Escalation of Memory Length in Finite Populations
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An Evolutionary Arms Race Between Coronaviruses and Mammalian Species Reflected in Positive Selection of the ACE2 Receptor Among Many Species
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.14.096131. this version posted May 15, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The Red Queen’s Crown: an evolutionary arms race between coronaviruses and mammalian species reflected in positive selection of the ACE2 receptor among many species Mehrdad Hajibabaei1,2,* and Gregory A. C. Singer2 1 Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada 2 Centre for Environmental Genomics Applications, eDNAtec Inc, St. John’s, NL, Canada * Correspondence: Mehrdad Hajibabaei ([email protected]) "Nothing in biology makes sense except in the light of evolution" (Theodosius Dobzhansky) Abstract The world is going through a global viral pandemic with devastating effects on human life and socioeconomic activities. This pandemic is the result of a zoonotic coronavirus, Severe Acute Respirsatory Syndrom Coronavirus 2 (SARS-CoV-2) which is believed to have originated in bats and transferred to humans possibly through an intermediate host species (Zhou et al. 2020; Coronaviridae Study Group of the International Committee on Taxonomy of Viruses 2020). The virus attacks host cells by attaching to a cell membrane surface protein receptor called ACE2 (Ge et al. 2013; Zhou et al. 2020). Given the critical role of ACE2 as a binding receptor for a number of coronaviruses, we studied the molecular evolution of ACE2 in a diverse range of mammalian species. Using ACE2 as the target protein, we wanted to specifically test the Red Queen hypothesis (Dawkins and Krebs 1979) where the parasite and host engage in an evolutionary arms race which can result in positive selection of their traits associated to their fitness and survival. -
Statistical Mechanics of Evolutionary Dynamics
Statistical Mechanics of Evolutionary Dynamics Kumulative Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Christian-Albrechts-Universit¨at zu Kiel vorgelegt von Torsten Rohl¨ Kiel 2007 Referent: Prof. Dr. H. G. Schuster Koreferent(en): Prof. Dr. G. Pfister Tagderm¨undlichenPr¨ufung: 4.Dezember2007 ZumDruckgenehmigt: Kiel,den12.Dezember2007 gez. Prof. Dr. J. Grotemeyer (Dekan) Contents Abstract 1 Kurzfassung 2 1 Introduction 3 1.1 Motivation................................... 3 1.1.1 StatisticalPhysicsandBiologicalSystems . ...... 3 1.1.1.1 Statistical Physics and Evolutionary Dynamics . ... 4 1.1.2 Outline ................................ 7 1.2 GameTheory ................................. 8 1.2.1 ClassicalGameTheory. .. .. .. .. .. .. .. 8 1.2.1.1 TheMatchingPenniesGame . 11 1.2.1.2 ThePrisoner’sDilemmaGame . 13 1.2.2 From Classical Game Theory to Evolutionary Game Theory.... 16 1.3 EvolutionaryDynamics. 18 1.3.1 Introduction.............................. 18 1.3.2 ReplicatorDynamics . 22 1.3.3 GamesinFinitePopulations . 25 1.4 SurveyofthePublications . 29 1.4.1 StochasticGaininPopulationDynamics. ... 29 1.4.2 StochasticGaininFinitePopulations . ... 31 1.4.3 Impact of Fraud on the Mean-Field Dynamics of Cooperative Social Systems................................ 36 2 Publications 41 2.1 Stochasticgaininpopulationdynamics . ..... 42 2.2 Stochasticgaininfinitepopulations . ..... 47 2.3 Impact of fraud on the mean-field dynamics of cooperative socialsystems . 54 Contents II 3 Discussion 63 3.1 ConclusionsandOutlook . 63 Bibliography 67 Curriculum Vitae 78 Selbstandigkeitserkl¨ arung¨ 79 Abstract Evolutionary dynamics is an essential component of a mathematical and computational ap- proach to biology. In recent years the mathematical description of evolution has moved to a description of any kind of process where information is being reproduced in a natural envi- ronment. In this manner everything that lives is a product of evolutionary dynamics. -
How to Win an Evolutionary Arms Race
Secure Systems Editor: S.W. Smith, [email protected] How to Win an Evolutionary Arms Race ust about every computer user today is engaged in an McAfee makes a mistake with a virus signature, it could disable or even evolutionary arms race with virus writers, spam dis- delete legitimate users’ applications (legitimate applications have already tributors, organized criminals, and other individuals been disabled by virus scanners; see http://news.com.com/2100-7350 attempting to co-opt the Internet for their own pur- -5361660.html). If Microsoft makes J a mistake, numerous machines poses. These adversaries are numerous, adaptable, persistent, and might no longer even boot. The time between vulnerability disclo- ANIL SOMAYAJI unscrupulous. They’re creating in- able way to communicate and col- sure and exploit distribution is some- Carleton dependent agents—mobile pro- laborate, we must adopt another, times only a few days. If software de- University grams—that, once released, take on perhaps radically different, model for velopers haven’t been previously lives of their own. Their attacks are securing our computers. notified, there’s little chance that becoming more sophisticated every To better understand this conclu- they can release a well-tested fix in day, and the situation will likely be- sion, we should first re-examine why this time frame. Further, with fast- come much worse unless we, as de- developers and users are embracing propagating worms and viruses, fenders, take drastic steps. automated update systems. antivirus developers must play catch- We can’t hope to completely de- up: Malware can infect thousands of feat all our attackers. -
Micro-Evolutionary Change and Population Dynamics of a Brood Parasite and Its Primary Host: the Intermittent Arms Race Hypothesis
Oecologia (1998) 117:381±390 Ó Springer-Verlag 1998 Manuel Soler á Juan J. Soler á Juan G. Martinez Toma sPe rez-Contreras á Anders P. Mùller Micro-evolutionary change and population dynamics of a brood parasite and its primary host: the intermittent arms race hypothesis Received: 7 May 1998 / Accepted: 24 August 1998 Abstract A long-term study of the interactions between Key words Brood parasitism á Clamator glandarius á a brood parasite, the great spotted cuckoo Clamator Coevolution á Parasite counter-defences á Pica pica glandarius, and its primary host the magpie Pica pica, demonstrated local changes in the distribution of both magpies and cuckoos and a rapid increase of rejection of Introduction both mimetic and non-mimetic model eggs by the host. In rich areas, magpies improved three of their defensive Avian brood parasites exploit hosts by laying eggs in mechanisms: nest density and breeding synchrony in- their nests, and parental care for parasitic ospring is creased dramatically and rejection rate of cuckoo eggs subsequently provided by the host. Parasitism has a increased more slowly. A stepwise multiple regression strongly adverse eect on the ®tness of hosts, given that analysis showed that parasitism rate decreased as host the young parasite ejects all host ospring or outcom- density increased and cuckoo density decreased. A lo- petes them during the nestling period (Payne 1977; gistic regression analysis indicated that the probability Rothstein 1990). Thus, there is strong selection acting on of changes in magpie nest density in the study plots was hosts to evolve defensive mechanisms against a brood signi®cantly aected by the density of magpie nests parasite which, in turn, will develop adaptive counter- during the previous year (positively) and the rejection defences. -
Snail Susceptibility to Crab Predation: a Case Study of Co-Evolution from Lake Tanganyika, East Africa
Snail susceptibility to crab predation: A case study of co-evolution from Lake Tanganyika, East Africa Student: Ava B. Rosales Mentors: Ellinor Michel & Saskia Marijnissen Introduction Co-evolution has been invoked as an explanation for Lake Tanganyika’s unusual endemic fauna. The crabs Platytelphusa armata and Potamonautes platynotus are molluscivores, found in the same habitats as the gastropods Lavigeria coronata, L. grandis, and L. nassa (West & Cohen 1994). As these are the largest gastropods in the Lavigeria species flock, and often the most exposed, we are determining whether shell size and sculpture provides protection from predation. We are also attempting to reveal the effectiveness of chela morphology among crab predators. The fine details of the predator-prey relationships will link the ecological processes with their potential evolutionary patterns. Methods Specimen collection was performed at two sites: Jakobsen’s Bay (4º 54.64’ S, 29º 35.92’ E) and Hilltop (4º 53.20’ S, 29º 36.75’ E), in the vicinity of Kigoma Bay, Tanzania. Snails were collected from the rocky littoral zone on the coast south of Jakobsen’s Beach by snorkel from 1-6 m. Crab traps baited with raw fish were used to catch crabs between 2-10 m depth from Jakobsen’s Bay as well as Hilltop. Snails and crabs were kept in aerated tanks filled with water collected from 1km off shore in Kigoma Bay. Crabs were acclimated and starved for 24-48 hours to increase their motivation to feed. Before the trials snail shells were scrubbed clean of algae to reveal scars and -
The Interface Theory of Perception
!1 The Interface Theory of Perception (To appear in The Stevens' Handbook of Experimental Psychology and Cognitive Neuroscience) DONALD D. HOFFMAN ABSTRACT Our perceptual capacities are products of evolution and have been shaped by natural selection. It is often assumed that natural selection favors veridical perceptions, namely, perceptions that accurately describe those aspects of the environment that are crucial to survival and reproductive fitness. However, analysis of perceptual evolution using evolutionary game theory reveals that veridical perceptions are generically driven to extinction by equally complex non-veridical perceptions that are tuned to the relevant fitness functions. Veridical perceptions are not, in general, favored by natural selection. This result requires a comprehensive reframing of perceptual theory, including new accounts of illusions and hallucinations. This is the intent of the interface theory of perception, which proposes that our perceptions have been shaped by natural selection to hide objective reality and instead to give us species-specific symbols that guide adaptive behavior in our niche. INTRODUCTION Our biological organs — such as our hearts, livers, and bones — are products of evolution. So too are our perceptual capacities — our ability to see an apple, smell an orange, touch a grapefruit, taste a carrot and hear it crunch when we take a bite. Perceptual scientists take this for granted. But it turns out to be a nontrivial fact with surprising consequences for our understanding of perception. The -
Trivers' Parental Investment and Sexual Selection: the Sex That Invests Most in Reproduction Will Be the Choosier Sex
Recent research reveals In an astonishing study recently undertaken in Western Europe, the following facts emerged: Married females choose to have affairs with males who are dominant, older, more physically attractive, more symmetrical in appearance, and married; females are much more likely to have an affair if their mates are subordinate, younger, physically unattractive, or have asymmetrical features; cosmetic surgery to improve a male's looks doubles his chances of having an adulterous affair; the more attractive a male, the less attentive he is as a father; roughly one in three of the babies born in Western Europe is the product of an adulterous affair. Why Have Sex? (I) We are involved in an “evolutionary arms race” against pathogens who reproduce faster than we do and therefore can modify their genetic structure to overcome our immune system. Sex allows us to modify our genetic structure, through our offspring, to win (for a time) this battle. Lifjeld and colleagues’ findings are yet another illustration of the fact that sex has one killer advantage over other, more efficient means of reproduction. By mixing the genes of two individuals, sex creates a third - the offspring - with a new, unique combination. This maintains genetic variation, fuelling evolution and keeping one step ahead of agents of infectious disease. As evolutionary biologist Jonathan Howard put it: if sex causes disease, then it might also be true that disease causes sex. (Nature 296-299 (2000) 1 Why Have Sex? (II) • Muller’s ratchet and Kondrashov’s solution • Deleterious mutations increase simply as the number of genes in an organism increases. -
Effects of Hybridization and Life History Tradeoffs on Pathogen Resistance in the Harvester Ants (Pogonomyrmex) Yainna M
University of Vermont ScholarWorks @ UVM Graduate College Dissertations and Theses Dissertations and Theses 2015 Effects of hybridization and life history tradeoffs on pathogen resistance in the Harvester ants (Pogonomyrmex) Yainna M. Hernaiz-Hernandez University of Vermont Follow this and additional works at: https://scholarworks.uvm.edu/graddis Part of the Biology Commons Recommended Citation Hernaiz-Hernandez, Yainna M., "Effects of hybridization and life history tradeoffs on pathogen resistance in the Harvester ants (Pogonomyrmex)" (2015). Graduate College Dissertations and Theses. 518. https://scholarworks.uvm.edu/graddis/518 This Thesis is brought to you for free and open access by the Dissertations and Theses at ScholarWorks @ UVM. It has been accepted for inclusion in Graduate College Dissertations and Theses by an authorized administrator of ScholarWorks @ UVM. For more information, please contact [email protected]. EFFECTS OF HYBRIDIZATION AND LIFE HISTORY TRADEOFFS ON PATHOGEN RESISTANCE IN THE HARVESTER ANTS (POGONOMY RMEX) A Thesis Presented by Yainna Hernáiz-Hernández to The Faculty of the Graduate College of The University of Vermont In Partial Fulfillment of the Requirements for the Degree of Master of Science Specializing in Biology May, 2015 Defense Date: March 26, 2015 Thesis Examination Committee: Sara Helms Cahan, Ph.D., Advisor Douglas Johnson, Ph.D., Chairperson Joseph Schall, Ph.D., Emeriti Faculty Cynthia J. Forehand, Ph.D., Dean of the Graduate College ABSTRACT A fundamental challenge faced by all organisms is the risk of infection by pathogens that can significantly reduce their fitness. The evolutionary dynamic between hosts and pathogens is expected to be a coevolutionary cycle, as pathogens evolve by increasing their level of virulence and hosts respond by increasing their level of resistance. -
Beyond Competition in Evolution and Social Learning Communities
Beyond Competition in Evolution and Social Learning communities. Jordan Pollack Brandeis University DEMO.CS.BRANDEIS.EDU EUCognition January 2008 My Lab’s Research ! How do biological systems progress without a designer? ! Can we understand open- ended evolution in enough formal detail to replicate the process using computer technology? ! What are beneficial applications? Demo.cs.brandeis.edu 1 Co-Evolution as Arms-race ! In Nature, Co-evolution means contingent development between species. ! But in Machine Learning the goal is an unstoppable “arms race” towards complexity. Demo.cs.brandeis.edu Canonical Coev. Algorithm Initialize random “genotypes” Pop. Evaluate Members Fitness computed By complete mixing y Output Done? Fittest Individuals n Select Parents New Generation Generate/Insert Offspring Demo.cs.brandeis.edu 2 Open-ended Evolution as Learning by Playing a game Detects Invents “tells” The Bluff (signals) Learns Knows probabilities what to draw Demo.cs.brandeis.edu Co-evolutionary Success Stories ! Prisoner Dilemma (Axelrod & Forrest) ! Pursuer Evader (Cliff, Reynolds …) ! Sorting Nets (Hillis, Juille) ! Game Players (Rosin, Angeline, Tesauro, Blair, Fogel) ! Cell Automata Rules (Packard, Juille) ! Robotics (Sims, Floreano, Funes, Lipson, Hornby) ! Education Technology (Sklar, Bader-Natal) (My students) Demo.cs.brandeis.edu 3 Coevolutionary Robots Evolutionary Computing Virtual Reality Simulation Artificial Lifeforms Demo.cs.brandeis.edu Can we turn Virtual Creatures Real? 3d Printing Machine 1999=$50,000 2009= $5000 CNC, CIM, -
A Co-Evolutionary Arms Race: Sierra Garter Snake Vs. Sierra Newt by Denise De Carion
FLOG A Co-Evolutionary Arms Race: Sierra garter snake vs. Sierra newt By Denise De Carion In the Tuolumne River watershed, there is a co-evolutionary arms race occurring between the Sierra garter snake (Thamnophis couchii) and the Sierra newt (Taricha sierrae) and it has become apparent that the Sierra garter snake is winning. The Sierra newt is an amphibious species whose conspicuous orange coloration provides a warning signal to predators (Petranka, 1998). This animal produces a potent neurotoxin called tetrodotoxin, which if ingested, binds to sodium ion channels in nerves and muscles, causing imminent mortality (Brodie, 2005). It is this molecular mechanism that allows the newt, which is slow-moving and often found out in exposed, shallow pool habitat, to avoid predation by almost all animals occupying higher trophic levels ―except for one. The Sierra garter snake has evolved an elevated resistance to tetrodotoxin, which prevents the toxin from binding to its pores. The deadly toxin is considered to be the phenotypic interface of interactions between these two species that has allowed them to co-evolve via natural selection. In other words, this example of a parallel “arms race” between predator and prey demonstrates that co-evolution of two species surrounding a toxin has been a result of each species having the genetic ability to respond and reciprocate to selection (Brodie et al., 2005). If you are planning to go ‘herping,’ or searching for reptiles and amphibians, on the Tuolumne River, the following words of advice should be followed. Sierra newts can be found in abundance during their breeding season, January through May, in a small tributary that is located on the other side of the river from the frequently visited campsite Indian Creek. -
The Bat–Moth Arms Race Hannah M
© 2016. Published by The Company of Biologists Ltd | Journal of Experimental Biology (2016) 219, 1589-1602 doi:10.1242/jeb.086686 REVIEW Evolutionary escalation: the bat–moth arms race Hannah M. ter Hofstede1,* and John M. Ratcliffe2,* ABSTRACT exclusive to the interactions between bats and moths. Most Echolocation in bats and high-frequency hearing in their insect prey adaptations that make bats better moth hunters also make them make bats and insects an ideal system for studying the sensory more effective hunters of other insects, and such adaptations are ecology and neuroethology of predator–prey interactions. Here, we therefore not moth specific. Likewise, some moths use their ears to review the evolutionary history of bats and eared insects, focusing on detect not only bats but also insect-eating birds or mates (Conner, the insect order Lepidoptera, and consider the evidence for 1999; Nakano et al., 2015). antipredator adaptations and predator counter-adaptations. Ears The evolutionary histories of predator and prey also differ. The ∼ evolved in a remarkable number of body locations across insects, with order Lepidoptera (moths and butterflies) originated 150 million the original selection pressure for ears differing between groups. years ago (mya; Misof et al., 2014), long before the origin of bats, Although cause and effect are difficult to determine, correlations which first took to the wing sometime between 60 and 95 mya between hearing and life history strategies in moths provide evidence (Bininda-Emonds et al., 2007). Although powered flight is a for how these two variables influence each other. We consider life defining characteristic of bats, laryngeal echolocation may have ∼ history variables such as size, sex, circadian and seasonal activity evolved only 50 mya (Simmons et al., 2008; Teeling, 2009; patterns, geographic range and the composition of sympatric bat Veselka et al., 2010). -
Cambrian Explosion Fact Sheet
Cambrian Explosion Fact Sheet The Cambrian Explosion was a burst of animal evolution that occurred 540 million years ago. It’s called an explosion because it happened in about 20 million years, a very short time on the geologic time scale. There were multicellular animals already living before this time: early animals – sponges, cnidarians and flatworm ancestors –all appeared before the Cambrian. But during the Cambrian Explosion the basic body plans—the designs – of most of the animal phyla that have ever lived appeared within those mere twenty million years. Almost all of the new body plans, 35 in all, were bilateral. During this evolutionary leap, came new active predators, changing the relationships among animals and creating new, more complex food webs. Scientists have found fossil evidence of the Cambrian Explosion at sites around the world. The most famous is the Burgess Shale in British Columbia, Canada. Other sites include: Chengjiang, Yunnan Province, China; the House Range, near Delta, Utah; and near the Aldan River in Siberia, Russia. In 2016, the causes of the Cambrian Explosion are still the topic of scientific debate. Scientists agree that there were probably both biological and non-biological causes interacting with each other. Some of the proposed causes are: • Genetics: in the Cambrian, the genetic code reached sufficient proportions to command and control the production of not just simple animals, such as sponges and jellies, but the more complex phyla of creatures. • Rise in oxygen levels: scientists are investigating whether or not oxygen levels rose significantly just before the Cambrian. Higher oxygen levels allow for more active predators.