent symmetry breaking motion "field drive." We show there emerge dynamic and spatial transitions similar to gas, crystalline, liquid, glass, and jammed states as a function of robot density, resource consumption rates, and resource recovery rates. Paradoxically the nongas states emerge from smooth, flat resource landscapes, not rough ones, and each state can directly move to a glassy state if the resource recovery rate is slow enough, at any robot density.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevLett.126.108002DOI Listing
March 2021

Our future in the Anthropocene biosphere.

Ambio 2021 Apr 14;50(4):834-869. Epub 2021 Mar 14.

CSIRO, Canberra, Australia.

The COVID-19 pandemic has exposed an interconnected and tightly coupled globalized world in rapid change. This article sets the scientific stage for understanding and responding to such change for global sustainability and resilient societies. We provide a systemic overview of the current situation where people and nature are dynamically intertwined and embedded in the biosphere, placing shocks and extreme events as part of this dynamic; humanity has become the major force in shaping the future of the Earth system as a whole; and the scale and pace of the human dimension have caused climate change, rapid loss of biodiversity, growing inequalities, and loss of resilience to deal with uncertainty and surprise. Taken together, human actions are challenging the biosphere foundation for a prosperous development of civilizations. The Anthropocene reality-of rising system-wide turbulence-calls for transformative change towards sustainable futures. Emerging technologies, social innovations, broader shifts in cultural repertoires, as well as a diverse portfolio of active stewardship of human actions in support of a resilient biosphere are highlighted as essential parts of such transformations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13280-021-01544-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7955950PMC
April 2021

Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes.

Science 2021 04 9;372(6540):363-370. Epub 2021 Mar 9.

Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada.

Given vaccine dose shortages and logistical challenges, various deployment strategies are being proposed to increase population immunity levels to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two critical issues arise: How timing of delivery of the second dose will affect infection dynamics and how it will affect prospects for the evolution of viral immune escape via a buildup of partially immune individuals. Both hinge on the robustness of the immune response elicited by a single dose as compared with natural and two-dose immunity. Building on an existing immuno-epidemiological model, we find that in the short term, focusing on one dose generally decreases infections, but that longer-term outcomes depend on this relative immune robustness. We then explore three scenarios of selection and find that a one-dose policy may increase the potential for antigenic evolution under certain conditions of partial population immunity. We highlight the critical need to test viral loads and quantify immune responses after one vaccine dose and to ramp up vaccination efforts globally.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.abg8663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8128287PMC
April 2021

Superinfection and the evolution of an initial asymptomatic stage.

R Soc Open Sci 2021 Jan 27;8(1):202212. Epub 2021 Jan 27.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.

Pathogens have evolved a variety of life-history strategies. An important strategy consists of successful transmission by an infected host before the appearance of symptoms, that is, while the host is still partially or fully asymptomatic. During this initial stage of infection, it is possible for another pathogen to superinfect an already infected host and replace the previously infecting pathogen. Here, we study the effect of superinfection during the first stage of an infection on the evolutionary dynamics of the degree to which the host is asymptomatic (host latency) in that same stage. We find that superinfection can lead to major differences in evolutionary behaviour. Most strikingly, the duration of immunity following infection can significantly influence pathogen evolutionary dynamics, whereas without superinfection the outcomes are independent of host immunity. For example, changes in host immunity can drive evolutionary transitions from a fully symptomatic to a fully asymptomatic first infection stage. Additionally, if superinfection relative to susceptible infection is strong enough, evolution can lead to a unique strategy of latency that corresponds to a local fitness minimum, and is therefore invasible by nearby mutants. Thus, this strategy is a branching point, and can lead to coexistence of pathogens with different latencies. Furthermore, in this new framework with superinfection, we also find that there can exist two interior singular strategies. Overall, new evolutionary outcomes can cascade from superinfection.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1098/rsos.202212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7890506PMC
January 2021

Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes.

medRxiv 2021 Feb 3. Epub 2021 Feb 3.

Department of Bioengineering, McGill University, Montreal QC H3A 0C3, Canada.

As the threat of Covid-19 continues and in the face of vaccine dose shortages and logistical challenges, various deployment strategies are being proposed to increase population immunity levels. How timing of delivery of the second dose affects infection burden but also prospects for the evolution of viral immune escape are critical questions. Both hinge on the strength and duration (i.e. robustness) of the immune response elicited by a single dose, compared to natural and two-dose immunity. Building on an existing immuno-epidemiological model, we find that in the short-term, focusing on one dose generally decreases infections, but longer-term outcomes depend on this relative immune robustness. We then explore three scenarios of selection, evaluating how different second dose delays might drive immune escape via a build-up of partially immune individuals. Under certain scenarios, we find that a one-dose policy may increase the potential for antigenic evolution. We highlight the critical need to test viral loads and quantify immune responses after one vaccine dose, and to ramp up vaccination efforts throughout the world.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1101/2021.02.01.21250944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7872380PMC
February 2021

Trajectory of individual immunity and vaccination required for SARS-CoV-2 community immunity: a conceptual investigation.

J R Soc Interface 2021 02 3;18(175):20200683. Epub 2021 Feb 3.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.

SARS-CoV-2 is an international public health emergency; high transmissibility and morbidity and mortality can result in the virus overwhelming health systems. Combinations of social distancing, and test, trace, and isolate strategies can reduce the number of new infections per infected individual below 1, thus driving declines in case numbers, but may be both challenging and costly. These interventions must also be maintained until development and (now likely) mass deployment of a vaccine (or therapeutics), since otherwise, many susceptible individuals are still at risk of infection. We use a simple analytical model to explore how low levels of infection, combined with vaccination, determine the trajectory to community immunity. Understanding the repercussions of the biological characteristics of the viral life cycle in this scenario is of considerable importance. We provide a simple description of this process by modelling the scenario where the effective reproduction number [Formula: see text] is maintained at 1. Since the additional complexity imposed by the strength and duration of transmission-blocking immunity is not yet clear, we use our framework to probe the impact of these uncertainties. Through intuitive analytical relations, we explore how the necessary magnitude of vaccination rates and mitigation efforts depends crucially on the durations of natural and vaccinal immunity. We also show that our framework can encompass seasonality or preexisting immunity due to epidemic dynamics prior to strong mitigation measures. Taken together, our simple conceptual model illustrates the importance of individual and vaccinal immunity for community immunity, and that the quantification of individuals immunized against SARS-CoV-2 is paramount.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1098/rsif.2020.0683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8086877PMC
February 2021

Economic and Behavioral Influencers of Vaccination and Antimicrobial Use.

Front Public Health 2020 21;8:614113. Epub 2020 Dec 21.

Princeton Environmental Institute, Princeton University, Princeton, NJ, United States.

Despite vast improvements in global vaccination coverage during the last decade, there is a growing trend in vaccine hesitancy and/or refusal globally. This has implications for the acceptance and coverage of a potential vaccine against COVID-19. In the United States, the number of children exempt from vaccination for "philosophical belief-based" non-medical reasons increased in 12 of the 18 states that allowed this policy from 2009 to 2017 (1). Meanwhile, the overuse and misuse of antibiotics, especially in young children, have led to increasing rates of drug resistance that threaten our ability to treat infectious diseases. Vaccine hesitancy and antibiotic overuse exist side-by-side in the same population of young children, and it is unclear why one modality (antibiotics) is universally seen as safe and effective, while the other (vaccines) is seen as potentially hazardous by some. In this review, we consider the drivers shaping the use of vaccines and antibiotics in the context of three factors: individual incentives, risk perceptions, and social norms and group dynamics. We illustrate how these factors contribute to the societal and individual costs of vaccine underuse and antimicrobial overuse. Ultimately, we seek to understand these factors that are at the nexus of infectious disease epidemiology and social science to inform policy-making.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpubh.2020.614113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779682PMC
January 2021

Corridors of Clarity: Four Principles to Overcome Uncertainty Paralysis in the Anthropocene.

Bioscience 2020 Dec 28;70(12):1139-1144. Epub 2020 Oct 28.

Economics, Athens University of Economics and Business, Athens, Greece, and at the University of Bologna, Bologna, Italy.

Global environmental change challenges humanity because of its broad scale, long-lasting, and potentially irreversible consequences. Key to an effective response is to use an appropriate scientific lens to peer through the mist of uncertainty that threatens timely and appropriate decisions surrounding these complex issues. Identifying such corridors of clarity could help understanding critical phenomena or causal pathways sufficiently well to justify taking policy action. To this end, we suggest four principles: Follow the strongest and most direct path between policy decisions on outcomes, focus on finding sufficient evidence for policy purpose, prioritize no-regrets policies by avoiding options with controversial, uncertain, or immeasurable benefits, aim for getting the big picture roughly right rather than focusing on details.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/biosci/biaa115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7750100PMC
December 2020

Asynchrony between virus diversity and antibody selection limits influenza virus evolution.

Elife 2020 11 11;9. Epub 2020 Nov 11.

Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.

Seasonal influenza viruses create a persistent global disease burden by evolving to escape immunity induced by prior infections and vaccinations. New antigenic variants have a substantial selective advantage at the population level, but these variants are rarely selected within-host, even in previously immune individuals. Using a mathematical model, we show that the temporal asynchrony between within-host virus exponential growth and antibody-mediated selection could limit within-host antigenic evolution. If selection for new antigenic variants acts principally at the point of initial virus inoculation, where small virus populations encounter well-matched mucosal antibodies in previously-infected individuals, there can exist protection against reinfection that does not regularly produce observable new antigenic variants within individual infected hosts. Our results provide a theoretical explanation for how virus antigenic evolution can be highly selective at the global level but nearly neutral within-host. They also suggest new avenues for improving influenza control.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.62105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7748417PMC
November 2020

Immune life history, vaccination, and the dynamics of SARS-CoV-2 over the next 5 years.

Science 2020 11 21;370(6518):811-818. Epub 2020 Sep 21.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

The future trajectory of the coronavirus disease 2019 (COVID-19) pandemic hinges on the dynamics of adaptive immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, salient features of the immune response elicited by natural infection or vaccination are still uncertain. We use simple epidemiological models to explore estimates for the magnitude and timing of future COVID-19 cases, given different assumptions regarding the protective efficacy and duration of the adaptive immune response to SARS-CoV-2, as well as its interaction with vaccines and nonpharmaceutical interventions. We find that variations in the immune response to primary SARS-CoV-2 infections and a potential vaccine can lead to markedly different immune landscapes and burdens of critically severe cases, ranging from sustained epidemics to near elimination. Our findings illustrate likely complexities in future COVID-19 dynamics and highlight the importance of immunological characterization beyond the measurement of active infections for adequately projecting the immune landscape generated by SARS-CoV-2 infections.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.abd7343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7857410PMC
November 2020

Robert May, 1936-2020: A man for all disciplines.

Proc Natl Acad Sci U S A 2020 09 10;117(38):23199-23201. Epub 2020 Sep 10.

Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.2016616117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7519286PMC
September 2020

Quorum sensing via dynamic cytokine signaling comprehensively explains divergent patterns of effector choice among helper T cells.

PLoS Comput Biol 2020 07 30;16(7):e1008051. Epub 2020 Jul 30.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America.

In the animal kingdom, various forms of swarming enable groups of autonomous individuals to transform uncertain information into unified decisions which are probabilistically beneficial. Crossing scales from individual to group decisions requires dynamically accumulating signals among individuals. In striking parallel, the mammalian immune system is also a group of decentralized autonomous units (i.e. cells) which collectively navigate uncertainty with the help of dynamically accumulating signals (i.e. cytokines). Therefore, we apply techniques of understanding swarm behavior to a decision-making problem in the mammalian immune system, namely effector choice among CD4+ T helper (Th) cells. We find that incorporating dynamic cytokine signaling into a simple model of Th differentiation comprehensively explains divergent observations of this process. The plasticity and heterogeneity of individual Th cells, the tunable mixtures of effector types that can be generated in vitro, and the polarized yet updateable group effector commitment often observed in vivo are all explained by the same set of underlying molecular rules. These rules reveal that Th cells harness dynamic cytokine signaling to implement a system of quorum sensing. Quorum sensing, in turn, may confer adaptive advantages on the mammalian immune system, especially during coinfection and during coevolution with manipulative parasites. This highlights a new way of understanding the mammalian immune system as a cellular swarm, and it underscores the power of collectives throughout nature.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1008051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7392205PMC
July 2020

Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans.

PLoS Comput Biol 2020 06 25;16(6):e1007892. Epub 2020 Jun 25.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America.

Seasonal influenza A viruses of humans evolve rapidly due to strong selection pressures from host immune responses, principally on the hemagglutinin (HA) viral surface protein. Based on mouse transmission experiments, a proposed mechanism for immune evasion consists of increased avidity to host cellular receptors, mediated by electrostatic charge interactions with negatively charged cell surfaces. In support of this, the HA charge of the globally circulating H3N2 has increased over time since its pandemic. However, the same trend was not seen in H1N1 HA sequences. This is counter-intuitive, since immune escape due to increased avidity (due itself to an increase in charge) was determined experimentally. Here, we explore whether patterns of local charge of H1N1 HA can explain this discrepancy and thus further associate electrostatic charge with immune escape and viral evolutionary dynamics. Measures of site-wise functional selection and expected charge computed from deep mutational scan data on an early H1N1 HA yield a striking division of residues into three groups, separated by charge. We then explored evolutionary dynamics of these groups from 1918 to 2008. In particular, one group increases in net charge over time and consists of sites that are evolving the fastest, that are closest to the receptor binding site (RBS), and that are exposed to solvent (i.e., on the surface). By contrast, another group decreases in net charge and consists of sites that are further away from the RBS and evolving slower, but also exposed to solvent. The last group consists of those sites in the HA core, with no change in net charge and that evolve very slowly. Thus, there is a group of residues that follows the same trend as seen for the entire H3N2 HA. It is possible that the H1N1 HA is under other biophysical constraints that result in compensatory decreases in charge elsewhere on the protein. Our results implicate localized charge in HA interactions with host cells, and highlight how deep mutational scan data can inform evolutionary hypotheses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1007892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7316228PMC
June 2020

Combating climate change with matching-commitment agreements.

Sci Rep 2020 06 19;10(1):10251. Epub 2020 Jun 19.

International Institute for Applied Systems Analysis, Laxenburg, A-2361, Austria.

Countries generally agree that global greenhouse gas emissions are too high, but prefer other countries reduce emissions rather than reducing their own. The Paris Agreement is intended to solve this collective action problem, but is likely insufficient. One proposed solution is a matching-commitment agreement, through which countries can change each other's incentives by committing to conditional emissions reductions, before countries decide on their unconditional reductions. Here, we study matching-commitment agreements between two heterogeneous countries. We find that such agreements (1) incentivize both countries to make matching commitments that in turn incentivize efficient emissions reductions, (2) reduce emissions from those expected without an agreement, and (3) increase both countries' welfare. Matching-commitment agreements are attractive because they do not require a central enforcing authority and only require countries to fulfil their promises; countries are left to choose their conditional and unconditional emissions reductions according to their own interests.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-63446-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7305217PMC
June 2020

Coalition-structured governance improves cooperation to provide public goods.

Sci Rep 2020 06 8;10(1):9194. Epub 2020 Jun 8.

ATP-group, P-2744-016, Porto Salvo, Portugal.

While the benefits of common and public goods are shared, they tend to be scarce when contributions are provided voluntarily. Failure to cooperate in the provision or preservation of these goods is fundamental to sustainability challenges, ranging from local fisheries to global climate change. In the real world, such cooperative dilemmas occur in multiple interactions with complex strategic interests and frequently without full information. We argue that voluntary cooperation enabled across overlapping coalitions (akin to polycentricity) not only facilitates a higher generation of non-excludable public goods, but it may also allow evolution toward a more cooperative, stable, and inclusive approach to governance. Contrary to any previous study, we show that these merits of multi-coalition governance are far more general than the singular examples occurring in the literature, and they are robust under diverse conditions of excludability, congestion of the non-excludable public good, and arbitrary shapes of the return-to-contribution function. We first confirm the intuition that a single coalition without enforcement and with players pursuing their self-interest without knowledge of returns to contribution is prone to cooperative failure. Next, we demonstrate that the same pessimistic model but with a multi-coalition structure of governance experiences relatively higher cooperation by enabling recognition of marginal gains of cooperation in the game at stake. In the absence of enforcement, public-goods regimes that evolve through a proliferation of voluntary cooperative forums can maintain and increase cooperation more successfully than singular, inclusive regimes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-65960-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7280206PMC
June 2020

Caring for the future can turn tragedy into comedy for long-term collective action under risk of collapse.

Proc Natl Acad Sci U S A 2020 06 20;117(23):12915-12922. Epub 2020 May 20.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544;

We will need collective action to avoid catastrophic climate change, and this will require valuing the long term as well as the short term. Shortsightedness and uncertainty have hindered progress in resolving this collective action problem and have been recognized as important barriers to cooperation among humans. Here, we propose a coupled social-ecological dilemma to investigate the interdependence of three well-identified components of this cooperation problem: 1) timescales of collapse and recovery in relation to time preferences regarding future outcomes, 2) the magnitude of the impact of collapse, and 3) the number of actors in the collective. We find that, under a sufficiently severe and time-distant collapse, how much the actors care for the future can transform the game from a tragedy of the commons into one of coordination, and even into a comedy of the commons in which cooperation dominates. Conversely, we also find conditions under which even strong concern for the future still does not transform the problem from tragedy to comedy. For a large number of participating actors, we find that the critical collapse impact, at which these game regime changes happen, converges to a fixed value of collapse impact per actor that is independent of the enhancement factor of the public good, which is usually regarded as the driver of the dilemma. Our results not only call for experimental testing but also help explain why polarization in beliefs about human-caused climate change can threaten global cooperation agreements.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1916545117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293627PMC
June 2020

Evolution of cooperation on temporal networks.

Nat Commun 2020 05 8;11(1):2259. Epub 2020 May 8.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.

Population structure is a key determinant in fostering cooperation among naturally self-interested individuals in microbial populations, social insect groups, and human societies. Traditional research has focused on static structures, and yet most real interactions are finite in duration and changing in time, forming a temporal network. This raises the question of whether cooperation can emerge and persist despite an intrinsically fragmented population structure. Here we develop a framework to study the evolution of cooperation on temporal networks. Surprisingly, we find that network temporality actually enhances the evolution of cooperation relative to comparable static networks, despite the fact that bursty interaction patterns generally impede cooperation. We resolve this tension by proposing a measure to quantify the amount of temporality in a network, revealing an intermediate level that maximally boosts cooperation. Our results open a new avenue for investigating the evolution of cooperation and other emergent behaviours in more realistic structured populations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-020-16088-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7210286PMC
May 2020

Dynamics in a simple evolutionary-epidemiological model for the evolution of an initial asymptomatic infection stage.

Proc Natl Acad Sci U S A 2020 05 8;117(21):11541-11550. Epub 2020 May 8.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544;

Pathogens exhibit a rich variety of life history strategies, shaped by natural selection. An important pathogen life history characteristic is the propensity to induce an asymptomatic yet productive (transmissive) stage at the beginning of an infection. This characteristic is subject to complex trade-offs, ranging from immunological considerations to population-level social processes. We aim to classify the evolutionary dynamics of such asymptomatic behavior of pathogens (hereafter "latency") in order to unify epidemiology and evolution for this life history strategy. We focus on a simple epidemiological model with two infectious stages, where hosts in the first stage can be partially or fully asymptomatic. Immunologically, there is a trade-off between transmission and progression in this first stage. For arbitrary trade-offs, we derive different conditions that guarantee either at least one evolutionarily stable strategy (ESS) at zero, some, or maximal latency of the first stage or, perhaps surprisingly, at least one unstable evolutionarily singular strategy. In this latter case, there is bistability between zero and nonzero (possibly maximal) latency. We then prove the uniqueness of interior evolutionarily singular strategies for power-law and exponential trade-offs: Thus, bistability is always between zero and maximal latency. Overall, previous multistage infection models can be summarized with a single model that includes evolutionary processes acting on latency. Since small changes in parameter values can lead to abrupt transitions in evolutionary dynamics, appropriate disease control strategies could have a substantial impact on the evolution of first-stage latency.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1920761117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261016PMC
May 2020

Dispersal Increases the Resilience of Tropical Savanna and Forest Distributions.

Am Nat 2020 05 8;195(5):833-850. Epub 2020 Apr 8.

Global change may induce changes in savanna and forest distributions, but the dynamics of these changes remain unclear. Classical biome theory suggests that climate is predictive of biome distributions, such that shifts will be continuous and reversible. This view, however, cannot explain the overlap in the climatic ranges of tropical biomes, which some argue may result from fire-vegetation feedbacks, maintaining savanna and forest as bistable states. Under this view, biome shifts are argued to be discontinuous and irreversible. Mean-field bistable models, however, are also limited, as they cannot reproduce the spatial aggregation of biomes. Here we suggest that both models ignore spatial processes, such as dispersal, which may be important when savanna and forest abut. We examine the contributions of dispersal to determining biome distributions using a 2D reaction-diffusion model, comparing results qualitatively to empirical savanna and forest distributions in sub-Saharan Africa. We find that the diffusion model resolves both the aforementioned limitations of biome models. First, local dispersive spatial interactions, with an underlying precipitation gradient, can reproduce the spatial aggregation of biomes with a stable savanna-forest boundary. Second, the boundary is determined not only by the amount of precipitation but also by the geometrical shape of the precipitation contours. These geometrical effects arise from continental-scale source-sink dynamics, which reproduce the mismatch between biome and climate. Dynamically, the spatial model predicts that dispersal may increase the resilience of tropical biome in response to global change: the boundary continuously tracks climate, recovering following disturbances, unless the remnant biome patches are too small.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1086/708270DOI Listing
May 2020
-->