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Svoboda J, Joshi S, Tkadlec J, Chatterjee K. Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating. PLoS Comput Biol 2024; 20:e1012008. [PMID: 38551989 PMCID: PMC11006194 DOI: 10.1371/journal.pcbi.1012008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/10/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024] Open
Abstract
Populations evolve by accumulating advantageous mutations. Every population has some spatial structure that can be modeled by an underlying network. The network then influences the probability that new advantageous mutations fixate. Amplifiers of selection are networks that increase the fixation probability of advantageous mutants, as compared to the unstructured fully-connected network. Whether or not a network is an amplifier depends on the choice of the random process that governs the evolutionary dynamics. Two popular choices are Moran process with Birth-death updating and Moran process with death-Birth updating. Interestingly, while some networks are amplifiers under Birth-death updating and other networks are amplifiers under death-Birth updating, so far no spatial structures have been found that function as an amplifier under both types of updating simultaneously. In this work, we identify networks that act as amplifiers of selection under both versions of the Moran process. The amplifiers are robust, modular, and increase fixation probability for any mutant fitness advantage in a range r ∈ (1, 1.2). To complement this positive result, we also prove that for certain quantities closely related to fixation probability, it is impossible to improve them simultaneously for both versions of the Moran process. Together, our results highlight how the two versions of the Moran process differ and what they have in common.
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Affiliation(s)
| | | | - Josef Tkadlec
- Computer Science Institute, Charles University, Prague, Czech Republic
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2
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Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants that modify population structure. J R Soc Interface 2023; 20:20230355. [PMID: 38016637 PMCID: PMC10684346 DOI: 10.1098/rsif.2023.0355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023] Open
Abstract
Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader's fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader's dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader's connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader's fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.
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Affiliation(s)
- Josef Tkadlec
- Department of Mathematics, Harvard University, Cambridge, MA 02138, USA
- Computer Science Institute, Charles University, Prague, Czech Republic
| | - Kamran Kaveh
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
| | - Krishnendu Chatterjee
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Martin A. Nowak
- Department of Mathematics, Harvard University, Cambridge, MA 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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3
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Smelikova E, Drevinek P, Nyc O, Brajerova M, Tkadlec J, Krutova M. To screen or not to screen medical students for carriage of multidrug-resistant pathogens? J Hosp Infect 2023; 140:15-23. [PMID: 37478913 DOI: 10.1016/j.jhin.2023.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND The carriage of multidrug-resistant (MDR) pathogens in medical students has not been studied extensively, despite the fact that they are in contact with patients and exposed to a hospital environment. AIM To investigate the intestinal and nasal carriage of MDR pathogens among medical students and its association with their lifestyle and demographic data. METHODS In 2021, first- and final-year medical students were invited to the study. Two rectal swabs were used for detection of extended-spectrum β-lactamase (ESBL)-producing, colistin-, tigecycline- or carbapenem-resistant Gram-negative bacteria and vancomycin-resistant enterococci. Nasal swab was used for Staphylococcus aureus culture. S. aureus isolates were characterized by spa typing; Gram-negative resistant isolates and meticillin-resistant S. aureus (MRSA) were subjected to whole-genome short and/or long sequencing. FINDINGS From 178 students, 80 (44.9%) showed nasal carriage of S. aureus; two isolates were MRSA. In rectal swabs, seven ESBL-producing strains were detected. Sixteen students were colonized by colistin-resistant bacteria, three isolates carried the mcr-1 gene (1.7%). The mcr-9 (10.7%, 19/178) and mcr-10 (2.2%, 4/178) genes were detected by quantitative polymerase chain reaction, but only two colistin-susceptible mcr-10-positive isolates were cultured. The S. aureus nasal carriage was negatively associated with antibiotic and probiotic consumption. S. aureus and colistin-resistant bacteria were detected more frequently among students in contact with livestock. CONCLUSION Medical students can be colonized by (multi)drug-resistant bacteria with no difference between first- and final-year students. The participation of students in self-screening increases their awareness of possible colonization by resistant strains and their potential transmission due to poor hand hygiene.
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Affiliation(s)
- E Smelikova
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - P Drevinek
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - O Nyc
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - M Brajerova
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - J Tkadlec
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - M Krutova
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic.
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Abstract
Direct reciprocity is a powerful mechanism for the evolution of cooperation based on repeated interactions between the same individuals. But high levels of cooperation evolve only if the benefit-to-cost ratio exceeds a certain threshold that depends on memory length. For the best-explored case of one-round memory, that threshold is two. Here, we report that intermediate mutation rates lead to high levels of cooperation, even if the benefit-to-cost ratio is only marginally above one, and even if individuals only use a minimum of past information. This surprising observation is caused by two effects. First, mutation generates diversity which undermines the evolutionary stability of defectors. Second, mutation leads to diverse communities of cooperators that are more resilient than homogeneous ones. This finding is relevant because many real-world opportunities for cooperation have small benefit-to-cost ratios, which are between one and two, and we describe how direct reciprocity can attain cooperation in such settings. Our result can be interpreted as showing that diversity, rather than uniformity, promotes evolution of cooperation.
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Affiliation(s)
- Josef Tkadlec
- Department of Mathematics, Harvard University, Cambridge, MA02138
| | - Christian Hilbe
- Max Planck Research Group ‘Dynamics of Social Behavior’, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Martin A. Nowak
- Department of Mathematics, Harvard University, Cambridge, MA02138
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA02138
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5
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Aloba BK, Kinnevey PM, Monecke S, Brennan GI, O'Connell B, Blomfeldt A, McManus BA, Schneider-Brachert W, Tkadlec J, Ehricht R, Senok A, Bartels MD, Coleman DC. An emerging Panton-Valentine leukocidin-positive CC5-meticillin-resistant Staphylococcus aureus-IVc clone recovered from hospital and community settings over a 17-year period from 12 countries investigated by whole-genome sequencing. J Hosp Infect 2023; 132:8-19. [PMID: 36481685 DOI: 10.1016/j.jhin.2022.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND A novel Panton-Valentine leukocidin (PVL)-positive meticillin-resistant Staphylococcus aureus (MRSA) clonal complex (CC)5-MRSA-IVc ('Sri Lankan' clone) was recently described from Sri Lanka. Similar isolates caused a recent Irish hospital outbreak. AIM To investigate the international dissemination and diversity of PVL-positive CC5-MRSA-IVc isolates from hospital and community settings using whole-genome sequencing (WGS). METHODS Core-genome single nucleotide polymorphism (cgSNP) analysis, core-genome multi-locus sequence typing (cgMLST) and microarray-based detection of antimicrobial-resistance and virulence genes were used to investigate PVL-positive CC5-MRSA-IVc (N = 214 including 46 'Sri Lankan' clone) from hospital and community settings in 12 countries over 17 years. Comparators included 29 PVL-positive and 23 PVL-negative CC5/ST5-MRSA-I/II/IVa/IVc/IVg/V. RESULTS Maximum-likelihood cgSNP analysis grouped 209/214 (97.7%) CC5-MRSA-IVc into Clade I; average of 110 cgSNPs between isolates. Clade III contained the five remaining CC5-MRSA-IVc; average of 92 cgSNPs between isolates. Clade II contained seven PVL-positive CC5-MRSA-IVa comparators, whereas the remaining 45 comparators formed an outlier group. Minimum-spanning cgMLST analysis revealed a comparably low average of 57 allelic differences between all CC5/ST5-MRSA-IVc. All 214 CC5/ST5-MRSA-IVc were identified as 'Sri Lankan' clone, predominantly spa type t002 (186/214) with low population diversity and harboured a similar range of virulence genes and variable antimicrobial-resistance genes. All 214 Sri Lankan clone isolates and Clade II comparators harboured a 9616-bp chromosomal PVL-encoding phage remnant, suggesting both arose from a PVL-positive meticillin-susceptible ancestor. Over half of Sri Lankan clone isolates were from infections (142/214), and where detailed metadata were available (168/214), most were community associated (85/168). CONCLUSIONS Stable chromosomal retention of pvl may facilitate Sri-Lankan clone dissemination.
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Affiliation(s)
- B K Aloba
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - P M Kinnevey
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - S Monecke
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany; Institut für Medizinische Mikrobiologie und Virologie, Uniklinikum Dresden, Dresden, Germany; InfectoGnostics Research Campus, Jena, Germany
| | - G I Brennan
- National MRSA Reference Laboratory, St. James's Hospital, Dublin, Ireland
| | - B O'Connell
- Department of Clinical Microbiology, St. James's Hospital, Dublin, Ireland
| | - A Blomfeldt
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - B A McManus
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - W Schneider-Brachert
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - J Tkadlec
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - R Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany; InfectoGnostics Research Campus, Jena, Germany; Institute of Physical Chemistry, Friedrich-Schiller University, Jena, Germany
| | - A Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - M D Bartels
- Department of Clinical Microbiology, Amager and Hvidovre Hospital, Hvidovre, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - D C Coleman
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland.
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Tkadlec J, Prasilova J, Drevinek P. 482 Fourier transform infrared spectroscopy for strain typing of Burkholderia cepacia complex and monitoring of strain carriage in chronically infected people with cystic fibrosis. J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)01172-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Chatterjee K, Svoboda J, Žikelić Đ, Pavlogiannis A, Tkadlec J. Social balance on networks: Local minima and best-edge dynamics. Phys Rev E 2022; 106:034321. [PMID: 36266862 DOI: 10.1103/physreve.106.034321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Structural balance theory is an established framework for studying social relationships of friendship and enmity. These relationships are modeled by a signed network whose energy potential measures the level of imbalance, while stochastic dynamics drives the network toward a state of minimum energy that captures social balance. It is known that this energy landscape has local minima that can trap socially aware dynamics, preventing it from reaching balance. Here we first study the robustness and attractor properties of these local minima. We show that a stochastic process can reach them from an abundance of initial states and that some local minima cannot be escaped by mild perturbations of the network. Motivated by these anomalies, we introduce best-edge dynamics (BED), a new plausible stochastic process. We prove that BED always reaches balance and that it does so fast in various interesting settings.
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Affiliation(s)
| | | | | | | | - Josef Tkadlec
- Department of Mathematics, Harvard University, Cambridge, Massachusetts 02138, USA
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8
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Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Infection dynamics of COVID-19 virus under lockdown and reopening. Sci Rep 2022; 12:1526. [PMID: 35087091 PMCID: PMC8795434 DOI: 10.1038/s41598-022-05333-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023] Open
Abstract
Motivated by COVID-19, we develop and analyze a simple stochastic model for the spread of disease in human population. We track how the number of infected and critically ill people develops over time in order to estimate the demand that is imposed on the hospital system. To keep this demand under control, we consider a class of simple policies for slowing down and reopening society and we compare their efficiency in mitigating the spread of the virus from several different points of view. We find that in order to avoid overwhelming of the hospital system, a policy must impose a harsh lockdown or it must react swiftly (or both). While reacting swiftly is universally beneficial, being harsh pays off only when the country is patient about reopening and when the neighboring countries coordinate their mitigation efforts. Our work highlights the importance of acting decisively when closing down and the importance of patience and coordination between neighboring countries when reopening.
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Affiliation(s)
| | - Josef Tkadlec
- Department of Mathematics, Harvard University, Cambridge, MA, 02138, USA
| | | | | | - Martin A Nowak
- Department of Mathematics, Harvard University, Cambridge, MA, 02138, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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9
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Melter O, Abdulla L, Harwill M, Vaniš V, Pavlíková M, Tkadlec J. SensiGram as a modified Gram staining procedure with higher sensitivity for detection of Gram-negative bacteria in blood culture. J Microbiol Methods 2021; 191:106344. [PMID: 34653524 DOI: 10.1016/j.mimet.2021.106344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
Affiliation(s)
- O Melter
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, V Úvalu 84, 15006 Prague 5, Czech Republic.
| | - L Abdulla
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, V Úvalu 84, 15006 Prague 5, Czech Republic
| | - M Harwill
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, V Úvalu 84, 15006 Prague 5, Czech Republic
| | - V Vaniš
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, V Úvalu 84, 15006 Prague 5, Czech Republic
| | - M Pavlíková
- Department of Probability and Mathematical Statistics, Charles University-Faculty of Mathematics and Physics, Prague, Czech Republic
| | - J Tkadlec
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, V Úvalu 84, 15006 Prague 5, Czech Republic
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10
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Abstract
Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.
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Affiliation(s)
- Josef Tkadlec
- grid.38142.3c000000041936754XDepartment of Mathematics, Harvard University, Cambridge, MA 02138 USA
| | - Andreas Pavlogiannis
- grid.7048.b0000 0001 1956 2722Department of Computer Science, Aarhus University, Aabogade 34, 8200 Aarhus, Denmark
| | - Krishnendu Chatterjee
- grid.33565.360000000404312247Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Martin A. Nowak
- grid.38142.3c000000041936754XDepartment of Mathematics, Harvard University, Cambridge, MA 02138 USA
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11
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Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS Comput Biol 2020; 16:e1007494. [PMID: 31951609 PMCID: PMC6968837 DOI: 10.1371/journal.pcbi.1007494] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/18/2019] [Indexed: 12/29/2022] Open
Abstract
The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process. Extensive literature exists on amplifiers of natural selection for the Birth-death Moran process, but no amplifiers are known for the death-Birth Moran process. Here we show that if amplifiers exist under death-Birth updating, they must be bounded and transient. Boundedness implies weak amplification, and transience implies amplification for only a limited range of the mutant fitness advantage. These results demonstrate that amplification depends on the specific mechanisms of the evolutionary process.
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Affiliation(s)
| | | | | | - Martin A. Nowak
- Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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12
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Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Population structure determines the tradeoff between fixation probability and fixation time. Commun Biol 2019; 2:138. [PMID: 31044163 PMCID: PMC6478818 DOI: 10.1038/s42003-019-0373-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 03/07/2019] [Indexed: 12/04/2022] Open
Abstract
The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these amplifiers of natural selection typically increase fixation time. Here we study population structures that achieve a tradeoff between fixation probability and time. First, we show that no amplifiers can have an asymptotically lower absorption time than the well-mixed population. Then we design population structures that substantially augment the fixation probability with just a minor increase in fixation time. Finally, we show that those structures enable higher effective rate of evolution than the well-mixed population provided that the rate of generating advantageous mutants is relatively low. Our work sheds light on how population structure affects the rate of evolution. Moreover, our structures could be useful for lab-based, medical, or industrial applications of evolutionary optimization.
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Affiliation(s)
| | | | | | - Martin A. Nowak
- Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University, Cambridge, MA 02138 USA
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13
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Ardon CB, Prens EP, Tkadlec J, Fuursted K, Abourayale S, Jemec GBE, Jenssen H. Virulent Staphylococcus lugdunensis with limited genetic diversity in hidradenitis suppurativa lesions. J Eur Acad Dermatol Venereol 2019; 33:e248-e250. [PMID: 30801776 DOI: 10.1111/jdv.15523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- C B Ardon
- Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands.,Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, DK-4000, Denmark
| | - E P Prens
- Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - J Tkadlec
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, V Úvalu 84, 150 06 Praha 5, Czech Republic
| | - K Fuursted
- Department of Microbiology and Infection Control, Staten Serum Institute, 5 Artillerivej, DK-2300, Copenhagen, Denmark
| | - S Abourayale
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, DK-4000, Denmark
| | - G B E Jemec
- Department of Dermatology, University Hospital Zealand, Sygehusvej 10, 4000 Roskilde, Denmark
| | - H Jenssen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, DK-4000, Denmark
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14
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Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak MA. Indirect reciprocity with private, noisy, and incomplete information. Proc Natl Acad Sci U S A 2018; 115:12241-12246. [PMID: 30429320 PMCID: PMC6275544 DOI: 10.1073/pnas.1810565115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Indirect reciprocity is a mechanism for cooperation based on shared moral systems and individual reputations. It assumes that members of a community routinely observe and assess each other and that they use this information to decide who is good or bad, and who deserves cooperation. When information is transmitted publicly, such that all community members agree on each other's reputation, previous research has highlighted eight crucial moral systems. These "leading-eight" strategies can maintain cooperation and resist invasion by defectors. However, in real populations individuals often hold their own private views of others. Once two individuals disagree about their opinion of some third party, they may also see its subsequent actions in a different light. Their opinions may further diverge over time. Herein, we explore indirect reciprocity when information transmission is private and noisy. We find that in the presence of perception errors, most leading-eight strategies cease to be stable. Even if a leading-eight strategy evolves, cooperation rates may drop considerably when errors are common. Our research highlights the role of reliable information and synchronized reputations to maintain stable moral systems.
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Affiliation(s)
- Christian Hilbe
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria;
| | - Laura Schmid
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Josef Tkadlec
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | | | - Martin A Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Mathematics, Harvard University, Cambridge, MA 02138
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15
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Tkadlec J, Peckova M, Sramkova L, Rohn V, Jahoda D, Raszka D, Berousek J, Mosna F, Vymazal T, Kvapil M, Drevinek P. The use of broad-range bacterial PCR in the diagnosis of infectious diseases: a prospective cohort study. Clin Microbiol Infect 2018; 25:747-752. [PMID: 30321604 DOI: 10.1016/j.cmi.2018.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/25/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Broad-range PCR has the potential to detect virtually any bacterial species via amplification and nucleotide sequencing of a DNA region common to all bacteria. We aimed to evaluate its usefulness and clinical relevance when applied to a wide variety of primary sterile materials. METHODS A prospective study including 1370 samples (75 heart valves, 151 joint tissue samples, 230 joint aspirates, 848 whole blood samples and 66 culture-negative cerebrospinal fluid samples) were studied by using a commercial PCR system for detecting 16S rDNA (Molzym). The PCR results were compared with culture and were considered to provide added diagnostic value only if the PCR approach revealed new pathogens that were missed by culture. RESULTS The added value of PCR was evident in 173 of 555 PCR-positive samples (0.126; 0.109-0.144 (proportion from all tested samples; 95% confidence interval)), most frequently in examinations of heart valves (0.56; 0.448-0.672) and joint tissue samples (0.219; 0.153-0.284). In contrast, the lowest rate of PCR with added value was noted for blood samples, regardless of the patient cohort they had been drawn from (nononcologic patients from intensive care: 0.065; 0.043-0.087, haematooncologic children: 0.048; 0.027-0.070). Moreover, PCR missed up to 7.1% of blood culture findings (0.071; 0.048-0.095) regarded as clinically relevant, which was the second highest failure rate after joint tissue samples (0.099; 0.052-0.147). CONCLUSIONS Broad-range PCR substantially increases detection rate of pathogens, especially from heart valves and joint samples. However, a concurrent risk of false-negative PCR results justifies the need for parallel culture.
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Affiliation(s)
- J Tkadlec
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Czech Republic
| | - M Peckova
- Institute of Applied Mathematics and Information Technologies, Faculty of Science, Charles University, Czech Republic
| | - L Sramkova
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Czech Republic
| | - V Rohn
- Department of Cardiovascular Surgery, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Czech Republic
| | - D Jahoda
- 1st Orthopaedic Department, 1st Faculty of Medicine, Charles University and Motol University Hospital, Czech Republic
| | - D Raszka
- 1st Orthopaedic Department, 1st Faculty of Medicine, Charles University and Motol University Hospital, Czech Republic
| | - J Berousek
- Department of Anaesthesiology and ICM, Motol University Hospital, Prague, Czech Republic
| | - F Mosna
- Department of Anaesthesiology and ICM, Motol University Hospital, Prague, Czech Republic
| | - T Vymazal
- Department of Anaesthesiology and ICM, Motol University Hospital, Prague, Czech Republic
| | - M Kvapil
- Department of Internal Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Czech Republic
| | - P Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Czech Republic.
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Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Commun Biol 2018; 1:71. [PMID: 30271952 PMCID: PMC6123726 DOI: 10.1038/s42003-018-0078-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/25/2018] [Indexed: 11/08/2022] Open
Abstract
Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures.
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Affiliation(s)
| | | | | | - Martin A Nowak
- Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University, Cambridge, MA, 02138, USA.
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17
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Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak MA. Language acquisition with communication between learners. J R Soc Interface 2018; 15:rsif.2018.0073. [PMID: 29593089 DOI: 10.1098/rsif.2018.0073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/02/2018] [Indexed: 11/12/2022] Open
Abstract
We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students.
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Affiliation(s)
| | | | | | - Martin A Nowak
- Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University, Cambridge, MA 02138, USA
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18
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Tkadlec J, Melter O, Bukáčková E, Fila L, Pantůček R, Indráková A, Botka T, Růičková V. 96 Staphylococcus aureus in Czech cystic fibrosis patients – prospective study. J Cyst Fibros 2014. [DOI: 10.1016/s1569-1993(14)60232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Tkadlec J, Melter O. [Small colony variants Staphylococcus aureus]. Klin Mikrobiol Infekc Lek 2013; 19:96-102. [PMID: 24579452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The phenomenon of dwarf colonies of S. aureus, the so-called small colony variants (SCVs), is associated with chronic and recurrent staphylococcal infections. Most frequently, these phenotypic variants differ from normal strains of S. aureus in colony size, morphology, pigmentation and other characteristics as well as molecular genetic changes. SCVs frequently emerge as a result of mutations in metabolically important and regulatory genes. The mutations are a cause of SCVs auxotrophy. From a clinical point of view, an increased ability of SCVs to resist antibiotic therapy and also an ability to persist within eukaryotic host cells are of importance.
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Affiliation(s)
- J Tkadlec
- Ustav lékarské mikrobiologie, 2. LF UK a FN Motel, Praha.
| | - O Melter
- Ustav lékarské mikrobiologie, 2. LF UK a FN Motel, Praha
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Melter O, Tkadlec J, Šulcová R, Skalická V, Kučerová T, Dřevínek P. 153 Direct detection and identification of controversial pathogens in CF – Pandoraea apista and Inquilinus limosus. J Cyst Fibros 2013. [DOI: 10.1016/s1569-1993(13)60295-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Tkadlec J, Bukáčková E, Fila L, Bartošová J, Dřevínek P, Melter O. 148 Direct detection, clonal analysis, and characterization of wild type and small colony variant strains of Staphylococcus aureus from the sputa of CF patients of the Prague CF centre. J Cyst Fibros 2013. [DOI: 10.1016/s1569-1993(13)60290-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Tkadlec J, Turunen E. Commutative bounded integral residuated orthomodular lattices are Boolean algebras. Soft comput 2010. [DOI: 10.1007/s00500-010-0572-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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Affiliation(s)
- Ivan Bruha
- Department Computing & Software, McMaster University, Hamilton, Ont., L8S4K1 Canada. E-mail:
| | - Josef Tkadlec
- Department of Mathematics, Faculty of Electrical Engineering, Czech Technical University, 16627 Praha, Czech Republic. E-mail:
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