1
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Zilio G, Deshpande JN, Duncan AB, Fronhofer EA, Kaltz O. Dispersal evolution and eco-evolutionary dynamics in antagonistic species interactions. Trends Ecol Evol 2024; 39:666-676. [PMID: 38637209 DOI: 10.1016/j.tree.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Dispersal evolution modifies diverse spatial processes, such as range expansions or biological invasions of single species, but we are currently lacking a realistic vision for metacommunities. Focusing on antagonistic species interactions, we review existing theory of dispersal evolution between natural enemies, and explain how this might be relevant for classic themes in host-parasite evolutionary ecology, namely virulence evolution or local adaptation. Specifically, we highlight the importance of considering the simultaneous (co)evolution of dispersal and interaction traits. Linking such multi-trait evolution with reciprocal demographic and epidemiological feedbacks might change basic predictions about coevolutionary processes and spatial dynamics of interacting species. Future challenges concern the integration of system-specific disease ecology or spatial modifiers, such as spatial network structure or environmental heterogeneity.
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Affiliation(s)
- Giacomo Zilio
- Institut des Sciences de l'Evolution - Montpellier (ISEM), University of Montpellier, CNRS, IRD, Montpellier, France; Centre d'Ecologie Fonctionelle et Evolutive (CEFE), University of Montpellier, CNRS, Montpellier, France.
| | - Jhelam N Deshpande
- Institut des Sciences de l'Evolution - Montpellier (ISEM), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Alison B Duncan
- Institut des Sciences de l'Evolution - Montpellier (ISEM), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Emanuel A Fronhofer
- Institut des Sciences de l'Evolution - Montpellier (ISEM), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Oliver Kaltz
- Institut des Sciences de l'Evolution - Montpellier (ISEM), University of Montpellier, CNRS, IRD, Montpellier, France.
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2
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Le Pennec G, Retel C, Kowallik V, Becks L, Feulner PGD. Demographic fluctuations and selection during host-parasite co-evolution interactively increase genetic diversity. Mol Ecol 2024; 33:e16939. [PMID: 36997280 DOI: 10.1111/mec.16939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/01/2023]
Abstract
Host-parasite interactions can cause strong demographic fluctuations accompanied by selective sweeps of resistance/infectivity alleles. Both demographic bottlenecks and frequent sweeps are expected to reduce the amount of segregating genetic variation and therefore might constrain adaptation during co-evolution. Recent studies, however, suggest that the interaction of demographic and selective processes is a key component of co-evolutionary dynamics and may rather positively affect levels of genetic diversity available for adaptation. Here, we provide direct experimental testing of this hypothesis by disentangling the effects of demography, selection and their interaction in an experimental host-parasite system. We grew 12 populations of a unicellular, asexually reproducing algae (Chlorella variabilis) that experienced either growth followed by constant population sizes (three populations), demographic fluctuations (three populations), selection induced by exposure to a virus (three populations), or demographic fluctuations together with virus-induced selection (three populations). After 50 days (~50 generations), we conducted whole-genome sequencing of each algal host population. We observed more genetic diversity in populations that jointly experienced selection and demographic fluctuations than in populations where these processes were experimentally separated. In addition, in those three populations that jointly experienced selection and demographic fluctuations, experimentally measured diversity exceeds expected values of diversity that account for the cultures' population sizes. Our results suggest that eco-evolutionary feedbacks can positively affect genetic diversity and provide the necessary empirical measures to guide further improvements of theoretical models of adaptation during host-parasite co-evolution.
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Affiliation(s)
- Guénolé Le Pennec
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Cas Retel
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Vienna Kowallik
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Albert-Ludwigs University Freiburg, Faculty of Environment and Natural Resources, Professorship of Forest Entomology and Protection, Stegen-Wittental, Germany
| | - Lutz Becks
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Aquatic Ecology and Evolution, Limnological Institute University of Konstanz, Konstanz, Germany
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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3
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Northrup GR, White A, Parratt SR, Rozins C, Laine AL, Boots M. The evolutionary dynamics of hyperparasites. J Theor Biol 2024; 582:111741. [PMID: 38280543 DOI: 10.1016/j.jtbi.2024.111741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024]
Abstract
Evolutionary theory has typically focused on pairwise interactions, such as those between hosts and parasites, with relatively little work having been carried out on more complex interactions including hyperparasites: parasites of parasites. Hyperparasites are common in nature, with the chestnut blight fungus virus CHV-1 a well-known natural example, but also notably include the phages of important human bacterial diseases. We build a general modeling framework for the evolution of hyperparasites that highlights the central role that the ability of a hyperparasite to be transmitted with its parasite plays in their evolution. A key result is that hyperparasites which transmit with their parasite hosts (hitchhike) will be selected for lower virulence, trending towards hypermutualism or hypercommensalism. We examine the impact on the evolution of hyperparasite systems of a wide range of host and parasite traits showing, for example, that high parasite virulence selects for higher hyperparasite virulence resulting in reductions in parasite virulence when hyperparasitized. Furthermore, we show that acute parasite infection will also select for increased hyperparasite virulence. Our results have implications for hyperparasite research, both as biocontrol agents and for their role in shaping community ecology and evolution and moreover emphasize the importance of understanding evolution in the context of multitrophic interactions.
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Affiliation(s)
- Graham R Northrup
- Center for Computational Biology, College of Engineering, University of California, Berkeley, CA, USA.
| | - Andy White
- Maxwell Institute for Mathematical Sciences, Heriot-Watt University, Edinburgh, UK; Department of Mathematics, Heriot-Watt University, Edinburgh, UK
| | - Steven R Parratt
- Department of Ecology, Evolution and Behaviour, University of Liverpool, Liverpool, UK
| | - Carly Rozins
- Department of Science and Technology Studies, Division of Natural Science, York University, Toronto, Ontario, Canada
| | - Anna-Liisa Laine
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | - Mike Boots
- Department of Integrative Biology, University of California Berkeley, CA, USA; Center for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, UK
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4
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Buckingham LJ, Ashby B. Separation of evolutionary timescales in coevolving species. J Theor Biol 2024; 579:111688. [PMID: 38096978 DOI: 10.1016/j.jtbi.2023.111688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/24/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
Many coevolutionary processes, including host-parasite and host-symbiont interactions, involve one species or trait which evolves much faster than the other. Whether or not a coevolutionary trajectory converges depends on the relative rates of evolutionary change in the two species, and so current adaptive dynamics approaches generally either determine convergence stability by considering arbitrary (often comparable) rates of evolutionary change or else rely on necessary or sufficient conditions for convergence stability. We propose a method for determining convergence stability in the case where one species is expected to evolve much faster than the other. This requires a second separation of timescales, which assumes that the faster evolving species will reach its evolutionary equilibrium (if one exists) before a new mutation arises in the more slowly evolving species. This method, which is likely to be a reasonable approximation for many coevolving species, both provides straightforward conditions for convergence stability and is less computationally expensive than traditional analysis of coevolution models, as it reduces the trait space from a two-dimensional plane to a one-dimensional manifold. In this paper, we present the theory underlying this new separation of timescales and provide examples of how it could be used to determine coevolutionary outcomes from models.
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Affiliation(s)
- Lydia J Buckingham
- Department of Mathematical Sciences, University of Bath, Bath, UK; Milner Centre for Evolution, University of Bath, Bath, UK.
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, Bath, UK; Milner Centre for Evolution, University of Bath, Bath, UK; Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada; The Pacific Institute on Pathogens, Pandemics and Society (PIPPS), Simon Fraser University, Burnaby, BC, Canada
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5
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O'Neill X, White A, Boots M. The evolution of parasite virulence under targeted culling and harvesting in wildlife and livestock. Evol Appl 2023; 16:1697-1707. [PMID: 38020874 PMCID: PMC10660816 DOI: 10.1111/eva.13594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/27/2023] [Accepted: 09/01/2023] [Indexed: 12/01/2023] Open
Abstract
There is a clear need to understand the effect of human intervention on the evolution of infectious disease. In particular, culling and harvesting of both wildlife and managed livestock populations are carried out in a wide range of management practices, and they have the potential to impact the evolution of a broad range of disease characteristics. Applying eco-evolutionary theory we show that once culling/harvesting becomes targeted on specific disease classes, the established result that culling selects for higher virulence is only found when sufficient infected individuals are culled. If susceptible or recovered individuals are targeted, selection for lower virulence can occur. An important implication of this result is that when culling to eradicate an infectious disease from a population, while it is optimal to target infected individuals, the consequent evolution can increase the basic reproductive ratio of the infection, R 0 , and make parasite eradication more difficult. We show that increases in evolved virulence due to the culling of infected individuals can lead to excess population decline when sustainably harvesting a population. In contrast, culling susceptible or recovered individuals can select for decreased virulence and a reduction in population decline through culling. The implications to the evolution of virulence are typically the same in wildlife populations, that are regulated by the parasite, and livestock populations, that have a constant population size where restocking balances the losses due to mortality. However, the well-known result that vertical transmission selects for lower virulence and transmission in wildlife populations is less marked in livestock populations for parasites that convey long-term immunity since restocking can enhance the density of the immune class. Our work emphasizes the importance of understanding the evolutionary consequences of intervention strategies and the different ecological feedbacks that can occur in wildlife and livestock populations.
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Affiliation(s)
- Xander O'Neill
- Department of MathematicsMaxwell Institute for Mathematical Sciences, Heriot‐Watt UniversityEdinburghUK
| | - Andy White
- Department of MathematicsMaxwell Institute for Mathematical Sciences, Heriot‐Watt UniversityEdinburghUK
| | - Mike Boots
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- Centre for Ecology and Conservation, BiosciencesUniversity of ExeterCornwallUK
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6
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Peters MAE, Mideo N, MacPherson A. The maintenance of genetic diversity under host-parasite coevolution in finite, structured populations. J Evol Biol 2023; 36:1328-1341. [PMID: 37610056 DOI: 10.1111/jeb.14207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/12/2023] [Accepted: 06/27/2023] [Indexed: 08/24/2023]
Abstract
As a corollary to the Red Queen hypothesis, host-parasite coevolution has been hypothesized to maintain genetic variation in both species. Recent theoretical work, however, suggests that reciprocal natural selection alone is insufficient to maintain variation at individual loci. As highlighted by our brief review of the theoretical literature, models of host-parasite coevolution often vary along multiple axes (e.g. inclusion of ecological feedbacks or abiotic selection mosaics), complicating a comprehensive understanding of the effects of interacting evolutionary processes on diversity. Here we develop a series of comparable models to explore the effect of interactions between spatial structures and antagonistic coevolution on genetic diversity. Using a matching alleles model in finite populations connected by migration, we find that, in contrast to panmictic populations, coevolution in a spatially structured environment can maintain genetic variation relative to neutral expectations with migration alone. These results demonstrate that geographic structure is essential for understanding the effect of coevolution on biological diversity.
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Affiliation(s)
- Madeline A E Peters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ailene MacPherson
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
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7
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Best A, Ashby B. How do fluctuating ecological dynamics impact the evolution of hosts and parasites? Philos Trans R Soc Lond B Biol Sci 2023; 378:20220006. [PMID: 36744565 PMCID: PMC9900711 DOI: 10.1098/rstb.2022.0006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Theoretical models of the evolution of parasites and their hosts have shaped our understanding of infectious disease dynamics for over 40 years. Many theoretical models assume that the underlying ecological dynamics are at equilibrium or constant, yet we know that in a great many systems there are fluctuations in the ecological dynamics owing to a variety of intrinsic or extrinsic factors. Here, we discuss the challenges presented when modelling evolution in systems with fluctuating ecological dynamics and summarize the main approaches that have been developed to study host-parasite evolution in such systems. We provide an in-depth guide to one of the methods by applying it to two worked examples of host evolution that have not previously been studied in the literature: when cycles occur owing to seasonal forcing in competition, and when the presence of a free-living parasite causes cycles, with accompanying interactive Python code provided. We review the findings of studies that have explored host-parasite evolution when ecological dynamics fluctuate, and point to areas of future research. Throughout we stress the importance of feedbacks between the ecological and evolutionary dynamics in driving the outcomes of infectious disease systems. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.
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Affiliation(s)
- A. Best
- School of Mathematics and Statistics, University of Sheffield, Sheffield S3 7RH, UK,Integrative Biology, University of California - Berkeley, Berkeley, CA 94720-5800, USA
| | - B. Ashby
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6,Department of Mathematics, University of Bath, Bath BA2 7AY, UK
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8
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Hite JL, Pfenning-Butterworth A, Auld SKJR. Commentary: Infectious disease — the ecological theater and the evolutionary play. Evol Ecol 2023. [DOI: 10.1007/s10682-023-10229-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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9
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Kikuchi D, Simon MW. Social learning of innovations in dynamic predator-prey systems. Am Nat 2023; 201:895-907. [DOI: 10.1086/724491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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10
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Broder ED, Gallagher JH, Wikle AW, Welsh GT, Zonana DM, Firneno TJ, Tinghitella RM. A well-studied parasitoid fly of field crickets uses multiple alternative hosts in its introduced range. Evol Ecol 2023. [DOI: 10.1007/s10682-022-10225-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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11
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Aavani P, Rice SH. When sexual selection in hosts benefits parasites. Infect Dis Model 2022; 7:561-570. [PMID: 36158519 PMCID: PMC9474839 DOI: 10.1016/j.idm.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/24/2022] [Accepted: 08/04/2022] [Indexed: 12/03/2022] Open
Abstract
In host-parasite coevolution, the parasite is selected to increase its infectivity while host is selected to resist the parasite infection. It is widely held that parasite-mediated sexual selection can further amplify the selective pressure on the host to overcome parasite infection. In this paper we focus on certain types of parasites, those that can impair the activity of the host immune function to prevent signs of sickness. We show that the effect of sexual selection can actually reduce the selective pressure on the host immune response to adapt to the parasite infection. We design a simple mathematical model for a population of sexually reproducing organism in which individuals are choosy, preferring traits that are correlated negatively with immune system activity. We introduce to this population a parasite that can suppress activation of the host's immune response. Our results show that even though the host immune system is likely to ultimately evolve and adapt to the parasite infection, when sexual selection is part of this process, it can slow down this evolution on the host and give the parasite more time to get established.
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Affiliation(s)
- Pooya Aavani
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.,Department of Biology, Emory University, Atlanta, GA, USA
| | - Sean H Rice
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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12
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Yang Y, Ma C, Zu J. Coevolutionary dynamics of host-pathogen interaction with density-dependent mortality. J Math Biol 2022; 85:15. [PMID: 35877051 PMCID: PMC9309463 DOI: 10.1007/s00285-022-01782-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/08/2022] [Accepted: 07/05/2022] [Indexed: 12/04/2022]
Abstract
This study explores the coevolutionary dynamics of host-pathogen interaction based on a susceptible-infected population model with density-dependent mortality. We assume that both the host's resistance and the pathogen's virulence will adaptively evolve, but there are inevitable costs in terms of host birth rate and disease-related mortality rate. Particularly, it is assumed that both the host resistance and pathogen virulence can affect the transmission rate. By using the approach of adaptive dynamics and numerical simulation, we find that the finally coevolutionary outcome depends on the strength of host-pathogen asymmetric interaction, the curvature of trade-off functions, and the intensity of density-dependent natural mortality. To be specific, firstly, we find that if the strengths of host-pathogen asymmetric interaction and disease-related mortality are relatively weak, or the density-dependent natural mortality is relatively strong, then the host resistance and pathogen virulence will evolve to a continuously stable strategy. However, if the strength of host-pathogen asymmetric interaction and disease-related mortality becomes stronger, then the host resistance and pathogen virulence will evolve periodically. Secondly, we find that if the intensities of both the birth rate trade-off function and the density-dependent natural mortality are relatively weak, but the strength of host-pathogen asymmetric interaction becomes relatively strong, then the evolution of host resistance will have a relatively strongly accelerating benefit, the evolutionary branching of host resistance will first arise. However, if the strength of host-pathogen asymmetric interaction is relatively weak, but the intensity of the trade-off function of disease-related mortality becomes relatively strong, then the evolution of pathogen virulence will have a relatively strongly decelerating cost, and the evolutionary branching of pathogen virulence will first arise. Thirdly, after the evolutionary branching of host resistance and pathogen virulence, we further study the coevolutionary dynamics of two-hosts-one-pathogen interaction and one-host-two-pathogens interaction. We find that if the evolutionary branching of host resistance arises firstly, then the finally evolutionary outcome contains a dimorphic host and a monomorphic pathogen population. If the evolutionary branching of pathogen virulence arises firstly, then the finally evolutionary outcome may contain a monomorphic host and a dimorphic pathogen population.
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Affiliation(s)
- Yantao Yang
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, PR China
- College of Mathematics and Computer Science, Yan'an University, Yan'an, 716000, PR China
| | - Chaojing Ma
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Jian Zu
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, PR China.
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13
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Amandine C, Ebert D, Stukenbrock E, Rodríguez de la Vega RC, Tiffin P, Croll D, Tellier A. Unraveling coevolutionary dynamics using ecological genomics. Trends Genet 2022; 38:1003-1012. [PMID: 35715278 DOI: 10.1016/j.tig.2022.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Coevolutionary interactions, from the delicate co-dependency in mutualistic interactions to the antagonistic relationship of hosts and parasites, are a ubiquitous driver of adaptation. Surprisingly, little is known about the genomic processes underlying coevolution in an ecological context. However, species comprise genetically differentiated populations that interact with temporally variable abiotic and biotic environments. We discuss the recent advances in coevolutionary theory and genomics as well as shortcomings, to identify coevolving genes that take into account this spatial and temporal variability of coevolution, and propose a practical guide to understand the dynamic of coevolution using an ecological genomics lens.
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Affiliation(s)
- Cornille Amandine
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France.
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Eva Stukenbrock
- Max Planck Institute for Terrestrial Microbiology, Max Planck Research Group, Fungal Biodiversity, Marburg, Germany
| | | | - Peter Tiffin
- Department of Plant and Microbial Biology, 250 Biological Sciences, 1445 Gortner Ave., University of Minnesota, Saint Paul, MN 55108, USA
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland.
| | - Aurélien Tellier
- Population Genetics, Department of Life Science Systems, Technical University of Munich, Liesel-Beckman-Str. 2, 85354 Freising, Germany.
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14
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Ashby B, Farine DR. Social information use shapes the coevolution of sociality and virulence. Evolution 2022; 76:1153-1169. [PMID: 35420704 PMCID: PMC9322624 DOI: 10.1111/evo.14491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 01/21/2023]
Abstract
Social contacts can facilitate the spread of both survival-related information and infectious diseases, but little is known about how these processes combine to shape host and parasite evolution. Here, we use a theoretical model that captures both infection and information transmission processes to investigate how host sociality (contact effort) and parasite virulence (disease-associated mortality rate) (co)evolve. We show that selection for sociality (and in turn, virulence) depends on both the intrinsic costs and benefits of social information and infection as well as their relative prevalence in the population. Specifically, greater sociality and lower virulence evolve when the risk of infection is either low or high and social information is neither very common nor too rare. Lower sociality and higher virulence evolve when the prevalence patterns are reversed. When infection and social information are both at moderate levels in the population, the direction of selection depends on the relative costs and benefits of being infected or informed. We also show that sociality varies inversely with virulence, and that parasites may be unable to prevent runaway selection for higher contact efforts. Together, these findings provide new insights for our understanding of group living and how apparently opposing ecological processes can influence the evolution of sociality and virulence in a range of ways.
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Affiliation(s)
- Ben Ashby
- Department of Mathematical SciencesUniversity of BathBathSomersetUK,Department of MathematicsSimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Damien R. Farine
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland,Max Planck Institute of Animal BehaviorRadolfzellGermany,Centre for the Advanced Study of Collective BehaviourUniversity of KonstanzKonstanzGermany
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15
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Buckingham LJ, Ashby B. Coevolutionary theory of hosts and parasites. J Evol Biol 2022; 35:205-224. [PMID: 35030276 PMCID: PMC9305583 DOI: 10.1111/jeb.13981] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/14/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
Host and parasite evolution are closely intertwined, with selection for adaptations and counter-adaptations forming a coevolutionary feedback loop. Coevolutionary dynamics are often difficult to intuit due to these feedbacks and are hard to demonstrate empirically in most systems. Theoretical models have therefore played a crucial role in shaping our understanding of host-parasite coevolution. Theoretical models vary widely in their assumptions, approaches and aims, and such variety makes it difficult, especially for non-theoreticians and those new to the field, to: (1) understand how model approaches relate to one another; (2) identify key modelling assumptions; (3) determine how model assumptions relate to biological systems; and (4) reconcile the results of different models with contrasting assumptions. In this review, we identify important model features, highlight key results and predictions and describe how these pertain to model assumptions. We carry out a literature survey of theoretical studies published since the 1950s (n = 219 papers) to support our analysis. We identify two particularly important features of models that tend to have a significant qualitative impact on the outcome of host-parasite coevolution: population dynamics and the genetic basis of infection. We also highlight the importance of other modelling features, such as stochasticity and whether time proceeds continuously or in discrete steps, that have received less attention but can drastically alter coevolutionary dynamics. We finish by summarizing recent developments in the field, specifically the trend towards greater model complexity, and discuss likely future directions for research.
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Affiliation(s)
- Lydia J. Buckingham
- Department of Mathematical SciencesUniversity of BathBathUK
- Milner Centre for EvolutionUniversity of BathBathUK
| | - Ben Ashby
- Department of Mathematical SciencesUniversity of BathBathUK
- Milner Centre for EvolutionUniversity of BathBathUK
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16
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Gupta A, Peng S, Leung CY, Borin JM, Medina S, Weitz JS, Meyer JR. Leapfrog dynamics in phage‐bacteria coevolution revealed by joint analysis of cross‐infection phenotypes and whole genome sequencing. Ecol Lett 2022; 25:876-888. [PMID: 35092147 PMCID: PMC10167754 DOI: 10.1111/ele.13965] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/21/2021] [Accepted: 11/10/2021] [Indexed: 01/21/2023]
Abstract
Viruses and their hosts can undergo coevolutionary arms races where hosts evolve increased resistance and viruses evolve counter-resistance. Given these arms race dynamics (ARD), both players are predicted to evolve along a single trajectory as more recently evolved genotypes replace their predecessors. By coupling phenotypic and genomic analyses of coevolving populations of bacteriophage λ and Escherichia coli, we find conflicting evidence for ARD. Virus-host infection phenotypes fit the ARD model, yet genomic analyses revealed fluctuating selection dynamics. Rather than coevolution unfolding along a single trajectory, cryptic genetic variation emerges and is maintained at low frequency for generations until it eventually supplants dominant lineages. These observations suggest a hybrid 'leapfrog' dynamic, revealing weaknesses in the predictive power of standard coevolutionary models. The findings shed light on the mechanisms that structure coevolving ecological networks and reveal the limits of using phenotypic or genomic data alone to differentiate coevolutionary dynamics.
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Affiliation(s)
- Animesh Gupta
- Department of Physics University of California San Diego La Jolla California USA
| | - Shengyun Peng
- School of Biological Sciences Georgia Institute of Technology Atlanta Georgia USA
| | - Chung Yin Leung
- School of Biological Sciences Georgia Institute of Technology Atlanta Georgia USA
| | - Joshua M. Borin
- Division of Biological Science University of California San Diego La Jolla California USA
| | - Sarah J. Medina
- Division of Biological Science University of California San Diego La Jolla California USA
| | - Joshua S. Weitz
- School of Biological Sciences Georgia Institute of Technology Atlanta Georgia USA
- School of Physics Georgia Institute of Technology Atlanta Georgia USA
| | - Justin R. Meyer
- Division of Biological Science University of California San Diego La Jolla California USA
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17
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Papkou A, Schalkowski R, Barg MC, Koepper S, Schulenburg H. Population size impacts host-pathogen coevolution. Proc Biol Sci 2021; 288:20212269. [PMID: 34905713 PMCID: PMC8670963 DOI: 10.1098/rspb.2021.2269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022] Open
Abstract
Ongoing host-pathogen interactions are characterized by rapid coevolutionary changes forcing species to continuously adapt to each other. The interacting species are often defined by finite population sizes. In theory, finite population size limits genetic diversity and compromises the efficiency of selection owing to genetic drift, in turn constraining any rapid coevolutionary responses. To date, however, experimental evidence for such constraints is scarce. The aim of our study was to assess to what extent population size influences the dynamics of host-pathogen coevolution. We used Caenorhabditus elegans and its pathogen Bacillus thuringiensis as a model for experimental coevolution in small and large host populations, as well as in host populations which were periodically forced through a bottleneck. By carefully controlling host population size for 23 host generations, we found that host adaptation was constrained in small populations and to a lesser extent in the bottlenecked populations. As a result, coevolution in large and small populations gave rise to different selection dynamics and produced different patterns of host-pathogen genotype-by-genotype interactions. Our results demonstrate a major influence of host population size on the ability of the antagonists to co-adapt to each other, thereby shaping the dynamics of antagonistic coevolution.
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Affiliation(s)
- Andrei Papkou
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universitaet Kiel, 24098 Kiel, Germany
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Rebecca Schalkowski
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universitaet Kiel, 24098 Kiel, Germany
| | - Mike-Christoph Barg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universitaet Kiel, 24098 Kiel, Germany
| | - Svenja Koepper
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universitaet Kiel, 24098 Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universitaet Kiel, 24098 Kiel, Germany
- Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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18
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Lerner N, Luizzi V, Antonovics J, Bruns E, Hood ME. Resistance Correlations Influence Infection by Foreign Pathogens. Am Nat 2021; 198:206-218. [PMID: 34260867 PMCID: PMC8283004 DOI: 10.1086/715013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
AbstractReciprocal selection promotes the specificity of host-pathogen associations and resistance polymorphisms in response to disease. However, plants and animals also vary in response to pathogen species not previously encountered in nature, with potential effects on new disease emergence. Using anther smut disease, we show that resistance (measured as infection rates) to foreign pathogens can be correlated with standing variation in resistance to an endemic pathogen. In Silene vulgaris, genetic variation in resistance to its endemic anther smut pathogen correlated positively with resistance variation to an anther smut pathogen from another host, but the relationship was negative between anther smut and a necrotrophic pathogen. We present models describing the genetic basis for assessing resistance relationships between endemic and foreign pathogens and for quantifying infection probabilities on foreign pathogen introduction. We show that even when the foreign pathogen has a lower average infection ability than the endemic pathogen, infection outcomes are determined by the sign and strength of the regression of the host's genetic variation in infection rates by a foreign pathogen on variation in infection rates by an endemic pathogen as well as by resistance allele frequencies. Given that preinvasion equilibria of resistance are determined by factors including resistance costs, we show that protection against foreign pathogens afforded by positively correlated resistances can be lessened or even result in elevated infection risk at the population level, depending on local dynamics. Therefore, a pathogen's emergence potential could be influenced not only by its average infection rate but also by resistance variation resulting from prior selection imposed by endemic diseases.
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Affiliation(s)
- Noah Lerner
- Department of Biology, Amherst College, Amherst, Massachusetts 01002
| | - Victoria Luizzi
- Department of Biology, Amherst College, Amherst, Massachusetts 01002
| | - Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Emily Bruns
- Department of Biology, University of Maryland, College Park, Maryland 20742
| | - Michael E. Hood
- Department of Biology, Amherst College, Amherst, Massachusetts 01002
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19
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Märkle H, John S, Cornille A, Fields PD, Tellier A. Novel genomic approaches to study antagonistic coevolution between hosts and parasites. Mol Ecol 2021; 30:3660-3676. [PMID: 34038012 DOI: 10.1111/mec.16001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
Host-parasite coevolution is ubiquitous, shaping genetic and phenotypic diversity and the evolutionary trajectory of interacting species. With the advances of high throughput sequencing technologies applicable to model and non-model organisms alike, it is now feasible to study in greater detail (a) the genetic underpinnings of coevolution, (b) the speed and type of dynamics at coevolving loci, and (c) the genomic consequences of coevolution. This review focuses on three recently developed approaches that leverage information from host and parasite full genome data simultaneously to pinpoint coevolving loci and draw inference on the coevolutionary history. First, co-genome-wide association study (co-GWAS) methods allow pinpointing the loci underlying host-parasite interactions. These methods focus on detecting associations between genetic variants and the outcome of experimental infection tests or on correlations between genomes of naturally infected hosts and their infecting parasites. Second, extensions to population genomics methods can detect genes under coevolution and infer the coevolutionary history, such as fitness costs. Third, correlations between host and parasite population size in time are indicative of coevolution, and polymorphism levels across independent spatially distributed populations of hosts and parasites can reveal coevolutionary loci and infer coevolutionary history. We describe the principles of these three approaches and discuss their advantages and limitations based on coevolutionary theory. We present recommendations for their application to various host (prokaryotes, fungi, plants, and animals) and parasite (viruses, bacteria, fungi, and macroparasites) species. We conclude by pointing out methodological and theoretical gaps to be filled to extract maximum information from full genome data and thereby to shed light on the molecular underpinnings of coevolution.
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Affiliation(s)
- Hanna Märkle
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Sona John
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Amandine Cornille
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Peter D Fields
- Department of Environmental Sciences, University of Basel, Zoology, Basel, Switzerland
| | - Aurélien Tellier
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
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20
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First record of chronic Fascioloides magna infection in roe deer ( Capreolus capreolus). INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2021; 15:173-176. [PMID: 34113543 PMCID: PMC8170357 DOI: 10.1016/j.ijppaw.2021.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 11/20/2022]
Abstract
Fascioloidosis is an allochthonous parasitic disease in Europe caused by the digenean trematode Fascioloides magna. The final hosts of F. magna in Europe are defined as definitive, aberrant and dead-end. Roe deer are aberrant hosts in which juvenile flukes permanently migrate through the liver parenchyma. Failure in pseudocysts formation leads to the death of both the host and the parasite. In this paper we present gross and histological findings of F. magna infection in 34 roe deer. The special emphasis is on the pseudocyst formation accompanied with new fluke's migratory channels observed in 7 animals, suggesting reinfection and prolonged survival of roe deer. No F. magna eggs were recovered from the faeces of the infected animals. These findings indicate that pseudocyst formation is essential for roe deer survival, but also point out the potential beginning of adaptation processes in roe deer, altering otherwise acute and fatal disease into a chronic one.
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21
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Bassar RD, Coulson T, Travis J, Reznick DN. Towards a more precise - and accurate - view of eco-evolution. Ecol Lett 2021; 24:623-625. [PMID: 33617684 DOI: 10.1111/ele.13712] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/03/2021] [Indexed: 11/28/2022]
Abstract
Over the past 15 years, the number of papers focused on 'eco-evo dynamics' has increased exponentially (Figure 1). This pattern suggests the rapid growth of a new, integrative discipline. We argue this overstates the case. First, the terms 'eco-evo dynamics' and 'eco-evo interactions' are used too imprecisely. As a result, many studies that claim to describe eco-evo dynamics are actually describing basic ecological or evolutionary processes. Second, these terms are often used as if the study of how ecological and evolutionary processes are intertwined is novel when, in fact, it is not. The result is confusion over what the term 'eco-evolution' and its derivatives describe. We advocate a more precise definition of eco-evolution that is more useful in efforts to understand and characterise the diversity of ecological and evolutionary processes and that focuses attention on the subset of those processes that occur only when ecological and evolutionary timescales are comparable. [Figure: see text].
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Affiliation(s)
| | - Tim Coulson
- Department of Zoology, University of Oxford, Oxford, UK
| | - Joseph Travis
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - David N Reznick
- Department of Biology, University of California, Riverside, CA, USA
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22
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MacPherson A, Keeling MJ, Otto SP. Feedback between coevolution and epidemiology can help or hinder the maintenance of genetic variation in host-parasite models. Evolution 2021; 75:582-599. [PMID: 33459348 DOI: 10.1111/evo.14165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 12/07/2020] [Indexed: 11/27/2022]
Abstract
Antagonistic coevolution has long been suggested to help maintain host genetic variation. Although ecological and epidemiological feedbacks are known to have important consequences on coevolutionary allele-frequency dynamics, their effects on the maintenance of genetic variation remains poorly understood. Here, we extend previous work on the maintenance of genetic variation in a classic matching alleles coevolutionary model by exploring the effects of ecological and epidemiological feedbacks, where both allele frequencies and population sizes are allowed to vary over time. We find that coevolution rarely maintains more host genetic variation than expected under neutral genetic drift alone. When and if coevolution maintains or depletes genetic variation relative to neutral drift is determined, predominantly, by two factors: the deterministic stability of the Red Queen allele-frequency cycles and the chance of allele fixation in the pathogen, as this results in directional selection and depletion of genetic variation in the host. Compared to purely coevolutionary models with constant host and pathogen population sizes, ecological and epidemiological feedbacks stabilize Red Queen cycles deterministically, but population fluctuations in the pathogen increase the rate of allele fixation in the pathogen, especially in epidemiological models. Our results illustrate the importance of considering the ecological and epidemiological context in which coevolution occurs when examining the impact of Red Queen cycles on genetic variation.
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Affiliation(s)
- Ailene MacPherson
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Matthew J Keeling
- Zeeman Institute of Systems Biology and Infectious Disease Research (SBIDER), University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Sarah P Otto
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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23
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MacPherson A, Keeling MJ, Otto SP. Coevolution fails to maintain genetic variation in a host-parasite model with constant finite population size. Theor Popul Biol 2020; 137:10-21. [PMID: 33340528 DOI: 10.1016/j.tpb.2020.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/17/2023]
Abstract
Coevolutionary negative frequency-dependent selection has been hypothesized to maintain genetic variation in host and parasites. Despite the extensive literature pertaining to host-parasite coevolution, the temporal dynamics of genetic variation have not been examined in a matching-alleles model (MAM) with a finite population size relative to the expectation under neutral genetic drift alone. The dynamics of the MA coevolution in an infinite population, in fact, suggests that genetic variation in these coevolving populations behaves neutrally. By comparing host heterozygosity to the expectation in a single-species model of neutral genetic drift we find that while this is also largely true in finite populations two additional phenomena arise. First, reciprocal natural selection acting on stochastic perturbations in host and pathogen allele frequencies results in a slight increase or decrease in genetic variation depending on the parameter conditions. Second, following the fixation of an allele in the parasite, selection in the MAM becomes directional, which then rapidly erodes genetic variation in the host. Hence, rather than maintain it, we find that, on average, matching-alleles coevolution depletes genetic variation.
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Affiliation(s)
- Ailene MacPherson
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.
| | - Matthew J Keeling
- Zeeman Institute of Systems Biology and Infectious Disease Research (SBIDER), University of Warwick, Coventry, United Kingdom
| | - Sarah P Otto
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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24
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Ashby B. When does parasitism maintain sex in the absence of Red Queen Dynamics? J Evol Biol 2020; 33:1795-1805. [PMID: 33073411 DOI: 10.1111/jeb.13718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/10/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022]
Abstract
Parasites can select for sexual reproduction in host populations, preventing replacement by faster-growing asexual genotypes. This is usually attributed to so-called 'Red Queen dynamics' (RQD), where antagonistic coevolution causes fluctuating selection in allele frequencies, which provides sex with an advantage over asex. However, parasitism may also maintain sex in the absence of RQD when sexual populations are more genetically diverse-and hence more resistant, on average-than clonal populations, allowing sex and asex to coexist at a stable equilibrium. Although the maintenance of sex due to RQD has been studied extensively, the conditions that allow sex and asex to stably coexist have yet to be explored in detail. In particular, we lack an understanding of how host demography and parasite epidemiology affect the maintenance of sex in the absence of RQD. Here, I use an eco-evolutionary model to show that both population density and the type and strength of virulence are important for maintaining sex, which can be understood in terms of their effects on disease prevalence and severity. In addition, I show that even in the absence of heterozygote advantage, asexual heterozygosity affects coexistence with sex due to variation in niche overlap. These results reveal which host and parasite characteristics are most important for the maintenance of sex in the absence of RQD, and provide empirically testable predictions for how demography and epidemiology mediate competition between sex and asex.
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Affiliation(s)
- Ben Ashby
- Department of Mathematical Sciences, University of Bath, Bath, UK
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25
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Bapteste E, Papale F. Modeling the evolution of interconnected processes: It is the song and the singers: Tracking units of selection with interaction networks. Bioessays 2020; 43:e2000077. [PMID: 33165956 DOI: 10.1002/bies.202000077] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 01/04/2023]
Abstract
Recently, Doolittle and Inkpen formulated a thought provoking theory, asserting that evolution by natural selection was responsible for the sideways evolution of two radically different kinds of selective units (also called Domains). The former entities, termed singers, correspond to the usual objects studied by evolutionary biologists (gene, genomes, individuals, species, etc.), whereas the later, termed songs, correspond to re-produced biological and ecosystemic functions, processes, information, and memes. Singers perform songs through selected patterns of interactions, meaning that a wealth of critical phenomena might receive novel evolutionary explanations. However, this theory did not provide an empirical approach to study evolution in such a broadened context. Here, we show that analyzing songs and singers, using patterns of interaction networks as a common ontology for both, offers a novel, actionable, inclusive and mathematical way to analyze not only the re-production but also the evolution and fitness of biological and ecosystemic interconnected processes.
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Affiliation(s)
- Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Bâtiment A 4ème étage, pièce 427, Paris, 75005, France
| | - François Papale
- Departement of Philosophy, University of Montreal, 2910 Édouard-Montpetit blvd, Montréal, QC, H3C 3J7, Canada
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26
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Märkle H, Tellier A. Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments. PLoS Comput Biol 2020; 16:e1007668. [PMID: 32203545 PMCID: PMC7156111 DOI: 10.1371/journal.pcbi.1007668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 04/14/2020] [Accepted: 01/19/2020] [Indexed: 01/27/2023] Open
Abstract
There is a long-standing interest in understanding host-parasite coevolutionary dynamics and associated fitness effects. Increasing amounts of genomic data for both interacting species offer a promising source to identify candidate loci and to infer the main parameters of the past coevolutionary history. However, so far no method exists to perform the latter. By coupling a gene-for-gene model with coalescent simulations, we first show that three types of biological costs, namely, resistance, infectivity and infection, define the allele frequencies at the internal equilibrium point of the coevolution model. These in return determine the strength of selective signatures at the coevolving host and parasite loci. We apply an Approximate Bayesian Computation (ABC) approach on simulated datasets to infer these costs by jointly integrating host and parasite polymorphism data at the coevolving loci. To control for the effect of genetic drift on coevolutionary dynamics, we assume that 10 or 30 repetitions are available from controlled experiments or several natural populations. We study two scenarios: 1) the cost of infection and population sizes (host and parasite) are unknown while costs of infectivity and resistance are known, and 2) all three costs are unknown while populations sizes are known. Using the ABC model choice procedure, we show that for both scenarios, we can distinguish with high accuracy pairs of coevolving host and parasite loci from pairs of neutrally evolving loci, though the statistical power decreases with higher cost of infection. The accuracy of parameter inference is high under both scenarios especially when using both host and parasite data because parasite polymorphism data do inform on costs applying to the host and vice-versa. As the false positive rate to detect pairs of genes under coevolution is small, we suggest that our method complements recently developed methods to identify host and parasite candidate loci for functional studies.
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Affiliation(s)
- Hanna Märkle
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Aurélien Tellier
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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27
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How long do Red Queen dynamics survive under genetic drift? A comparative analysis of evolutionary and eco-evolutionary models. BMC Evol Biol 2020; 20:8. [PMID: 31931696 PMCID: PMC6958710 DOI: 10.1186/s12862-019-1562-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/12/2019] [Indexed: 11/26/2022] Open
Abstract
Background Red Queen dynamics are defined as long term co-evolutionary dynamics, often with oscillations of genotype abundances driven by fluctuating selection in host-parasite systems. Much of our current understanding of these dynamics is based on theoretical concepts explored in mathematical models that are mostly (i) deterministic, inferring an infinite population size and (ii) evolutionary, thus ecological interactions that change population sizes are excluded. Here, we recall the different mathematical approaches used in the current literature on Red Queen dynamics. We then compare models from game theory (evo) and classical theoretical ecology models (eco-evo), that are all derived from individual interactions and are thus intrinsically stochastic. We assess the influence of this stochasticity through the time to the first loss of a genotype within a host or parasite population. Results The time until the first genotype is lost (“extinction time”), is shorter when ecological dynamics, in the form of a changing population size, is considered. Furthermore, when individuals compete only locally with other individuals extinction is even faster. On the other hand, evolutionary models with a fixed population size and competition on the scale of the whole population prolong extinction and therefore stabilise the oscillations. The stabilising properties of intra-specific competitions become stronger when population size is increased and the deterministic part of the dynamics gain influence. In general, the loss of genotype diversity can be counteracted with mutations (or recombination), which then allow the populations to recurrently undergo negative frequency-dependent selection dynamics and selective sweeps. Conclusion Although the models we investigated are equal in their biological motivation and interpretation, they have diverging mathematical properties both in the derived deterministic dynamics and the derived stochastic dynamics. We find that models that do not consider intraspecific competition and that include ecological dynamics by letting the population size vary, lose genotypes – and thus Red Queen oscillations – faster than models with competition and a fixed population size.
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28
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Živković D, John S, Verin M, Stephan W, Tellier A. Neutral genomic signatures of host-parasite coevolution. BMC Evol Biol 2019; 19:230. [PMID: 31856710 PMCID: PMC6924072 DOI: 10.1186/s12862-019-1556-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022] Open
Abstract
Background Coevolution is a selective process of reciprocal adaptation in hosts and parasites or in mutualistic symbionts. Classic population genetics theory predicts the signatures of selection at the interacting loci of both species, but not the neutral genome-wide polymorphism patterns. To bridge this gap, we build an eco-evolutionary model, where neutral genomic changes over time are driven by a single selected locus in hosts and parasites via a simple biallelic gene-for-gene or matching-allele interaction. This coevolutionary process may lead to cyclic changes in the sizes of the interacting populations. Results We investigate if and when these changes can be observed in the site frequency spectrum of neutral polymorphisms from host and parasite full genome data. We show that changes of the host population size are too smooth to be observable in its polymorphism pattern over the course of time. Conversely, the parasite population may undergo a series of strong bottlenecks occurring on a slower relative time scale, which may lead to observable changes in a time series sample. We also extend our results to cases with 1) several parasites per host accelerating relative time, and 2) multiple parasite generations per host generation slowing down rescaled time. Conclusions Our results show that time series sampling of host and parasite populations with full genome data are crucial to understand if and how coevolution occurs. This model provides therefore a framework to interpret and draw inference from genome-wide polymorphism data of interacting species.
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Affiliation(s)
- Daniel Živković
- Section of Population Genetics, Technical University of Munich, Freising, Germany.
| | - Sona John
- Section of Population Genetics, Technical University of Munich, Freising, Germany
| | - Mélissa Verin
- Section of Population Genetics, Technical University of Munich, Freising, Germany.,Department of Mathematics and Statistics, Queen's University, Kingston, Ontario, Canada
| | - Wolfgang Stephan
- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Aurélien Tellier
- Section of Population Genetics, Technical University of Munich, Freising, Germany.
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